Publications

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
[inhibition of hepatitis c virus by antisense oligodeoxynucleotide in vitro].	to study inhibitory effect of antisense oligodeoxynucleotide (asodn) on hcv in vitro.	1997	9772458
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
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
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
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
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
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
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
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
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
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
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-drb102x, drb10401) 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
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
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
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
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
peptide agonists of the thrombopoietin receptor.	we have screened a variety of l-amino acid peptide libraries against the extracellular domain of the human thrombopoietin (hutpo) receptor, c-mpl. a large number of peptide ligands were recovered and categorized into two families. peptides from each family compete with the binding of hutpo and with the binding of peptides from the other familiy. representative peptides were synthesized and found to activate the full-length hutpo receptor expressed in ba/f3 cells to promote proliferation. these p ...	1998	11012174
dna fingerprinting analysis by a pcr based method for monitoring the genotoxic effects of heavy metals pollution.	environmental pollutants can have deleterious effects on living organisms. at high concentrations, or at high activities, they can cause acute toxicity damaging cells, tissues and organs. chronic toxification, on the other hand, can also cause serious damage from bio-accumulation. plants, as biological indicators, can measure both the actual and the potential effects of pollutants, when they are used to measure effects of heavy metals. we have applied a system of "molecular fingerprinting" based ...	1998	9839398
a free energy analysis by unfolding applied to 125-mers on a cubic lattice.	a common approach to the protein folding problem involves computer simulation of folding using lattice models of amino acid sequences. key factors for good performance in such models are the correct choice of the temperature and the average interaction energy between residues. in order to push the lattice approach to its limit it is important to have a method to adjust these parameters for optimal folding that is not limited by our ability to successfully simulate folding in a reasonable time.	1998	9502320
the detection of oligonucleotide n3'-->p5' phosphoramidate/rna duplexes with capillary gel electrophoresis.	oligonucleotide n3'-->p5' phosphoramidates (3'-phosphoramidates) are dna analogs that are presently under investigation as potential therapeutic agents. these compounds may also hold promise as a diagnostic tool. here, we describe a rapid method for the analysis of single-stranded rna fragments utilizing 3'-phosphoramidate oligonucleotides as probes in conjunction with capillary gel electrophoresis (cge). 3'-phosphoramidate 9-mers were mixed with complimentary rna, and cge was used to monitor du ...	1998	9694262
identification, composition, and asymmetric formation mechanism of glycidyl methacrylate/butyl methacrylate copolymers up to 7000 da from electrospray ionization ultrahigh-resolution fourier transform ion cyclotron resonance mass spectrometry.	glycidyl methacrylate (gma) and butyl methacrylate (bma) have the same nominal mass (142 da) but differ in exact mass by 0.036 da (ch(4) vs o). therefore, copolymers formed from the two isobaric monomers exhibit a characteristic isobaric distribution due to different monomer compositions. here, we show that electrospray ionization ft-icr mass spectrometry at 9.4 t resolves the isobaric components of copolymers as large as 7000 da with a resolving power (m/δm(50%)) of ∼500 000 in a gel permeation ...	1998	21644659
mermade: an oligodeoxyribonucleotide synthesizer for high throughput oligonucleotide production in dual 96-well plates.	we have designed and constructed a machine that synthesizes two standard 96-well plates of oligonucleotides in a single run using standard phosphoramidite chemistry. the machine is capable of making a combination of standard, degenerate, or modified oligos in a single plate. the run time is typically 17 hr for two plates of 20-mers and a reaction scale of 40 nm. the reaction vessel is a standard polypropylene 96-well plate with a hole drilled in the bottom of each well. the two plates are placed ...	1998	9685322
enhancement of insect antifreeze protein activity by solutes of low molecular mass.	antifreeze proteins (afps) lower the non-equilibrium freezing point of water (in the presence of ice) below the melting point, thereby producing a difference between the freezing and melting points that has been termed thermal hysteresis. in general, the magnitude of the thermal hysteresis depends upon the specific activity and concentration of the afp. this study describes several low-molecular-mass solutes that enhance the thermal hysteresis activity of an afp from overwintering larvae of the ...	1998	9662495
in vitro inhibition of ras-raf association by short peptides.	seven amino acid peptides were tested as in vitro inhibitors of oncogenic ras-raf association. the sequences of these peptides were derived from the h-ras effector region (amino acids 25 to 51) and the ras binding domain of raf-1 (amino acids 64 to 105). eleven out of the twenty-one ras 7-mers tested inhibited formation of the ras-raf complex by at least 20% at 100 microm. the most potent of these inhibitory peptides contained the effector residues 32 to 37 or 40 to 45. of the raf-1 peptides tes ...	1998	9636675
conformations of nicked and gapped dna structures by nmr and molecular dynamic simulations in water.	we have analyzed and compared the molecular structures and dynamics of dna duplexes containing a nick or a gap of one nucleotide where the base in front of the gap is a guanine. the continuous strand has the sequence 5'(cagagtcxctggctc) where the residue x is absent for the nick, 14-mer, and where it is a g residue for the gap. duplexes were formed with the two corresponding 7-mers. neither of these is phosphorylated adjacent at the nick site, but it is a good model for a single strand break. fo ...	1998	9521727
spectroscopic studies of single-stranded dna ligands and oxazole yellow dyes.	interactions between short single-stranded dna ligands and fluorescent dna indicator dyes were used to investigate binding selectivity of the ligands. conformational differences among four dna ligands of different sequence and structure, including two that form a g-quartet and two that do not, were confirmed by circular dichroism spectroscopy. their interactions with indicator dyes yo-pro-1 iodide (yo) and yoyo-1 iodide (yoyo) were probed using measurements of dye absorbance; induced circular di ...	1998	9547012
sequence dependent n-terminal rearrangement and degradation of peptide nucleic acid (pna) in aqueous solution.	the stability of the pna (peptide nucleic acid) thymine monomer ¿n-[2-(thymin-1-ylacetyl)]-n-(2-aminoaminoethyl)glycine¿ and those of various pna oligomers (5-8-mers) have been measured at room temperature (20 degrees c) as a function of ph. the thymine monomer undergoes n-acyl transfer rearrangement with a half-life of 34 days at ph 11 as analyzed by 1h nmr; and two reactions, the n-acyl transfer and a sequential degradation, are found by hplc analysis to occur at measurable rates for the oligo ...	1998	11543609
effect of single benzo[a]pyrene diol epoxide-deoxyguanosine adducts on the action of dna polymerases in vitro.	neither sequenase 2.0 nor klenow fragment were able to extend 12-mer primers using the eight templates (16-mers) derived by placing each of the four isomeric benzo[a]pyrene diol epoxide-deoxyguanosine adducts at the 13th nucleotide from the 3'-end of two different sequence contexts. using an 11-mer primer to get a running start did not overcome the adduct induced block of primer extension except for the klenow fragment and one of the two sequence contexts, indicating primer extension is dependen ...	1998	9664121
oligonucleotides bearing 5-formyl-2'-o-methyluridine: preference in binding affinity to the nf-kappa b (p50)2 homo- and p50/p65 heterodimers.	5-formyl-2'-o-methyluridine was incorporated into the various positions of oligonucleotide 26-mers containing the nf-kappa b binding sequence. some of them showed binding selectivity toward the homo- and heterodimers of subunits of nf-kappa b.	1998	9873704
kinetic steps for alpha-helix formation.	the kinetics of alpha-helix formation in polyalanine and polyglycine eicosamers (20-mers) were examined using torsional-coordinate molecular dynamics (md). of one hundred fifty-five md experiments on extended (ala)20 carried out for 0.5 ns each, 129 (83%) formed a persistent alpha-helix. in contrast, the extended state of (gly)20 only formed a right-handed alpha-helix in two of the 20 md experiments (10%), and these helices were not as long or as persistent as those of polyalanine. these simulat ...	1998	9829694
blackbody infrared radiative dissociation of oligonucleotide anions.	the dissociation kinetics of a series of doubly deprotonated oligonucleotide 7-mers [d(a)7(2-), d(aattaat)2-, d(ttaatta)2-, and d(ccggccg)2-] were measured using blackbody infrared radiative dissociation in a fourier-transform mass spectrometer. the oligonucleotides dissociate first by cleavage at the glycosidic bond leading to the loss of a neutral nucleobase, followed by cleavage at the adjacent (5') phosphodiester bond to produce structurally informative a-base and w type ions. from the tempe ...	1998	9794082
clinical implications of p53 autoantibodies in the sera of patients with non-small-cell lung cancer.	the presence of autoantibodies to p53 protein has been associated with the presence of p53 (also known as tp53) gene mutations in primary tumors and with poor prognosis. this study was undertaken to determine the clinical significance of p53 autoantibodies in patients with non-small-cell lung cancer (nsclc).	1998	9790550
cellular and molecular characterization of a major soybean allergen.	soybean proteins share a large number of cross-reacting allergens with other members of the legume family; however, soy-allergic patients rarely react clinically to other members of the legume family. gly m bd 30k, an ige-binding protein with a molecular weight of 30 kd, was identified in soybean extracts by western ige-immunoblot analysis. this monomeric allergen was shown to have an n-terminal amino acid sequence and amino acid composition identical to that of the seed 34-kd protein, p34, a th ...	1998	9751845
bacteriophage p2 and p4 morphogenesis: structure and function of the connector.	the connector, the structure located between the bacteriophage capsid and tail, is interesting from several points of view. the connector is in many cases involved in the initiation of the capsid assembly process, functions as a gate for dna transport in and out of the capsid, and is, as implied by the name, the structure connecting a tail to the capsid. occupying a position on a 5-fold axis in the capsid and connected to a coaxial 6-fold tail, it mediates a symmetry mismatch between the two. to ...	1998	9614863
molecular characterization and sequencing of antifreeze proteins from larvae of the beetle dendroides canadensis.	the deduced amino acid sequences of antifreeze proteins (afps) from larvae of the beetle dendroides canadensis were determined from both complementary dnas (cdnas) and from peptide sequencing. these consisted of proteins with a 25-residue signal peptide and mature proteins 83 (dendroides antifreeze protein; dafp-1) or 84 (dafp-2) amino acids in length which differed at only two positions. peptide sequencing yielded sequences which overlapped exactly with those of the deduced cdna sequences of da ...	1998	9591363
sequence dependence and characteristics of bends induced by site-specific polynuclear aromatic carcinogen-deoxyguanosine lesions in oligonucleotides.	the tumorigenic metabolite of benzo[a]pyrene, the (+)-7r,8s,9s,10r enantiomer, and the nontumorigenic mirror-image isomer, (-)-7s,8r,9r, 10s, of r7,t8-dihydroxy-t9,10-epoxy-7,8,9, 10-tetrahydrobenzo[a]pyrene (anti-bpde) bind covalently to the exocyclic amino group of deoxyguanosine (n2-dg) in native dna. these adducts can cause structural perturbations such as dna bends, which in turn may influence the cellular processing of these lesions. the characteristics of bends in site-specifically modifi ...	1998	9538018
mapping of the interleukin-10/interleukin-10 receptor combining site.	the discontinuous interleukin-10(il-10)/interleukin-10 receptor (il-10r) combining site was mapped using sets of overlapping peptides derived from both binding partners bound to continuous cellulose membranes. low affinity binding of single regions of the discontinuous contact sites on il-10 and il-10r could be identified due to (1) high peptide density on the membrane support, (2) incubation with high protein concentrations, (3) indirect immunodetection of the ligates after electrotransfer onto ...	1998	9568901
oxazole yellow dye interactions with short dna oligomers of homogeneous base composition and their hybrids.	interactions between short single-stranded dna oligomers of homogeneous base composition and the fluorescent probes oxazole yellow (yo) and its homodimer yoyo are described. the oligomers included 15-mers and 30-mers of polyda, polydt, polydg, and polydc. interactions between the dyes and dna hybrids formed from complementary homogeneous strands of equal length were also investigated. no interactions were observed between the dyes and the monomeric monophosphate nucleosides a, g, t, or c. the dy ...	1998	9547011
genetic and alkaloid analysis of papaver species and their f1 hybrid by rapd, hplc and elisa.	total dna was extracted from the leaves of a f1 hybrid and its parents, papaver bracteatum lindle and p. pseudo-orientale medw. analysis of random-amplified polymorphic dna (rapd) using ten arbitrary oligonucleotide 10-mers, showed that f1 hybrid was confirmed to be genetically intermediate of both parental plants compared with the genetic distance between f1 hybrid and individual parents. furthermore, the comparison of the band patterns between a f1 hybrid, p. bracteatum and p. pseudo-orientale ...	1998	9530831
comparison of mass spectrometric techniques for generating molecular weight information on a class of ethoxylated oligomers.	the results of fast atom bombardment (fab), time-of-flight secondary ion mass spectrometry (tof-sims), matrix-assisted laser desorption/ionization (mald/i), electrospray ionization (esi), and field desorption (fd) analyses of ethoxylated oligomers of 2,4,7,9-tetramethyl-5-decyne-4,7-diol (surfynol(®) 104) were compared.each of these desorption mass spectrometry (ms) techniques can produce spectra of unfragmented cationized oligomers. from the observed ion series we calculate average molecular we ...	1998	27518863
synthesis, biophysical properties, and nuclease resistance properties of mixed backbone oligodeoxynucleotides containing cationic internucleoside guanidinium linkages: deoxynucleic guanidine/dna chimeras.	the synthesis of mixed backbone oligodeoxynucleotides (18-mers) consisting of positively charged guanidinium linkages along with negatively charged phosphodiester linkages is carried out. the use of a base labile-protecting group for guanidinium linkage offers a synthetic strategy similar to standard oligonucleotide synthesis. the nuclease resistance of the oligodeoxyribonucleotides capped with guanidinium linkages at 5' and 3' ends are reported. the hybridization properties and sequence specifi ...	1998	9736687
hybridization of complementary strand and single-base mutated oligonucleotides detected with an on-line acoustic wave sensor.	the hybridization of a biotinylated 25-mer oligonucleotide probe with complementary, non-complementary and single-base mutated 25-mer targets at the liquid-solid (neutravidin-modified) interface of a thickness-shear mode acoustic wave device was studied. the sensor was incorporated into an on-line configuration capable of both variable flow and stop-flow experiments. under ambient temperature conditions different signals were obtained for the complementary and non-complementary cases. at higher ...	1998	10209884
dr (mhc class ii) ligands: an approach to rheumatoid arthritis therapeutics.	the presentation of peptide antigens to t-cells by mhc class ii proteins is a central process in cellular and humoral immune responses. blockade of this presentation event via synthetic ligands that bind to disease-associated mhcs (such as dr1 and dr4) may be useful for the treatment of autoimmune diseases such as rheumatoid arthritis, type 1 diabetes, multiple sclerosis, lupus erthymatosis and graves disease. recently reported synthetic ligands for dr1 and dr4 are short modified peptides (2-7 m ...	1998	10197051
in vitro evaluation of the haemostatic value of the lfb-von willebrand factor concentrate.	the structural and functional studies of the concentrate of von willebrand factor (vwf) manufactured by lfb have been first performed as part of the preclinical development of this product specially intended for the treatment of von willebrand disease. the electrophoretic analyses showed the high purity of lfb-vwf concentrate (specific activity of 100 iu of ristocetin cofactor activity per milligram of protein) and the multimeric pattern attesting the presence of high molecular weight multimeter ...	1998	10028317
triplex formation by oligonucleotides containing 5-(1-propynyl)-2'-deoxyuridine: decreased magnesium dependence and improved intracellular gene targeting.	oligonucleotides capable of sequence-specific triple helix formation have been proposed as dna binding ligands useful for modulation of gene expression and for directed genome modification. however, the effectiveness of such triplex-forming oligonucleotides (tfos) depends on their ability to bind to their target sites within cells, and this can be limited under physiologic conditions. in particular, triplex formation in the pyrimidine motif is favored by unphysiologically low ph and high magnesi ...	1999	10026270
low-energy (5-25 ev) electron damage to homo-oligonucleotides.	radiation-induced damage to homo-oligonucleotides is investigated by electron-stimulated desorption of neutral fragments from chemisorbed organic films. six and 12 mers of cytidine phosphate (poly dcs) and thymidine phosphate (poly dts) are chemisorbed from various solutions onto a crystalline gold substrate by a thiol modification at the 3' end and are irradiated under ultra-high vacuum conditions with 5-25 ev electrons. the mass selected neutral desorption yields consist mainly of fragments of ...	1999	10073671
electrospray quadrupole mass spectrometry analysis of model oligonucleotides and polymerase chain reaction products: determination of base substitutions, nucleotide additions/deletions, and chemical modifications.	esi fticr mass spectrometry is the only technique currently used for accurate molecular weight analysis of pcr products above 100 bp in size. this is important in demonstrating the potential for ms in making major contributions in the molecular biology and genomics areas. in the near future, it is more likely that less expensive, more user friendly ms techniques will be used for high-throughput analyses (including maldi tof and esi quadrupole). there have been numerous reports on the use of mald ...	1999	10424176
the role of linkers in the reassembly of the 3.6 mda hexagonal bilayer hemoglobin from lumbricus terrestris.	the extent and kinetics of reassembly of the four groups of linkers l1-l4 with 213 kda subassemblies of twelve globin chains d, (bac)3(d)3, isolated from the approximately 3.6 mda hexagonal bilayer (hbl) hemoglobin (hb) of lumbricus terrestris, was investigated using gel filtration. the reassembled hbl's were characterized by scanning transmission electron microscopic (stem) mass mapping and their subunit content determined by reversed-phase chromatography. in reassembly by method (a), the linke ...	1999	10373372
trans-(nh3)(2)pt(ii)-modified deoxyoligonucleotides as potential antisense agents: cross-linking reactions between two 12-mers.	an approach is presented which probes the possible use of trans-[(nh3)(2)ptcl](+)-modified deoxyoligonucleotides in the antisense strategy. it consists of (1) the selective platination of an oligonucleotide containing 11 pyrimidine (t, c) bases as well as a single guanine (g) as a pt-anchoring group at the 5'-end to give trans-[(nh3)(2)pt¿5'-d(g(n7)t(2)c(2)t(2)c(2)t(2)c¿cl](10-) 1 ("antisense strand") and (2) subsequent hybridization with the purine 12-mer 5'-d(ga(2)g(2)a(2)g(2)a(2)g)(11-) ("sen ...	1999	10550694
electrochemical polymerization of aniline investigated using on-line electrochemistry/electrospray mass spectrometry.	a thin-layer electrochemical flow cell coupled on-line with electrospray mass spectrometry (ec/es-ms) was used to investigate the soluble products from the controlled-potential anodic polymerization of aniline in h(2)o and h(2)o/ch(3)oh (1/1 v/v) with ammonium acetate and acetic acid or ammonium hydroxide as electrolytes (ph 4, 6.5, or 9). at a working electrode (glassy carbon) potential of 1.0 v versus ag/agcl, singly protonated aniline oligomers containing as many as 10 aniline units (10-mer) ...	1999	21662856
sequence specific hybridization properties of methylphosphonate oligodeoxynucleotides.	methylphosphonate oligodeoxynucleotides (mpo's) with isomerically pure rp-configurated methylphosphonates (mp's) were synthesized by block coupling of apt and tpa dinucleoside methylphosphonates (dmp's, p indicating mp-linkage). oligonucleotide duplexes (20 mers) with these rp-mp's showed almost the same melting temperatures (tm) as those with phosphorodiester bonds. further a dependence of the duplex stability from the nucleosides (bases) adjacent to the mp moiety was observed. for the first ti ...	1999	10447202
abasic sites in duplex dna: molecular modeling of sequence-dependent effects on conformation.	molecular modeling calculations using junction minimization of nucleic acids (jumna) have been used to study sequence effects on the conformation of abasic sites within duplex dna. we have considered lesions leading to all possible unpaired bases (x), adenine, guanine, cytosine, or thymine contained within two distinct sequence contexts, cxc and gxg. calculations were carried out on dna 11-mers using extensive conformational search techniques to locate the most stable abasic conformations and us ...	1999	10585943
observation of daunomycin and nogalamycin complexes with duplex dna using electrospray ionisation mass spectrometry.	the noncovalent binding of the antitumour drugs daunomycin and nogalamycin to duplex dna has been studied using electrospray ionisation mass spectrometry (esi-ms). the conditions for the preparation of drug/duplex dna complexes and for their detection by esi-ms have been optimised. ions corresponding to these complexes were most abundant relative to free dna when prepared in the ph range 8-9, and using gentle esi interface conditions. self-complementary oligonucleotides, 5'-d(ggctagcc)-3' or 5'- ...	1999	10589098
lattice-fluid model for gas-liquid chromatography.	lattice-fluid models describe molecular ensembles in terms of the number of lattice sites occupied by molecular species (r-mers) and the interactions between neighboring molecules. the lattice-fluid model proposed by sanchez and lacombe (macromolecules, 1978;11:1145-1156) was used to model specific retention volume data for a series of n-alkane solutes with n-alkane, polystyrene, and poly(dimethylsiloxane) stationary liquid phases. theoretical equations were derived for the specific retention vo ...	1999	10588340
a novel strategy to generate biologically active neo-glycosaminoglycan conjugates.	heparin and heparan sulfate are structurally related polysaccharides with a variety of biological effects/functions. most of these effects are due to interactions, of varying specificity, between the negatively charged polysaccharide chains and proteins. while such interactions generally involve a single saccharide domain of decasaccharide size or less, ternary complexes of two protein molecules binding to separate domains on a single polysaccharide chain are known to occur. to facilitate studie ...	1999	10561458
dna homo as a new landmark for nucleic acid properties. ab initio calculations and experimental mapping.	of the non-covalent binding forces in dna-drug or dna-protein interaction, electrostatic interaction, stacking interaction, hydrogen bonds and hydrophobic effect have been well established. however, only a few homo-lumo interaction in dna have been reported. we examined the ab initio calculations of b-dna duplex 5-mers. based on the calculated results, we investigated the mapping of homo experimentally and found that dna cleavage patterns with co(ii) and bpo (benzoyl peroxide) were in good agree ...	1999	10780408
synthesis of oligonucleotides containing the oxidatively modified kappab site: unique binding affinity to the nfkappab p50 homodimer.	synthesis of oligonucleotide 26-mers including single 5-formyl-2'-deoxyuridine (1) or 5-formyl-2'-o-methyluridine (2) in place of thymidine at the kappab site has been accomplished. one of the 26-mers with 1 was critically discriminated by the nfkappab p50 homodimer in binding.	1999	10780365
the importance of coulombic end effects: experimental characterization of the effects of oligonucleotide flanking charges on the strength and salt dependence of oligocation (l8+) binding to single-stranded dna oligomers.	binding constants kobs, expressed per site and evaluated in the limit of zero binding density, are quantified as functions of salt (sodium acetate) concentration for the interactions of the oligopeptide ligand kwk6nh2 (designated l8+, with zl = 8 charges) with three single-stranded dna oligomers (ss dt-mers, with \|zd\| = 15, 39, and 69 charges). these results provide the first systematic experimental information about the effect of changing \|zd\| on the strength and salt dependence of oligocation- ...	1999	9916032
inhibitory effect of telomere-mimic phosphorothioate oligodeoxy nucleotides (s-odns) on human tumor cell lines.	to clarify the inhibitory effect of telomere-mimic oligonucleotides on human cancer cell lines, we synthesized 18-mers (18t; n = 3), 24-mers (24t; n = 4) and 30-mers (30t; n = 5) of telomere-mimic phosphorothioate oligodeoxy nucleotides [5'-d(tta ggg)n-3'] and examined their effects on the proliferation of human tumor cells by xtt assay. after 7 days of continuous exposure to 24t and 30t at concentrations ranging from 0.1 to 10 microm, concentration-dependent cell growth inhibition was observed ...	1999	10545800
cellular uptake of adamantyl conjugated peptide nucleic acids.	peptide nucleic acids (pna) (15-mers) conjugated to adamantyl acetic acid and labeled with fluorescein have been prepared, and their (liposome mediated) uptake in human cells in culture (hela, imr-90 and mda-mb-453) has been studied by confocal fluorescence microscopy. it is found that adamantyl-pnas show greatly improved (endosomal) cellular uptake, but that this uptake is dependent on the cell line. cellular uptake of such lipophilic pnas is further mediated by cationic liposomes, and in some ...	1999	10563765
human apurinic/apyrimidinic endonuclease is processive.	apurinic/apyrimidinic endonuclease (ap endo) is believed to play a critical role in repair of oxidative damage of dna and is proposed to initiate repair of most abasic sites in the base excision repair pathway. ap endo makes a single nick 5' to an abasic site in double-stranded dna. in this study, we investigated whether ap endo locates an abasic site through a processive or a distributive mechanism. we used a linear multi-abasic site substrate (concatemer), synthesized by ligating together iden ...	1999	10600117
genetic variation between susceptible and non-susceptible snails to schistosoma infection using random amplified polymorphic dna analysis (rapds).	susceptibility of snails to infection by certain trematodes and their suitability as hosts for continued development has been a bewildering problem in host-parasite relationships. the present work emphasizes our interest in snail genetics to determine what genes or gene products are specifically responsible for susceptibility of snails to infection. high molecular weight dna was extracted from both susceptible and non-susceptible snails within the same species biomphalaria tenagophila. rapd was ...	1999	10602543
the stem hairpin loop structure of p2sp1 rna is required for rna-cleaving activity.	we studied the hairpin-loop structure of an rna fragment (guuucguacaaac) (r13) with the sequence corresponding to the self-cleavage domain in the precursor of an rna molecule from bacteriophage t4-infected escherichia coli cells (p2sp1 rna). in order to determine the influence of the hairpin-loop structure on these sequence-specific cleavage reactions, we have synthesized oligoribonucleotides containing hairpin-loop, double-helical stem-loop, and single-stranded rna structures. the cleavage was ...	1999	10673038
structural basis for triplet repeat disorders: a computational analysis.	over a dozen major degenerative disorders, including myotonic distrophy, huntington's disease and fragile x syndrome, result from unstable expansions of particular trinucleotides. remarkably, only some of all the possible triplets, namely cag/ctg, cgg/ccg and gaa/ttc, have been associated with the known pathological expansions. this raises some basic questions at the dna level. why do particular triplets seem to be singled out? what is the mechanism for their expansion and how does it depend on ...	1999	10743558
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
variation in genotype and aggressiveness of ralstonia solanacearum race 1 isolated from tomato in taiwan.	abstract a population of ralstonia solanacearum race 1 from tomato (lycopersicon esculentum) was analyzed for genetic polymorphism and aggressiveness on tomato. the 46 strains were collected from main tomato-growing areas in taiwan. genetic analysis was achieved by two polymerase chain reaction (pcr)-based methods: rep-, eric-, and box-pcr (collectively as rep-pcr) and random amplified polymorphic dna (rapd) techniques. rapd (with three 10-mers) and rep-pcr revealed 35 and 30 haplotypes, respect ...	1999	18944778
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
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
peptide ligands to human immunodeficiency virus type 1 gp120 identified from phage display libraries.	we have used phage-displayed peptide libraries to identify novel ligands to the human immunodeficiency virus type 1 (hiv-1) envelope glycoprotein gp120. screening of libraries of random 12-mers, 7-mers, and cyclic 9-mers produced two families of gp120 binding peptides. members of a family with the prototype sequence rinnipwseamm (peptide 12p1) inhibit the interaction between gp120 and both four-domain soluble cd4 (4dcd4) and monoclonal antibody (mab) 17b, a neutralizing antibody that covers the ...	1999	10364331
murine b-cell and t-cell epitopes of the allergen hev b 5 from natural rubber latex.	hev b 5, a proline-rich acidic protein with a predominantly random secondary structure, is a major allergen in natural rubber latex and a candidate for specific immunotherapy of latex allergy. as a first step in the identification of candidate peptides for immunotherapy, we have begun to identify the b-cell and t-cell epitopes of hev b 5 in balb/c mice. the mice were immunized with a hev b 5 fusion protein. the b-cell epitopes were determined by the spots method using overlapping octamers or by ...	1999	10378685
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
monomer-dimer equilibrium constants of rna in the dimer initiation site of human immunodeficiency virus type 1.	the genome of the human immunodeficiency virus (hiv) exists as a dimer of two identical rna molecules hydrogen bonded to each other near their 5' ends. the dimer, known to be important for viral infectivity, is formed by two monomers interacting through a stem-loop structure called the dimer initiation site (dis). an initially formed intermediate, the "kissing" dimer, is unstable and rearranges to the stable, duplex form. in this report we use nondenaturing polyacrylamide gel electrophoresis to ...	1999	10433723
effect of the ionic environment on the molecular structure of bacteriophage spp1 portal protein.	bacteriophage spp1 portal protein is a large cyclical homo-oligomer composed of 13 subunits. the solution structure and assembly behavior of this protein with high-point rotational symmetry was characterized. the purified protein was present as a monodisperse population of 13-mers, named gp6h, at univalent salt concentrations in the hundred millimolar range (>/= 250 mm nacl) or in the presence of bivalent cations in the millimolar range (>/= 5 mm mgcl2). gp6h had a slightly higher sedimentation ...	1999	10491118
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