| only the two end helixes of eight tandem amphipathic helical domains of human apo a-i have significant lipid affinity. implications for hdl assembly. | human apolipoprotein a-i (apo a-i) possesses multiple tandem repeating 22-mer amphipathic alpha-helixes. computer analysis and studies of model synthetic peptides and recombinant protein-lipid complexes of phospholipids have suggested that apo a-i interacts with hdl surface lipids through cooperation among its individual amphipathic helical domains. to delineate the overall lipid-associating properties of apo a-i, the first step is to understand the lipid-associating properties of individual amp ... | 1996 | 8620350 |
| proliferative t cell responses to human papillomavirus type 16 l1 peptides in patients with cervical dysplasia. | human papillomavirus type 16 (hpv-16) can cause genital warts, cervical dysplasias and carcinoma of the cervix. cell-mediated immunity is thought to be important in protection against the virus and in its elimination, but little is known about the mechanisms involved. in a cross-sectional study we have demonstrated proliferative t cell responses to peptides representing the hpv-16 l1 capsid protein (aa 199-409) in the peripheral blood of 63% of patients (n = 41) with histological evidence of cer ... | 1996 | 8627247 |
| synthesis and immunological characterization of 104-mer and 102-mer peptides corresponding to the n- and c-terminal regions of the plasmodium falciparum cs protein. | we investigated the immunogenicity and the conformational properties of the non-repetitive sequences of the plasmodium falciparum circumsporozoite (cs) protein. two polypeptides of 104 and 102 amino acids long, covering, respectively, the n- and c-terminal regions of the cs protein, were synthesized using solid phase fmoc chemistry. the crude polypeptides were purified by a combination of size exclusion chromatography and rp-hplc. sera of mice immunized with the free polypeptides emulsified in i ... | 1995 | 8643099 |
| kinetic and thermodynamic analysis of the interaction between trap (trp rna-binding attenuation protein) of bacillus subtilis and trp leader rna. | in bacillus subtilis, expression of the tryptophan biosynthetic genes is regulated in response to tryptophan by an rna-binding protein called trap (trp rna-binding attenuation protein). trap has been shown to contain 11 identical subunits arranged in a symmetrical ring. kinetic and thermodynamic parameters of the interaction between tryptophan-activated trap and trp leader rna were studied. results from glycerol gradients and mobility shift gels indicate that two trap 11-mers bind to each trp le ... | 1996 | 8647825 |
| 32p-postlabelling of diastereomeric 7-alkylguanine adducts of butadiene monoepoxide. | the reaction of 3,4-epoxy-1-butene (bmo) with deoxyguanosine-3'-monophosphate (3'-dgmp) resulted in the formation of two pairs of diastereomeric 7-alkyl-3'-dgmp derivatives corresponding to two isomers c¿-1 and c¿-2. the t4 polynucleotide kinase-mediated phosphorylation with [gamma-32p]-atp showed preferential labelling of diastereo- mers of the c¿-1 isomer. the diastereomers 1 and 2 of the c¿-1 isomer had labelling efficiencies of 42%. however, the labelling efficiencies of diastereomers 3 and ... | 1996 | 8681446 |
| long-range sequence analysis in xq28: thirteen known and six candidate genes in 219.4 kb of high gc dna between the rcp/gcp and g6pd loci. | dna comprising 219 447 bp was sequenced in nine cosmids and verified at > 99.9% precision. of the standard repetitive elements, 187 alus make up 20.6% of the sequence, but there were only 27 mers (2.9%) and 17 l1 fragments (1.6%). this may be characteristic of such high gc (57%) regions. the sequence also includes an 11.3 kb tract duplicated with 99.2% identity at a distance of 38 kb. the region is 80-90% transcribed and 12.5% translated. thirteen known genes and their exon-intron borders are al ... | 1996 | 8733135 |
| characterization and comparison of synthetic immobile and mobile holliday junctions. | eight synthetic holliday junction (hj) oligonucleotides containing an immobile or a mobile junction were characterized by gel electrophoresis, ultraviolet absorption and circular dichroism (cd) spectroscopy. four 24-mer deoxyribonucleotides formed stable immobile and mobile hjs in 0.1 m nacl at 5 mum strand concentration at room temperature. however, the immobile hj constructed from four 18-mers was less stable, and four 12-mers did not form the hj structure under the conditions used. a comparis ... | 1996 | 8743565 |
| inhibition of growth of human tumor cell lines in nude mice by an antisense of oligonucleotide inhibitor of protein kinase c-alpha expression. | a 20-mer phosphorothioate oligodeoxynucleotide (isis 3521) designed to hybridize sequences in the 3'-untranslated region of human protein kinase c-alpha (pkc-alpha) mrna has been shown to inhibit the expression of pkc-alpha in multiple human cell lines. in human bladder carcinoma (t-24) cells, inhibition of pkc-alpha was both concentration dependent and oligonucleotide sequence specific. isis 3521 had a ic50 of 50-100 nm for pkc-alpha mrna reduction and was without effect on the expression of ot ... | 1996 | 8758918 |
| de novo antimicrobial peptides with low mammalian cell toxicity. | de novo antimicrobial peptides with the sequences: (klakkla)n, (klaklak)n (where n = 1,2,3), (kalkalk)3, (klgkklg)n, and (kaakkaa)n (where n = 2,3), were prepared as the c-terminus amides. these peptides were designed to be perfectly amphipathic in helical conformations. peptide antibacterial activity was tested against escherichia coli, pseudomonas aeruginosa, and staphylococcus aureus. peptide cytotoxicity was tested against human erythrocytes and 3t3 mouse fibroblasts. the 3t3 cell testing wa ... | 1996 | 8759631 |
| differential display protocol with selected primers that preferentially isolates mrnas of moderate- to low-abundance in a microscopic system. | a modified reverse transcription polymerase chain reaction (rt-pcr)-based differential display procedure with selected primers (spr) was developed to increase the bias toward isolating moderate- to low-abundance transcripts that are differentially expressed during synapse formation in a microscopic neuronal system, the embryonic chicken ciliary ganglion. major modifications, in comparison with available arbitrarily primed rt-pcr protocols, include the use of (i) experimentally selected primer pa ... | 1996 | 8780874 |
| mutational analysis of the estrogen receptor ligand-binding domain: influence of ligand structure and stereochemistry on transactivation. | the mouse estrogen receptor (mer) exhibits ligand stereochemical specificity for indenestrol a (ia), a stilbestrol estrogen. ia has a chiral c3 methyl group, and the mer preferentially binds the s-enantiomer (ia-s), resulting in elevated biological activity when compared with the ia-r enantiomer. to elucidate the mechanisms for this stereochemical recognition, we have constructed a series of mers with individual amino acid substitutions at met521, his528, met532, and val537. the abilities of yea ... | 1996 | 8782086 |
| optimization of the rate of dna hybridization and rapid detection of methicillin resistant staphylococcus aureus dna using fluorescence polarization. | the hybridization rate of two complementary single-stranded dna 24-mers was determined at various nacl concentrations using a fluorescence polarization method. the rate was taken as the rate constant of the second order reaction, obtained by mathematical fitting of the time course curves of hybridization. the rate increased with the nacl concentration, plateauing in the concentration range of about 1-2 m. over the temperature range of 46 degrees c to 56 degrees c, it was found that in 0.8 m nacl ... | 1996 | 8861999 |
| internal autocrine regulation by erythropoietin of erythroleukemic cell proliferation. | antisense oligomers (18 mers) corresponding to the erythropoietin and erythropoietin receptor 5' coding sequences cause marked suppression of proliferation of several lines of erythroleukemic cells. in these systems, phosphorothioate protected sense oligomers are inhibitory, while the unmodified sense oligomers have no significant effect on cell growth. these data indicate that proliferation of some erythroleukemic cells is under internal autocrine regulation by erythropoietin and its receptor. | 1996 | 8862443 |
| the bundling of actin with polyethylene glycol 8000 in the presence and absence of gelsolin. | actin filament and bundle formation occur in the cytosol under conditions of very high total macromolecular concentration. in this study we have utilized the inert molecule polyethylene glycol 8000 (peg) as a means of simulating crowded conditions in vitro. column-purified ca-actin was polymerized in the absence and presence of gelsolin (to regulate mean filament lengths between 50 and 5000 mers) and peg (2-8%) using various concentrations of kcl and/or 2 mm divalent cations. bundling was charac ... | 1996 | 8874022 |
| protection against measles virus encephalitis by monoclonal antibodies binding to a cystine loop domain of the h protein mimicked by peptides which are not recognized by maternal antibodies. | after immunization with measles virus (mv) several monoclonal antibodies (mabs) were obtained, which reacted with peptides corresponding to the amino acids 361-410 of the haemagglutinin protein (mv-h). three of these mabs (bh6, bh21 and bh216) inhibited haemagglutination, neutralized mv in vitro and protected animals from a lethal challenge of rodent-adapted neurotropic mv. these mabs reacted with the 15-mer peptides h381 and h386 defining their overlapping region 386-395 as a sequential neutral ... | 1996 | 8887481 |
| a comparison of the sensitivity of epidural and myogenic transcranial motor-evoked responses in the detection of acute spinal cord ischemia in the rabbit. | monitoring motor-evoked responses to transcranial stimulation (tc-mers) provides information about the functional status of the spinal cord during operations that pose the risk of spinal cord ischemia. responses can be recorded from the epidural space (epidural tc-mers) or from muscle (myogenic tc-mers). in this study the relative sensitivity of epidural and myogenic tc-mers to acute spinal cord ischemia was compared. spinal cord ischemia was produced by infrarenal aortic balloon occlusion in ni ... | 1996 | 8895279 |
| chlamydia trachomatis major outer membrane protein (momp) epitopes that activate hla class ii-restricted t cells from infected humans. | we localized peptide epitopes within the chlamydia trachomatis (ct) major outer membrane protein (momp) that activate human t cells. t-momp' cells were prepared by culturing pbl from 38 humans who had ct infections in the presence of ct serovar e momp. some epitopes were first localized by quantifying proliferative responses of t-momp' cells to overlapping momp segments (sixths) that were produced in escherichia coli. further localization was achieved by using overlapping synthetic 16-22 mers th ... | 1996 | 8906834 |
| 3'-5' l-capped-antisense oligodeoxynucleotides targeted at the sv40 t-antigen gene: pharmacological and biological properties. | this paper reports on some pharmacological and biological properties of 22-mer antisense oligodeoxynucleotides which contain an l-deoxyribonucleoside at each terminus. compared with natural compounds, of which they retain the dna hybridizing ability and the cell uptake mechanism, the l-22-mers exhibited an increased resistance to phosphodiesterase degradation, an apparent higher intracellular concentration and a longer intracellular half life. antiviral activity was not prominent. | 1996 | 8914127 |
| characterization of pcr products from bacilli using electrospray ionization fticr mass spectrometry. | a procedure for rapid purification of polymerase chain reaction (pcr) products allowing precise molecular weight determination using electrospray ionization-fourier transform ion cyclotron resonance (esi-fticr) mass spectrometry is described. pcr amplification utilized the dna polymerase from pyrococcus furiosus (pfu) which, unlike taq, does not incorporate a nontemplated terminal deoxyadenosine phosphate. an 89-base pair nucleotide portion of the spacer region between the 16s and 23s ribosomal ... | 1996 | 8914480 |
| structural origins of bulky oxidative dna adducts (type ii i-compounds) as deduced by oxidation of oligonucleotides of known sequence. | bulky dna adducts, previously termed type ii i-compounds, are detected by 32p-postlabeling following treatment of dna with several fenton-type oxygen radical-generating reagents, i.e., mixtures of fe(ii) or ni(ii) and h2o2. in an attempt to characterize the chemical nature and mechanism(s) of formation of these novel adducts, 16 single-stranded deoxyribooligonucleotides (20- and 21-mers) of known sequence were oxidized with fe(ii) or ni(ii) and h2o2, and the products were analyzed by 32p-postlab ... | 1996 | 8924599 |
| [the improvement of a direct dna sequencing method by devising the primer design: detection of lipoprotein lipase gene aberrations]. | we developed an improved method of direct dna sequencing which makes it possible to detect heterozygous mutations in an exon and the splicing consensus regions (acceptor and donor) in introns even in the cases where there is limited information available regarding the base sequences of the introns flanking the exon. human lipoprotein lipase (lpl) gene was utilized to develop this method, since the reported intron base sequences of the lpl gene are limited to 40 bases. we constructed pcr primers ... | 1996 | 8937192 |
| in vitro interaction between a chloroplast transit peptide and chloroplast outer envelope lipids is sequence-specific and lipid class-dependent. | interaction of artificial lipid bilayers (liposomes) with the purified transit peptide (ss-tp) of the precursor form of the small subunit for ribulose-2,5-bisphosphate carboxylase/oxygenase (prssu) has been studied using a vesicle-disruption assay (calcein dye release) and electron microscopy. employing purified forms of escherichia coli-expressed prssu, mature small subunit, glutathione s-transferase-transit peptide fusion protein, and ss-tp in dye release studies demonstrated that lipid intera ... | 1996 | 8955132 |
| co-operativity of hexamer ligation. | the spel-6 (sequential rimer elongation by ligation of 6-mers) procedure is based on the assembly of dna primers by ligation of three or more hexamers taken from a library of 4096 hexamers. in this way, the synthesized primers enable dna sequencing by primer walking. ligation by both t4 dna ligase and rhodothermus marinus thermophilic dna ligase is highly cooperative. sequencing ladders obtained with 18-60-nucleotide (nt) primers (produced by ligation of three to ten hexamers using t4 dna ligase ... | 1996 | 8955646 |
| synthesis and biological activity of dna damaging agents that form decoy binding sites for the estrogen receptor. | it is a goal of cancer chemotherapy to achieve the selective killing of tumor cells while minimizing toxicity to normal tissues. we describe the design of selective toxins forming dna adducts that attract the estrogen receptor (er), a transcription factor that is overexpressed in many human breast and ovarian tumors. the compounds consist of 4-(3-aminopropyl)-n,n-(2-chloroethyl)-aniline linked to 2-(4'-hydroxyphenyl)-3-methyl-5-hydroxy-indole. the former moiety is a dna damaging nitrogen mustard ... | 1996 | 8986764 |
| muts interaction with mismatch and alkylated base containing dna molecules detected by optical biosensor. | an optical biosensor was used to monitor interactions between the escherichia coli dna mismatch repair molecule muts and various immobilized oligonucleotides. while associating poorly with single-stranded dna, muts was capable of rapid association/dissociation from homoduplex dna. the interaction of muts with oligonucleotide 30-mers containing single site mismatches demonstrated that during the dissociation phase, muts binding was greatest to a g-g mismatch, followed by g-t > a-a > c-t, a-c. bin ... | 1996 | 9003535 |
| polydeoxyguanine motifs in a 12-mer phosphorothioate oligodeoxynucleotide augment binding to the v3 loop of hiv-1 gp120 and potency of hiv-1 inhibition independency of g-tetrad formation. | phosphorothioate oligodeoxynucleotides belong to a class of polyanions that bind to the third variable domain (v3) of hiv-1 gp120 and inhibit infectivity of a wide variety of hiv-1 isolates. this potent v3 binding of phosphorothioate oligodeoxynucleotides, which is relatively independent of the nucleotide sequence of the oligodeoxynucleotides, decreases with chain length (below 18-mers) and is low for 8-mers. however, recent studies have observed a nucleotide sequence-dependent augmentation of p ... | 1996 | 9012864 |
| studying functional significance of the sequence 980-1061 in the central domain of human 18s rrna using complementary dna probes. | region 980-1061 in human 18s rrna has been chosen on the basis of our previous results, indicating that cross-linking sites of the alkylating mrna analogs are located within this region. in the present study, we have used 10 dna 15-mers complementary to various overlapping sequences within the 18s rrna positions 980-1061. their abilities to bind selectively to the target rrna sequences were proved by hydrolysis of 18s rrna within heteroduplexes with the corresponding probes by rnase h. four sequ ... | 1997 | 9061030 |
| effects of modifications near the 2-, 3- and 4-fold symmetry axes on human ferritin renaturation. | ferritin is a protein of 24 subunits which assemble into a shell with 432 point symmetry. it can be denatured reversibly in acidic guanidine hydrochloride, with the formation of poorly populated renaturation intermediates. in order to increase the accumulation of intermediates and to study the mechanism of ferritin renaturation, we analysed variants of the human ferritin h-chain altered at the n-terminus (delta(1-13)), near the 4-fold axis (leu-169 --> arg), the 3-fold axis (asp-131 --> ile + gl ... | 1997 | 9065764 |
| retroviral oligonucleotide distributions correlate with biased nucleotide compositions of retrovirus sequences, suggesting a duplicative stepwise molecular evolution. | a computer-assisted analysis was made of 24 complete nucleotide sequences selected from the vertebrate retroviruses to represent the ten viral groups. the conclusions of this analysis extend and strengthen the previously made hypothesis on the moloney murine leukemia virus: the evolution of the nucleotide sequence appears to have occurred mainly through at least three overlapping levels of duplication: (1) the distributions of overrepresented (3-6)-mers are consistent with the universal rule of ... | 1997 | 9069182 |
| cytoplasmic dna in entamoeba histolytica: its biological significance. | we report a study on the dna organization in entamoeba histolytica using a ribosomal dna probe. the rdna genes were found forming mers which were separated in a typical ladder pattern by pulse field electrophoresis. dna rosette structures were visualized through electron microscopy in dna eluted from bands recognized by the ribosomal probe. the in situ hybridization experiments using a dna probe suggested that the rdna genes are portioned between the nucleus and a cytoplasmic structure. these fi ... | 1997 | 9078580 |
| repair of o6-benzylguanine by the escherichia coli ada and ogt and the human o6-alkylguanine-dna alkyltransferases. | o6-methylguanine is removed from dna via the transfer of the methyl group to a cysteine acceptor site present in the dna repair protein o6-alkylguanine-dna alkyltransferase. the human alkyltransferase is inactivated by the free base o6-benzylguanine, raising the possibility that substantially larger alkyl groups could also be accepted as substrates. however, the escherichia coli alkyltransferase, ada-c, is not inactivated by o6-benzylguanine. the ada-c protein was rendered capable of reaction by ... | 1997 | 9079656 |
| probing structure/function relationships of hiv-1 reverse transcriptase with styrene oxide n2-guanine adducts. | details of the interactions between the human immunodeficiency virus (hiv-1) reverse transcriptase and substrate dna were probed both by introducing site-specific and stereospecific modifications into dna and by altering the structure of potential critical residues in the polymerase. unadducted 11-mer dnas and 11-mer dnas containing r and s enantiomers of styrene oxide at n2-guanine were ligated with two additional oligonucleotides to create 63-mers that served as templates for hiv-1 reverse tra ... | 1997 | 9079681 |
| [rapid detection of the escherichia cori verotoxin gene using fluorescence polarization]. | the effects of nacl concentration, temperature and base-pair mismatches on the hybridization of two complementary single-stranded dna 24-mers were investigated using a fluorescence polarization method. over a temperature range of 46 degrees c to 56 degrees c in 0.8 m nacl it was found that hybridization was essentially complete in under 10 minutes and that rapid in vitro determination of the target dna was possible when the sample dna had three or less base-pair mismatches in the 24-mer sequence ... | 1997 | 9086791 |
| sequence specific mutagenesis of the major (+)-anti-benzo[a]pyrene diol epoxide-dna adduct at a mutational hot spot in vitro and in escherichia coli cells. | in the supf gene, most (+)-anti-benzo[a]pyrene diol epoxide ((+)-anti-b[a]pde) mutagenesis hot spots in escherichia coli are in 5'-gg sequences [rodriguez and loechler (1993) carcinogenesis 14, 373-383]. a major hot spot was detected at g1 in the sequence 5'-gcg1g2-ccaaag, whereas g2 yielded very few mutants. in order to investigate the details of such sequence context effects of (+)-anti-b[a]pde mutagenesis, we have constructed 25-mer oligonucleotides and single-stranded m13 genomes containing ... | 1997 | 9114972 |
| evaluation of weight loss protocols for dogs. | several canine weight loss protocols were evaluated to determine their relative safety and efficacy. dogs were fed 100%, 75%, 60%, or 50% of maintenance energy requirements (mers) using the dogs' target body weights. no indications of adverse health effects were observed with any weight loss protocol. triiodothyronine (t3) levels and apparent mers decreased in dogs restricted to 50% to 60% of their mers. the rate of weight loss was correlated linearly with degree of calorie restriction, although ... | 1997 | 9138236 |
| estrogen receptor residues required for stereospecific ligand recognition and activation. | the mouse estrogen receptor (mer) has been shown to exhibit stereospecific binding of certain stilbene estrogen agonists. the region of the mer involved in the stereochemical recognition of ligands was further defined using a stilbene isomer, indenestrol b (ib). the ib compound has a chiral carbon bearing an ethyl substituent, and the wild type uterine mer has been shown to bind the enantiomers, ib-s and ib-r, with similar affinity. the wild type mer expressed in yeast exhibited a very minor pre ... | 1997 | 9139802 |
| differentiation of acinetobacter baumannii biotypes by amplification of 16s-23s rrna intergenic spacer sequences. | isolates of acinetobacter baumannii (32 strains) from blood samples obtained from patients in five chilean hospitals were identified and biotyped according to their phenotypic properties. they were also submitted to random amplified polymorphic dna (rapd) using eight randomly designed 10-mers and the core sequence of m13 phage (15-mers) as well as amplification of the spacer regions between 16s and 23s genes in the prokaryotic rrna genetic loci. with some primers, rapd discriminated between biot ... | 1996 | 9141712 |
| comparative pharmacokinetics, tissue distribution, and tumor accumulation of phosphorothioate, phosphorodithioate, and methylphosphonate oligonucleotides in nude mice. | the goals of this study were to systematically compare the pharmacokinetics and tissue distribution of phosphorothioate (ps), methylphosphonate (mp), and phosphorodithioate (ps2) oligonucleotide analogs; 15-mers of sequence d-tac gcc aac agc tcc (5'-3') complementary to the aug region of k-ras were radiolabeled with carbon-14. oligomers were administered as a single dose in the tail vein of nude mice harboring a k-ras-dependent human pancreatic tumor (cfpac1). the kinetics of ps, ps2, and mp oli ... | 1997 | 9149842 |
| the recb protein of escherichia coli translocates along single-stranded dna in the 3' to 5' direction: a proposed ratchet mechanism. | to investigate the role that the individual subunits play in the atp-dependent helicase activity of the recbcd protein we have investigated the ability of the recb, recc and recd proteins to displace various 20-mer oligonucleotides annealed to either end or to the centre of an oligonucleotide 60 bases long. the results show that the only subunit which can displace the 20-mers in the absence of the other subunits is the recb protein. moreover, the 20-mer is displaced only if it is annealed to the ... | 1997 | 9150267 |
| x-ray diffraction analysis of scrapie prion: intermediate and folded structures in a peptide containing two putative alpha-helices. | small proteinaceous infectious particles called prions cause certain neurodegenerative diseases in human and animals. limited proteolysis of infectious scrapie prions prp(sc) yields an n-truncated polypeptide termed prp 27-30, which encompasses residues 90 to 231 of prp(sc) and which assembles into 100 to 200 a wide amyloid rods. it has been hypothesized that the infectious prion is converted from its non-infectious cellular form (prp(c)) by means of an alpha-helical to beta-sheet conformational ... | 1997 | 9159477 |
| comparison of the three-dimensional structures of recombinant human h and horse l ferritins at high resolution. | mammalian ferritins are 24-mers assembled from two types of polypeptide chain which provide the molecule with different functions. h(eavy) chains catalyse the first step in iron storage, the oxidation of iron(ii). l(ight) chains promote the nucleation of the mineral ferrihydrite enabling storage of iron(iii) inside the protein shell. we report here the comparison of the three-dimensional structures of recombinant human h chain (huhf) and horse l chain (holf) ferritin homopolymers, which have bee ... | 1997 | 9159481 |
| misincorporation of dntps opposite 1,n2-ethenoguanine and 5,6,7,9-tetrahydro-7-hydroxy-9-oxoimidazo[1,2-a]purine in oligonucleotides by escherichia coli polymerases i exo- and ii exo-, t7 polymerase exo-, human immunodeficiency virus-1 reverse transcriptase, and rat polymerase beta. | 1,n2-ethenoguanine (1,n2-epsilon-gua) and 5,6,7,9-tetrahydro-7-hydroxy-9-oxoimidazo[1,2-a]purine (ho-ethanogua) are two modified bases formed in the reaction of dna with 2-chlorooxirane, the epoxide derivative of vinyl chloride. the oligonucleotides (19-mers), 5'-cagtgggtg*tccgaattga-3', were prepared, with each of these modified bases substituted for g at g*. ho-ethanodeoxyguanosine exists predominantly as a mixture of diastereomers of the closed cyclic hemiaminal form, 5,6,7,9-tetrahydro-7-hyd ... | 1997 | 9166777 |
| a hexameric phosphorothioate oligonucleotide telomerase inhibitor arrests growth of burkitt's lymphoma cells in vitro and in vivo. | a phosphorothioate oligonucleotide (ps-odn) with sequence identical to the repeat sequence of the mammalian telomere, 5'-d(ttaggg)-3', was incubated with a burkitt's lymphoma-derived (oma-bl1) cell line. this hexanucleotide inhibits telomerase activity in cell lysates, lengthens cell doubling time, and induces apoptosis. concatenated repeats (12-, 18-, and 24-mers) of the 5'-d(ttaggg)-3' motif induce similar cellular responses. scrambled sequences do not efficiently inhibit telomerase activity o ... | 1997 | 9169084 |
| selecting effective antisense reagents on combinatorial oligonucleotide arrays. | an array of 1,938 oligodeoxynucleotides (ons) ranging in length from monomers to 17-mers was fabricated on the surface of a glass plate and used to measure the potential of oligonucleotide for heteroduplex formation with rabbit beta-globin mrna. the oligonucleotides were complementary to the first 122 bases of mrna comprising the 5' utr and bases 1 to 69 of the first exon. surprisingly few oligonucleotides gave significant heteroduplex yield. antisense activity, measured in a rnase h assay and b ... | 1997 | 9181575 |
| significant role of electrostatic interactions for stabilization of protein assemblies. | contribution of electrostatic interactions to stability of bpti orthorhombic, pig-insulin cubic crystals, and horse l ferritin crystals was evaluated with numerical calculation of poisson-boltzmann equation based on a dielectric model. the stability of a ferritin molecule (24-mer) composed of 24 subunits was also evaluated. it was found that the surface charge-charge interactions at separation distances (< 5 a) were insensitive to variations in the ionic strength, and thus stabilized assembled s ... | 1997 | 9204125 |
| a specificity comparison of four antisense types: morpholino, 2'-o-methyl rna, dna, and phosphorothioate dna. | cell-free translation studies were carried out to compare the efficacy and specificity of four antisense structural types: dna, phosphorothioate dna (s-dna), 2'-o-methyl rna, and morpholino oligos, a novel antisense structural type. in these studies, translational inhibition was assessed for two 20-mers of each structural type, where one 20-mer was complementary to its target sequence in rabbit alpha-globin mrna and the other 20-mer contained three mispairs to that same target sequence. it is sh ... | 1997 | 9212905 |
| effect of transcriptional regulatory sequences on autonomous replication of plasmids in transient mammalian systems. | transcriptional regulatory sequences often influence the efficiency of dna replication, directly or indirectly, in bacteria, yeast, and animal virus systems. we have tested several transcriptional regulatory sequences for affecting dna replication, based on puc vector, in transient systems. autonomous replication of transfected plasmids was assayed by pcr amplification of the fragments derived from the plasmids, which had replicated in mammalian cells. by this highly efficient method of detectin ... | 1997 | 9212977 |
| kinetics of oxidized cytosine repair by endonuclease iii of escherichia coli. | endonuclease iii of escherichia coli excises a broad range of oxidized, hydrated and ring-fragmented pyrimidines from dna. the kinetic parameters were compared for repair of three potentially mutagenic oxidized cytosine lesions: 5,6-dihydroxy-5, 6-dihydro-2'-deoxyuridine (uracil glycol or ug), 5-hydroxy-2'-deoxycytidine (5-ohc), and 5-hydroxy-2'-deoxyuridine (5-ohu). site-specifically modified 40-mer oligonucleotides containing each of the three lesions in the same sequence context were synthesi ... | 1997 | 9214309 |
| inhibitory effects of telomere-mimic phosphorothioate oligonucleotides on various human tumor cells in vitro. | we tested the cell growth inhibitory effects of telomere-mimic oligomers, 5'-d(ttaggg)n-3' where n = 1, 2, 3 or 4 in the following 8 human tumor cell lines: 2780 ovarian carcinoma, hep-2 squamous cell carcinoma, vamt-1 mesothelioma, dnd-1a melanoma, molt-3 all, jurkat lymphoma, daudi burkitt lymphoma, and jar choriocarcinoma. as controls, 1 scrambled 6-mer and 2 scrambled 24-mers were tested. among the compounds tested, the 6-mer and 12-mer were not active in any of the cell lines studied. incre ... | 1997 | 9252662 |
| identification of aptamers against the dna template for in vitro transcription of the hiv-1 tar element. | we have extracted from a random population of about 10(9) oligodeoxynucleotides a series of 21-mers that are able to bind to a folded dna 76-mer used as a template for in vitro transcription of the tar element of the retrovirus hiv-1, by the t7 rna polymerase. five aptastrucs, that is, aptamers able to bind to the structure, out of 15 analyzed sequences, share the consensus motif 5'-pyggg(tg)pyc, complementary in part to a weak double-stranded region of the target. (the parentheses indicate that ... | 1997 | 9303189 |
| estimating the entropy of dna sequences. | the shannon entropy is a standard measure for the order state of symbol sequences, such as, for example, dna sequences. in order to incorporate correlations between symbols, the entropy of n-mers (consecutive strands of n symbols) has to be determined. here, an assay is presented to estimate such higher order entropies (block entropies) for dna sequences when the actual number of observations is small compared with the number of possible outcomes. the n-mer probability distribution underlying th ... | 1997 | 9344742 |
| murine transporter associated with antigen presentation (tap) preferences influence class i-restricted t cell responses. | the transporter associated with antigen presentation (tap) complex shuttles cytosolic peptides into the exocytic compartment for association with nascent major histocompatibility complex class i molecules. biochemical studies of murine and human tap have established that substrate length and cooh-terminal residue identity are strong determinants of transport efficiency. however, the existence of these specificities in the intact cell and their influences on t cell responses have not been demonst ... | 1997 | 9362526 |
| dna-dependent transregulation by ie1 of autographa californica nuclear polyhedrosis virus: ie1 domains required for transactivation and dna binding. | ie1 is the principal early transregulator of autographa californica multicapsid nuclear polyhedrosis virus (acmnpv). the 582-residue protein stimulates viral transcription and binds as a dimer to 28-bp palindromic repeats (28-mers) comprising the acmnpv homologous region (hr) transcription enhancers. to define ie1 domains responsible for hr-dependent transactivation, we first constructed a series of ie1 fusions to the dna binding domain of the yeast gal4 transactivator. in transfection assays, g ... | 1997 | 9371585 |
| molecular basis for the binding promiscuity of an anti-p24 (hiv-1) monoclonal antibody. | multiple binding capabilities utilized by specific protein-to-protein interactions in molecular recognition events are being documented increasingly but remain poorly understood at the molecular level. we identified five unrelated peptides that compete with each other for binding to the paratope region of the monoclonal anti-p24 (hiv-1) antibody cb4-1 by using a synthetic positional scanning combinatorial library xxxx[b1,b2,b3,x1,x2,x3]xxxx (14 mers; 68,590 peptide mixtures in total) prepared by ... | 1997 | 9413989 |
| partial characterization of guinea pig cholinephosphotransferase cdna. | an alternative molecular biology strategy is needed to characterize cholinephosphotransferase (cpt) gene because of the complexity of the problem associated with the solubilization of the membrane-bound enzyme without denaturation. we have synthesized five heterologous oligonucleotide probes based on the published yeast cpt gene sequence. each probe (24 to 30 mers) was used as either forward or reverse flanking primers in combination with lambda gt11 primers to amplify a segment of dna from a gu ... | 1997 | 9425300 |
| genomic signatures: tracing the origin of retroelements at the nucleotide level. | we investigate the nucleotide sequences of 23 retroelements (4 mammalian retroviruses, 1 human, 3 yeast, 2 plant, and 13 invertebrate retrotransposons) in terms of their oligonucleotide composition in order to address the problem of relationship between retrotransposons and retroviruses, and the coadaptation of these retroelements to their host genomes. we have identified by computer analysis over-represented 3-through 6-mers in each sequence. our results indicate retrotransposons are heterogene ... | 1997 | 9440280 |
| capture of single-stranded dna assisted by oligonucleotide modules. | real-time biospecific interaction analysis was employed to monitor direct capture of a hepatitis c virus (hcv) derived polymerase chain reaction (pcr) product by nucleic acid hybridization. different formats for hybridization were used to study the interaction between a single-stranded hcv pcr product and capture oligonucleotides immobilized on a sensor chip via streptavidin-biotin chemistry. by employing a prehybridization step in solution with nonbiotin oligonucleotides complementary to the si ... | 1998 | 9451504 |
| biologically active oligodeoxyribonucleotides--ix. synthesis and anti-hiv-1 activity of hexadeoxyribonucleotides, tgggag, bearing 3'- and 5'-end-modification. | we have determined that hexadeoxyribonucleotides (5'tgggag3'), with modified aromatic groups such as a trityl group at the 5'-end, have anti-hiv-1 activity in vitro. the 6-mer bearing a 3,4-dibenzyloxybenzyl (3,4-dbb) group at the 5'-end had the most potent activity and the least cytotoxicity. when the 3'-end of the 5'-(3,4-dbb)-modified 6-mer was substituted with a 2-hydroxyethylphosphate, a 2-hydroxyethylthiophosphate, or a methylphosphate group at the 3'-end, anti-hiv-1 activity increased. mo ... | 1997 | 9459021 |
| random amplification of polymorphic dna is useful for the differentiation of several anthropophilic dermatophytes. | the efficacy of random amplification of polymorphic dna (rapd) analysis, a polymerase chain reaction (pcr)-based technology, as a tool for differentiation of several anthropophilic dermatophytes, that is, trichophyton mentagrophytes var. interdigitale, t. rubrum and epidermophyton floccosum, was examined. total cellular dna extracted by a mini-preparation method were used as template dnas and pcrs were performed using five primers, all of which were synthesized 10-mers. all of the primers genera ... | 1997 | 9470403 |
| cyclobutane thymine dimers with a disrupted phosphodiester bond are refractory to t4 endonuclease v digestion but have increased sensitivity to uvrabc nuclease. | uv irradiation induces the dimerization of synthetic single-stranded, 80-mer oligonucleotides with self-complementary, alternating purine-pyrimidine sequences, and terminal 5'- and 3'-thymines; this process can be reversed by photoreactivation. the uv-induced 160-mers are sensitive to digestion by the restriction enzyme snabi, but monomers are insensitive to digestion, indicating that uv irradiation stabilizes the formation of double-stranded dna. these results suggest that uv irradiation of the ... | 1998 | 9521643 |
| replication origin of the broad host range plasmid rk2. positioning of various motifs is critical for initiation of replication. | the 393-base pair minimal origin, oriv, of plasmid rk2 contains three iterated motifs essential for initiation of replication: consensus sequences for binding the bacterial dnaa protein, dnaa boxes, which have recently been shown to bind the dnaa protein; 17-base pair direct repeats, iterons, which bind the plasmid encoded replication protein, trfa; and a + t-rich repeated sequences, 13-mers, which serve as the initial site of helix destabilization. to investigate how the organization of the rk2 ... | 1998 | 9525957 |
| base specificity of oligonucleotide digestion by calf spleen phosphodiesterase with matrix-assisted laser desorption ionization analysis. | calf spleen phosphodiesterase cleaves oligonucleotide strands in a stepwise manner from the 5' end and can be used in combination with matrix-assisted laser desorption ionization (maldi) mass spectrometry to perform ladder sequencing. the relative intensities of ladder peaks in the mass spectra of a series of 5-mers and 7-mers show that the rate of digestion is influenced by strand sequence. sequences terminating in a or g at the 5' end are found to react two to three times faster than sequences ... | 1998 | 9527844 |
| serological detection of attenuated hiv-1 variants with nef gene deletions. | to investigate whether members of a transfusion-linked cohort (the sydney bloodbank cohort) infected with a nef-deleted strain of hiv-1 could be differentiated from individuals infected with wild-type strains of hiv-1 by characterizing the nef antibody response of cohort members. | 1998 | 9583594 |
| further characterization of the binding of human recombinant interleukin 2 to heparin and identification of putative binding sites. | we have previously provided compelling evidence that human recombinant interleukin 2 (il-2) binds to the sulfated polysaccharides heparin, highly sulfated heparan sulfate and fucoidan. here we show that il-2 binding is dependent on heparin chain length, but with fragments as small as 15-mers retaining binding activity. the addition of exogenous heparin has no effect on the in vitro biological activity of il-2. in addition soluble il-2 receptor alpha and beta polypeptides do not compete with hepa ... | 1998 | 9597549 |
| affinity purification of recombinant cholera toxin b subunit oligomer expressed in bacillus brevis for potential human use as a mucosal adjuvant. | for use as a mucosal adjuvant for human vaccines, a simple method has been developed for the affinity purification of recombinant cholera toxin b subunit which had been expressed in a safe host, bacillus brevis. recombinant cholera toxin b subunit, adsorbed quantitatively to a d-galactose-agarose column, was eluted with an 0.1-0.4 m d-galactose gradient with a yield of > 90%. the cholera toxin b subunit preparation was similar to the native cholera toxin b subunit with respect to gm1 binding abi ... | 1998 | 9626936 |
| sequence context profoundly influences the mutagenic potency of trans-opened benzo[a]pyrene 7,8-diol 9,10-epoxide-purine nucleoside adducts in site-specific mutation studies. | the postoligomerization method was used to prepare oligonucleotide 16-mers that contained dado or dguo adducts, derived from trans opening of each enantiomer of the two diastereomeric benzo[a]pyrene 7,8-diol 9,10-epoxides, in two sequence contexts. these 16 oligonucleotides, along with the four corresponding oligonucleotides containing unsubstituted purines, were ligated into single-stranded dna from bacteriophage m13mp7l2 and transfected into escherichia coli smh77. the mutagenic effects of rep ... | 1998 | 9636059 |
| computerized polymorphic marker identification: experimental validation and a predicted human polymorphism catalog. | a computational system for the prediction of polymorphic loci directly and efficiently from human genomic sequence was developed and verified. a suite of programs, collectively called pompous (polymorphic marker prediction of ubiquitous simple sequences) detects tandem repeats ranging from dinucleotides up to 250 mers, scores them according to predicted level of polymorphism, and designs appropriate flanking primers for pcr amplification. this approach was validated on an approximately 750-kilob ... | 1998 | 9636181 |
| recognition of a common mycobacterial t-cell epitope in mpb59 of mycobacterium bovis. | bovine tuberculosis, which persists as a residual level of infection in many european countries, has implications not only for the economy of farming communities but also for human health. the aim of this study was to identify a common mycobacterial antigen which was recognized in bovine tuberculosis and to characterize the response to this antigen at the epitope level. a t-cell clone, phenotype cd4+, raised from an animal experimentally infected with mycobacterium bovis was shown to proliferate ... | 1998 | 9640240 |
| differentially expressed aortic genes in cholesterol-fed rabbits. | in order to identify key genes involved in the development of atherosclerotic lesions, differentially expressed genes in atherosclerotic plaques obtained from diet-induced hypercholesterolemic rabbit aorta were screened using the differential display (dd) rt-pcr technique. aortic rnas were isolated from rabbits fed cholesterol-supplemented (2% cholesterol in lab-chow, w/w) chow diet for 12 weeks, followed by the synthesis of cdnas by reverse-transcription using 2-base anchored oligo (dt) (5'-t11 ... | 1998 | 9666470 |
| identification of epitopes within beta lactoglobulin recognised by polyclonal antibodies using phage display and pepscan. | two different epitope mapping techniques were used to identify linear epitopes recognised by polyclonal igg antibodies from rabbits immunised with bovine beta lactoglobulin (blg), which is generally regarded as a major allergen in milk. the first, pepscan, was used to investigate the binding of several rabbit polyclonal antisera to sequential overlapping peptides (12-mers) across the sequence of blg. each peptide was synthesized on a different polypropylene pin, and a standard elisa procedure wa ... | 1998 | 9671121 |
| t-cell recognition of mycobacterial proteins mpb70 and mpb64 in cattle immunized with antigen and infected with mycobacterium bovis. | defined antigenic reagents and knowledge of t-cell responses are required for the design of improved diagnostic tests for bovine tuberculosis. the limited species distribution of mycobacterium bovis antigens mpb70 and mpb64 has indicated their potential for inclusion in future tests. the strategy adopted in this study was to define bovine t-cell responses to these antigens at the epitope level, using cattle immunized with recombinant forms of the antigens, and to compare these responses with cat ... | 1998 | 9714409 |
| high-level expression of the angiotensin-converting-enzyme-inhibiting peptide, yg-1, as tandem multimers in escherichia coli. | to produce a large quantity of the angiotensin-converting- enzyme(ace)-inhibiting peptide yg-1, which consists of ten amino acids derived from yeast glyceraldehyde-3-phosphate dehydrogenase, a high-level expression was explored with tandem multimers of the yg-1 gene in escherichia coli. the genes encoding yg-1 were tandemly multimerized to 9-mers, 18-mers and 27-mers, in which each of the repeating units in the tandem multimers was connected to the neighboring genes by a dna linker encoding pro- ... | 1998 | 9720202 |
| identification of troponin c antagonists from a phage-displayed random peptide library. | affinity purification of a phage-displayed library, expressing random peptide 12-mers at the n terminus of protein iii, has identified 10 distinct novel sequences which bind troponin c specifically. the troponin c-selected peptides yield a consensus binding sequence of (v/l)(d/e)xlkxxlxxla. sequence comparison revealed as much as a 62.5% similarity between phit5, the peptide sequence of the phage clone with the highest level of binding to troponin c, and the n-terminal region of troponin i isofo ... | 1998 | 9722581 |
| biologically active oligodeoxyribonucleotides. 5. 5'-end-substituted d(tgggag) possesses anti-human immunodeficiency virus type 1 activity by forming a g-quadruplex structure. | a series of hexadeoxyribonucleotides (6-mers), d(tgggag), substituted with a variety of aromatic groups at the 5'-end were synthesized and tested for anti-human immunodeficiency virus type 1 (hiv-1) activity. while unmodified d(tgggag) (31) had no anti-hiv-1 activity, compound 23 with a 3,4-di(benzyloxy)benzyl (dbb) group at the 5'-end potently inhibited the hiv-1iiib-induced cytopathicity of mt-4 cells in vitro (ic50 = 0.37 microm) without cytotoxicity up to 40 microm. a thermal denaturation st ... | 1998 | 9733490 |
| analysis of 2-chloro-2'-deoxyadenosine incorporation into cellular dna by quantitative polymerase chain reaction. | thermus aquaticus (taq) dna polymerase elongation is blocked by several dna adducts. this property has been exploited in polymerase chain reaction (pcr) methods to analyze cellular dna damage and repair after exposure to damaging agents. such methods have not been applied previously to detect nucleoside analog incorporation into cellular dna. 2-chloro-2'-deoxyadenosine (cldado), a deoxyadenosine analog, is clinically effective for hairy cell leukemia. cldado is taken up by cells, converted to th ... | 1998 | 9735141 |
| desensitization and sensitization of cells to fluoropyrimidines with different antisenses directed against thymidylate synthase messenger rna. | previous studies have shown that the cytotoxicity of fluoropyrimidines is mediated, in large part, by inhibition of the enzyme thymidylate synthase (ts). the aim of this study was to determine whether the chemosensitivity of human cancer cells to fluoropyrimidines could be increased by decreasing ts expression with antisense oligodeoxyribonucleotides (odns). odns (18-mers) targeted at the aug translational initiation site of ts mrna inhibited translation in a sequence- and dose-dependent manner ... | 1998 | 9748143 |
| tumour-specific mhc-class-ii-restricted responses after in vitro sensitization to synthetic peptides corresponding to gp100 and annexin ii eluted from melanoma cells. | in a search for potentially tumour-specific mhc-class-ii-restricted antigens, the immunogenicity of endogenous peptides that had been eluted from hla-dr molecules of the human melanoma cell line fm3 (hla-drb1*02x, drb1*0401) was tested in vitro. two 16-mers representing gp100 positions 44-59, and annexin ii positions 208-223 bound well to isolated drb1*0401 molecules and are discussed here. hla-dr-matched normal donors' t cells were cultured with peptide-pulsed artificial antigen-presenting cell ... | 1998 | 9755876 |
| [inhibition of hepatitis c virus by antisense oligodeoxynucleotide in vitro]. | to study inhibitory effect of antisense oligodeoxynucleotide (asodn) on hcv in vitro. | 1997 | 9772458 |
| nucleotide excision repair in the third kingdom. | nucleotide excision repair, a general repair mechanism for removing dna damage, is initiated by dual incisions bracketing the lesion. in procaryotes, the dual incisions result in excision of the damage in 12- to 13-nucleotide-long oligomers, and in eucaryotes they result in excision of the damage in the form of 24- to 32-nucleotide-long oligomers. we wished to find out if archaea perform excision repair. using cell extracts from methanobacterium thermoautotrophicum, we found that this organism r ... | 1998 | 9791138 |
| inter-species differentiation of benign theilerias by genomic fingerprinting with arbitrary primers. | a method was developed to obtain reproducible dna fingerprints from five distinct purified benign theileria genomic dnas by pcr-based amplification. randomly amplified polymorphic dna (rapd) profiles were obtained from 10 randomly designed 12-mers. however, nine of the 10 primers could generate the difference in rapd-pcr profiles which allowed discrimination of theileria species. the method has advantage of being simple, fast and sensitive for diagnosis and characterization of the parasites sinc ... | 1998 | 9806494 |
| flow cytometric analysis of the in situ accessibility of escherichia coli 16s rrna for fluorescently labeled oligonucleotide probes. | in situ identification of whole fixed bacterial cells by hybridization with fluorescently labeled, rrna-targeted oligonucleotide probes is often limited by low signal intensities. in addition to an impermeability of the cell periphery and a low cellular rrna content, the three-dimensional structure of the ribosome may hinder the access of oligonucleotides to their target sites. until now, a systematic study on the accessibility of 16s rrna target sites had not been done. here, we report fluoresc ... | 1998 | 9835591 |
| genomic dna sequencing by spel-6 primer walking using hexamer ligation. | dna sequencing by spel-6 (sequential primer elongation by ligation of 6-mers) primer walking is based on the rapid assembly of true primers by ligation of several (three to 10) contiguous hexamers complementary to a dna template saturated with escherichia coli single-stranded dna-binding protein. to prove the usefulness and to check the reliability of this method, a 3-kb dna fragment carrying the genes encoding the ecoviii restriction-modification (rm) system was sequenced with low redundancy (2 ... | 1998 | 9858694 |
| oxidation of guanines in the iron-responsive element rna: similar structures from chemical modification and recent nmr studies. | the translation or stability of the mrnas from ferritin, maconitase, erythroid aminoevulinate synthase and the transferrin receptor is controlled by the binding of two iron regulatory proteins to a family of hairpin-forming rna sequences called iron-responsive elements (ires). the determination of high-resolution nuclear magnetic resonance (nmr) structures of ire variants suggests an unusual hexaloop structure, leading to an intra-loop g-c base pair and a highly exposed loop guanine, and a speci ... | 1998 | 9862796 |
| single base discrimination of cenp-b repeats on mouse and human chromosomes with pna-fish. | the satellite repeat structure of the mammalian centromere contains the cenp-b protein binding site. using the peptide nucleic acid-fluorescence in situ hybridization (pna-fish), we show by direct pna-dna binding that all detectable cenp-b sites in a mammalian genome might have the same sequence. two species-specific pna 17-mers, pmm and pmc, were identified from cenp-b binding sites of mus musculus and m. caroli, respectively. fluorescence in situ hybridization confirmed that pmc hybridized to ... | 1999 | 9892726 |
| sequence context effects on mutational properties of cis-opened benzo[c]phenanthrene diol epoxide-deoxyadenosine adducts in site-specific mutation studies. | diastereomeric n6-substituted dado adducts (cis b[c]phde-2/1r and cis b[c]phde-2/1s) that correspond to cis-opening at c-1 of the enantiomeric benzo[c]phenanthrene 3,4-diol 1,2-epoxides in which the epoxide oxygen and the benzylic hydroxyl group are trans (de-2) were synthetically incorporated into oligonucleotide 16-mers. each adduct was placed at the fourth nucleotide from the 5'-end of each of two different oligonucleotide sequences derived from the e. coli supf gene. each adduct was also pla ... | 1999 | 9894012 |
| oligomerization and phase separation in globular protein solutions. | we have chemically crosslinked a globular protein, gamma iiib-crystallin, to produce a system of well-defined oligomers: monomers, dimers, trimers and a mixture of higher n-mers. gel electrophoresis, size exclusion chromatography, quasielastic light scattering spectroscopy, and electrospray ionization mass spectrometry were used to characterize the oligomers formed. the liquid-liquid phase separation boundaries of the various oligomers were measured. we find that at a given concentration the pha ... | 1998 | 9894340 |
| biologically active oligodeoxyribonucleotides. part 11: the least phosphate-modification of quadruplex-forming hexadeoxyribonucleotide tgggag, bearing 3-and 5-end-modification, with anti-hiv-1 activity. | we have found that a hexadeoxyribonucleotide (5'tgggag3', r-95288), koizumi, m. et al. bioorganic & medicinal chemistry, 1997, 5, 2235, bearing a 3,4-dibenzyloxybenzyl (3,4-dbb) group at the 5'-end and a 2-hydroxyethylphosphate at the 3'-end, has high anti-hiv-1 activity and the least cytotoxicity in vitro and in vivo. in order to synthesize more potent hexadeoxyribonucleotides, we substituted phosphodiester (p-o) bonds in the 6-mer with the least phosphorothioate (p-s), phosphoramidate (p-n), o ... | 1998 | 9925303 |
| oligodeoxynucleotides as probes for in situ hybridization with transmission electron microscopy to specifically localize phytoplasma in plant cells. | phytoplasmas are plant-pathogenic mollicutes restricted to phloem. they belong to several groups in a unique phylogenetic clade. non-related phytoplasmas may infect the same plant species, often with similar symptoms. hence methods are needed to specifically localize phytoplasmas and to study their multiplication and movement in their hosts. conditions for post-embedding in situ hybridization (ish) with transmission electron microscopy using oligodeoxynucleotides as probes for labelling of phyto ... | 1999 | 10024432 |
| differential display cloning of genes induced in regenerating neurons. | mammalian adult motor and sensory neurons are thought to reexpress a complement of genes that are originally expressed during development when they regenerate following injury. therefore, one strategy for identifying key genes involved in development of the peripheral nervous system is to identify those genes reexpressed in the regenerating system. to test this hypothesis, we used the single-base anchor method of mrna differential display to study changes in gene expression in regenerating adult ... | 1998 | 10049646 |
| hybridization of antisense oligonucleotides with the 3'part of trna(phe). | the interaction of antisense oligodeoxyribonucleotides with yeast trna(phe) was investigated. 14-15-mers complementary to the 3'-terminal sequence including the acca end bind to the trna under physiological conditions. at low oligonucleotide concentrations the binding occurs at the unique complementary site. at higher oligonucleotide concentrations, the second oligonucleotide molecule binds to the complex due to non-perfect duplex formation in the t-loop stabilized by stacking between the two bo ... | 1999 | 10050762 |
| iron homeostasis alteration in transgenic tobacco overexpressing ferritin. | intracellular iron concentration requires tight control and is regulated both at the uptake and storage levels. our knowledge of the role that the iron-storage protein ferritins play in plants is still very limited. overexpression of this protein, either in the cytoplasm or the plastids of transgenic tobacco, was obtained by placing soybean ferritin cdna cassettes under the control of the camv 35s promoter. the protein accumulated in 4- and 6-day-old seedlings and in leaves of 3-week-old plants ... | 1999 | 10069070 |
| mutational consequences of replication of m13mp7l2 constructs containing cis-opened benzo[a]pyrene 7,8-diol 9, 10-epoxide-deoxyadenosine adducts. | the four adducts that arise by cis ring opening of the four optically active benzo[a]pyrene diol epoxides by the exocyclic n6-amino group of deoxyadenosine were incorporated synthetically into each of two different oligonucleotide 16-mers, 5'-tttxgagtctgctccc-3' [context i(a)] and 5'-cagxtttagagtctgc-3' [context ii(a)], at the x position. the eight resultant oligonucleotides were separately ligated into bacteriophage m13mp7l2 and replicated in escherichia coli that had been sos-induced, and the ... | 1999 | 10077488 |
| defined oligonucleotide tag pools and pcr screening in signature-tagged mutagenesis of essential genes from bacteria. | we describe a fast and simple method for signature-tagged mutagenesis (stm) using defined oligonucleotides for tag construction into mini-tn5 and pcr instead of hybridization for rapid screening of bacterial mutants in vivo. a collection of 12 unique 21-mers were synthesized as complementary dna strands to tag bacterial mutants constructed by insertional mutagenesis using putmini-tn5km2 plasmids. tags were tested in a combination of assays by pcr and compared to hybridization for specificity and ... | 1999 | 10090989 |
| dynamic epigenetic regulation of initial o-glycosylation by udp-n-acetylgalactosamine:peptide n-acetylgalactosaminyltransferases. site-specific glycosylation of muc1 repeat peptide influences the substrate qualities at adjacent or distant ser/thr positions. | in search of possible epigenetic regulatory mechanisms ruling the initiation of o-glycosylation by polypeptide:n-acetylgalactosaminyltransferases, we studied the influences of mono- and disaccharide substituents of glycopeptide substrates on the site-specific in vitro addition of n-acetylgalactosamine (galnac) residues by recombinant galnac-ts (rgalnac-t1, -t2, and -t3). the substrates were 20-mers (hgv20) or 21-mers (ahg21) of the muc1 tandem repeat peptide carrying galnacalpha or galbeta1-3gal ... | 1999 | 10187769 |
| redox reactivity of animal apoferritins and apoheteropolymers assembled from recombinant heavy and light human chain ferritins. | the redox reactivities of air-oxidized apo horse spleen ferritin (hosf) and apo rat liver ferritin (raf) were examined by microcoulometry and reductive optical titrations. microcoulometry on several independent lots of commercial hosf revealed two distinct types of redox activity: one requiring 3-4 electrons and one requiring 6-7 electrons for full reduction of the protein shell. aporaf required 8-9 electrons to fully reduce the oxidized form. reductive optical titrations confirmed the microcoul ... | 1999 | 10194323 |
| assembly of the herpes simplex virus procapsid from purified components and identification of small complexes containing the major capsid and scaffolding proteins. | an in vitro system is described for the assembly of herpes simplex virus type 1 (hsv-1) procapsids beginning with three purified components, the major capsid protein (vp5), the triplexes (vp19c plus vp23), and a hybrid scaffolding protein. each component was purified from insect cells expressing the relevant protein(s) from an appropriate recombinant baculovirus vector. procapsids formed when the three purified components were mixed and incubated for 1 h at 37 degrees c. procapsids assembled in ... | 1999 | 10196320 |
| mutation of an active site residue in escherichia coli uracil-dna glycosylase: effect on dna binding, uracil inhibition and catalysis. | the role of the conserved histidine-187 located in the leucine intercalation loop of escherichia coli uracil-dna glycosylase (ung) was investigated. using site-directed mutagenesis, an ung h187d mutant protein was created, overproduced, purified to apparent homogeneity, and characterized in comparison to wild-type ung. the properties of ung h187d differed from ung with respect to specific activity, substrate specificity, dna binding, ph optimum, and inhibition by uracil analogues. ung h187d exhi ... | 1999 | 10200172 |
| interaction of seqa and dam methylase on the hemimethylated origin of escherichia coli chromosomal dna replication. | preferential binding of seqa protein to hemimethylated oric, the origin of escherichia coli chromosomal replication, delays methylation by dam methylase. because the seqa-oric interaction appears to be essential in timing of chromosomal replication initiation, the biochemical functions of seqa protein and dam methylase at the 13-mer l, m, and r region containing 4 gatc sequences at the left end of oric were examined. we found that seqa protein preferentially bound hemimethylated 13-mers but not ... | 1999 | 10206949 |
| polymer solution-filled column for the analysis of antisense phosphorothioates by capillary electrophoresis. | a capillary electrophoresis (ce) column filled with 13% poly(ethylene glycol) (peg) solution is demonstrated to resolve different lengths of antisense phosphorothioates in 100 mm tris-borate (ph 9.0) buffer containing 30% formamide at 50 degrees c. two sets of mixtures composed of 15-20 mers of either antisense phosphorothioate or phosphodiester oligonucleotides were synthesized based on a sequence of the antisense orientation directed against dna-methyltransferase (denoted as mt-as) and were us ... | 1999 | 10217170 |
| specific binding of human msh2.msh6 mismatch-repair protein heterodimers to dna incorporating thymine- or uracil-containing uv light photoproducts opposite mismatched bases. | previous studies have demonstrated recognition of dna-containing uv light photoproducts by bacterial (feng, w.-y., lee, e., and hays, j. b. (1991) genetics 129, 1007-1020) and human (mu, d., tursun, m., duckett, d. r., drummond, j. t., modrich, p., and sancar, a. (1997) mol. cell. biol. 17, 760-769) long-patch mismatch-repair systems. mismatch repair directed specifically against incorrect bases inserted during semi-conservative dna replication might efficiently antagonize uv mutagenesis. to tes ... | 1999 | 10358035 |