| hoechst 33258 tethered by a hexa(ethylene glycol) linker to the 5'-termini of oligodeoxynucleotide 15-mers: duplex stabilization and fluorescence properties. | a fluorescent hoechst 33258 derivative has been prepared in which a hexa(ethylene glycol) linker is attached to the terminal phenol residue. conjugation of this derivative to dna sequences is accomplished by a reversed coupling protocol, one in which the 5'-terminal nucleoside residue of a fully protected dna sequence is converted to a terminal phosphoramidite. in the presence of the hoechst derivative and tetrazole the final coupling reaction is achieved to generate the conjugated nucleic acid. ... | 1997 | 11671444 |
| a picomole-scale method for charge derivatization of peptides for sequence analysis by mass spectrometry. | a highly activated ester containing a fixed positive charge, s-pentafluorophenyl [tris(2,4,6-trimethoxyphenyl)phosphonium]acetate bromide (tmpp-acsc6f5 bromide), has been synthesized as a reagent for n-terminal modification of peptides. stable in aqueous acetonitrile solution during extended storage, tmpp-acsc6f5 bromide reacts with unprotected peptides through p-(dimethylamino)pyridine (dmap)-promoted amidation in aqueous acetonitrile (15 min, ambient temperature) to form n-tmpp-ac derivatives ... | 1997 | 8997893 |
| detection of oligonucleotides by external injection into an ion trap storage/reflection time-of-flight device. | the detection of oligonucleotides has been studied using external injection of matrix-assisted laser desorption/ionization (maldi) produced ions into a quadrupole ion trap storage device. the ions stored in the trap are then detected by pulsed dc injection into a reflection time-of-flight mass spectrometer. it is shown that by using a low acceleration voltage from the probe tip and external injection into the trap that 3-mers to 9-mers can be stored for 20-50 ms and detected as intact ions. in c ... | 1997 | 9299762 |
| improved resolution in the detection of oligonucleotides up to 60-mers in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using pulsed-delayed extraction with a simple high voltage transistor switch. | pulsed-delayed extraction using a simple high voltage transistor switch together with various sample purification approaches were used to enhance the resolution in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (maldi-tofms) of oligonucleotides up to 60 bases long. this switch can provide a 0-3 kv voltage pulse with a 75 ns fall time. a resolution of 500-900 was typically observed for samples from 5-mers to 60-mers using pulsed-delayed extraction (pde) with the swit ... | 1997 | 9204573 |
| dna mobility anomalies are determined primarily by polyacrylamide gel concentration, not gel pore size. | the dependence of dna mobility anomalies on gel pore size has been studied in polyacrylamide gels with a wide variety of compositions, using molecular weight ladders containing multiple copies of normal (12b) and anomalously slowly migrating (12a) 147-base pair restriction fragments from plasmid pbr322 as the migrating probe molecules. if the gel pore size is increased by decreasing the total acrylamide concentration (%t) at constant cross-linker ratio (%c), the usual method of increasing gel po ... | 1997 | 9059818 |
| hairpin loops consisting of single adenine residues closed by sheared a.a and g.g pairs formed by the dna triplets aaa and gag: solution structure of the d(gtacaaagtac) hairpin. | the dna undecamers gtacaaagtac (aaa 11-mer) and gtacgaggtac (gag 11-mer) have been studied in solution by high-resolution nmr spectroscopy. both duplexes form stable hairpins containing single deoxyadenosine loops and stems containing five base-pairs that are closed at the loop end by sheared axa and gxc pairs, respectively. these molecules thus contain new aaa and gag loop turn motifs. all protons, including the chiral h5'/h5" protons of the loop residues, were assigned using noesy, dqf-cosy an ... | 1996 | 9000625 |
| conformational properties of z-forming dna oligomers bearing terminal unpaired bases. | three sets of semi-self-complementary deoxyribonucleotide decamers with the sequence xx-(5mecg)4, (5mecg)4-xx, or y-(5mecg)4-y, where xx = aa, cc, gg, or tt and y = a, c, g, or t, were synthesized along with the self-complementary octamer (5mecg)4. the 8-mer duplex readily undergoes a b-to-z conformational conversion upon increasing the nacl concentration with a transitional midpoint of approximately 1.1 m nacl. the 10-mers should form 8-bp duplexes a with core sequence of [(5mecg)4]2 with 5'-xx ... | 1996 | 8968605 |
| incorporation of two anthraquinonylmethyl groups into the 2'-o-positions of oligonucleotides: increased affinity and sequence specificity of anthraquinone-modified oligonucleotides in hybrid formation with dna and rna. | oligonucleotide 15-mers containing one or two anthraquinonylmethyl groups at specified sugar residues have been prepared on an automated dna/rna synthesizer by using 5'-o-dimethoxytrityl 2'-o-(2-anthraquinonylmethyl)uridine 3'-o-(2-cyanoethyl)-n, n-diisopropylphosphoramidite. the purification of the modified oligonucleotides was done with denaturing polyacrylamide gel electrophoresis. the base compositions and the presence of anthraquinone group(s) in the oligonucleotides were verified with enzy ... | 2006 | 8950490 |
| alternate-strand triplex formation: modulation of binding to matched and mismatched duplexes by sequence choice in the pu-pu-py block. | in double-stranded dna, tandem blocks of purines (pu) and pyrimidines (py) can form triplexes by pairing with oligonucleotides which also consist of blocks of purines and pyrimidines, using both py.pu.py (y-type) and pu.pu.py (r-type) pairing motifs in a scheme called "alternate-strand recognition," or asr [jayasena, s. d., & johnston, b. h. (1992) biochemistry 31, 320-327; beal p. a., & dervan, p. b. (1992) j. am. chem. soc. 114, 1470-1478]. we investigated the relative contributions of the py. ... | 1996 | 8873599 |
| specificity and degeneracy in peptide binding to hla-b7-like class i molecules. | the hla-b7-like binding supertype includes several different hla-b molecules. herein, the primary and secondary anchor specificities of the five most common hla-b7-like molecules (b*0702, b*3501, b51, b*5301, and b*5401) were defined by the use of molecular binding assays, analogue peptides, and large sets of peptides corresponding to naturally occurring sequences. all five b7-like molecules analyzed preferentially bound 9-mers, with a stringent requirement for proline in position 2, while a var ... | 1996 | 8871647 |
| a fast conformational search strategy for finding low energy structures of model proteins. | we describe a new computer algorithm for finding low-energy conformations of proteins. it is a chain-growth method that uses a heuristic bias function to help assemble a hydrophobic core. we call it the core-directed chain growth method (cg). we test the cg method on several well-known literature examples of hp lattice model proteins [in which proteins are modeled as sequences of hydrophobic (h) and polar (p) monomers], ranging from 20-64 monomers in two dimensions, and up to 88-mers in three di ... | 1996 | 8897604 |
| multi-facility survey of oligonucleotide synthesis and an examination of the performance of unpurified primers in automated dna sequencing. | the purity of 208 crude synthetic 25- and 50-base oligonucleotides synthesized in 71 dna core facilities was assessed by capillary electrophoresis (ce), and the average coupling efficiency of each synthesis was determined. the median average coupling efficiencies of the 25-mers and 50-mers were 98.9% and 98.7%, respectively, and 85% of the samples exceeded the minimum industry standard of 98% average coupling efficiency. the overall yields estimated by on-line trityl monitors showed poor agreeme ... | 1996 | 8891221 |
| synthesis of 6-deoxy-5-thio-d-glucose. | three routes were investigated for the conversion of d-glucose into the title compound. in the first approach, reduction of the 5,6-thiirane ring of 5,6-dideoxy-5, 6-epithio-1,2-o-isopropylidene-alpha-d-glucofuranose (17) as well as that of its 3-o-allyl derivative (13) with lithium aluminium hydride was investigated; 17 afforded the corresponding 6-deoxy derivative besides di-, tri-, and poly-mers, whereas only polymers were formed from 13. in the second approach, the oxirane ring of 3-o-allyl- ... | 1996 | 8823905 |
| spectroscopic probe for the detection of local dna bending at an aaa triplet. | spectroscopic evidence of a dna bend in solution is presented by analyzing model 15-mer duplexes spin-labeled with the five-atom-tethered nitroxide duap located in the major groove. three 15-mers containing aatt with duap enzymatically incorporated into three different positions yielded nearly identical line shapes while a fourth 15-mer containing aaatt produced an epr spectrum with significant additional line broadening. these results are interpreted according to the dynamic cylinder model wher ... | 1996 | 8755708 |
| random sequential adsorption of k-mers on a square lattice: the large k regime. | | 1996 | 9965151 |
| a recipe for designing water-soluble, beta-sheet-forming peptides. | based on observations of solubility and folding properties of peptide 33-mers derived from the beta-sheet domains of platelet factor-4 (pf4), interleukin-8 (il-8), and growth related protein (gro-alpha), as well as other beta-sheet-forming peptides, general guidelines have been developed to aid in the design of water soluble, self-association-induced beta-sheet-forming peptides. cd, 1h-nmr, and pulsed field gradient nmr self-diffusion measurements have been used to assess the degree of folding a ... | 1996 | 8819163 |
| structure determination of a lone alpha-helical antifreeze protein from winter flounder. | the x-ray crystal structure of a lone alpha-helical antifreeze protein from winter flounder has been determined to 1.5 a using a combination of molecular-replacement and isomorphous-replacement techniques. molecular replacement involved a multiparameter search using x-plor with two 37-mers of alanine in idealized alpha-helical conformations as the search models. identified were a large number of potential solutions from which the correct solution was not distinguishable. commitment of the top 16 ... | 1996 | 15299670 |
| autoimmune mechanisms involved in the pathogenesis of rheumatoid arthritis. | rheumatoid arthritis (ra) was one of the first systemic disorders to be considered an autoimmune disease. two major aspects of ra suggest a fundamental immune-mediated derangement in the disease: (1) presence of often massive lymphocytic infiltrates and activated cd4(+) t cells within the inflamed hypertrophied synovium, and (2) production of large amounts of rheumatoid factor (rf) by b-cells and plasma cells in the involved synovium itself. the actual tissue damage to joints and extra-articular ... | 1996 | 8934924 |
| oligomerization of uridine phosphorimidazolides on montmorillonite: a model for the prebiotic synthesis of rna on minerals. | the 5'-phosphorimidazolide of uridine reacts on na(+)-montmorillonite 22a in aqueous solution to give oligomers as long as 7 mers. the maximum chain length increases to 9 mers and the overall oligomer yield increases when 9:1 impu, a5' ppa mixtures react under the same conditions. the oligomer yield and maximum chain length decreases with the structure of the added pyrophosphate in the order a5' ppa > a5' ppu > u5' ppu. structure analysis of individual oligomer fractions was performed by selecti ... | 1996 | 8765685 |
| selection of hammerhead ribozymes for optimum cleavage of interleukin 6 mrna. | four guc triplets in the coding region of the mrna of interleukin 6 (il-6) were examined for their suitabilty to serve as a target for hammerhead ribozome-mediated cleavage. this selection procedure was performed with the intention to downregulate il-6 production as a potential treatment of those diseases in which il-6 overexpression is involved. hammerhead ribozymes and their respective short synthetic substrates (19-mers) were synthesized for these four guc triplets. notwithstanding the identi ... | 1996 | 8670082 |
| combining the technique of rna fingerprinting and differential display to obtain differentially expressed mrna. | we have modified recently developed methods of rna fingerprinting and differential display based on arbitrarily primed pcr which can be used for detection and cloning of differentially expressed mrnas. our protocol requires only a single cdna synthesis for each different rna sample, in contrast to the multiple cdna reactions required for differential display method, followed by selective amplification of cdna sequence fraction by arbitrary and oligo(dt) primers. we have shown that the longer pri ... | 1996 | 8645264 |
| downregulation of msx-2 expression results in chondrogenesis in the medial region of the avian mandible. | homeobox-containing genes are thought to be regulators of pattern formation during vertebrate development. we have previously characterized regions in the developing chick mandible expressing either msx-1 or msx-2 in terms of their chondrogenic potential, rates of cell proliferation, and their correlation with regions of cell death. these experiments suggest that msx-1 may be involved in outgrowth of the mandibular arch, and msx-2 may be involved in delineating the non-chondrogenic region of the ... | 1996 | 9084645 |
| refined peptide hla-b*3501 binding motif reveals differences in 9-mer to 11-mer peptide binding. | hla-b*3501 is associated with subacute thyroiditis and fast progression of aids. an important prerequisite to investigate the t-cell recognition of hla-b*3501-restricted antigens is the characterization of peptide-hla-b*3501 interactions. in this study, peptide-hla-b*3501 interactions were determined in quantitative peptide binding assays. the results were statistically analyzed to evaluate the influence of both anchor and nonanchor positions and the predictability of peptide binding. the bindin ... | 1996 | 8952961 |
| electrospray tandem mass spectrometry of nucleotides. | the tandem mass spectra (ms/ms) following electrospray ionization of nucleotides (from 2- to 6-mers) have been examined under a range of collision and ionization conditions. in general, abundant peaks due to the free bases and phosphate groups are observed, along with a limited number of sequence ions. a number of strategies for increasing the extent of the observed fragmentation were investigated. increasing the skimmer potential of the ion source, thereby increasing the initial internal energy ... | 1996 | 8563014 |
| the synthesis and biological activities of oligodeoxynucleotides that are covalently linked to psoralen at their 5' ends. | four oligodeoxynucleotides (15-mers), designated 13 through 16, and the corresponding conjugates, designated 17 through 20, in which psoralen was covalently linked to the 5' end of each oligonucleotide were synthesized. compounds 16 and 20 contained a sequence that was complementary to part of the first four codons and the upstream sequence close to the ribosome-binding site of c-ha-ras mrna. compounds 16 and 20 inhibited the growth of cells that had been transformed by the c-ha-ras plasmid, wit ... | 1995 | 8872455 |
| oligonucleotide analogues containing 4'-c-(hydroxymethyl)uridine: synthesis, evaluation and mass spectrometric analysis. | 2',3'-di-o-tert-butyldimethylsilyl-4'-c-(hydroxymethyl)uridine was synthesized and converted into the phosphoramidite building blocks 9 and 13. novel oligodeoxynucleotide analogues containing 4'-c-hydroxymethyl linked phosphodiester internucleoside linkages and 3'-hydroxyl linked phosphodiester internucleotide linkages were synthesized on an automated dna-synthesizer. the latter modification introduced an additional 4'-c-hydroxymethyl functionality. oligodeoxynucleotides with one or two modifica ... | 1995 | 8634829 |
| structure-activity relationships of cytotoxic cholesterol-modified dna duplexes. | short dna duplexes with cholesterol linked at the 3'-terminus of each strand have unique, selective cytotoxic properties. the structural requirements for biological activity were explored through chemical synthesis of analogs and testing in cultured hepatoma cells. effects of modifications to the sequence, backbone, 3'-sterol, 3'-linker, and 5'-terminus were evaluated. self-complementary 3'-modified oligodeoxynucleotide (odn) 10-mers were prepared from solid supports bearing the modification and ... | 1995 | 7473587 |
| the fundamentals of applying electrospray ionization mass spectrometry to low mass poly(methyl methacrylate) polymers. | electrospray ionization (esi) is capable of ionizing many soluble polymers. the esi spectra are complex because of overlap of the multiply charged ions of the oligomer distribution, causing current computer transform programs to fail. however, it is possible to determine the origin of the multiply charged ions, making it feasible to write a program designed to transform esi polymer spectra. to assess the value of such a program for polymer analysis, isolated monodisperse methyl methacrylate (mma ... | 1995 | 24214034 |
| synthesis and biochemical evaluation of rna containing an intrahelical disulfide crosslink. | several factors impede the elucidation of rna structure and function by x-ray and nmr methods, including the complexity of folded rna motifs, the tendency of rna to aggregate, and its ability to fold into multiple isomeric structures. the ability to constrain the process of rna folding to give a single, homogeneous product would assist these investigations. we therefore set out to develop a synthetic procedure for the site-specific insertion of a disulfide crosslink into oligoribonucleotides. we ... | 1995 | 9383473 |
| inhibition of platelet heparitinase by phosphorothioate dna oligonucleotides. | in view of the role that heparitinase and heparanase enzymes are thought to play in regulating the proliferation of smooth muscle cells, inhibitors of these enzymes may have therapeutic value in the treatment of vascular hyperplasia. here we report that phosphorothioate oligodeoxynucleotides inhibit platelet heparitinase and related enzymes in vitro. the inhibition is greatly enhanced by the presence of a ggg motif in the oligonucleotide, and also increases with oligonucleotide for two phosphoro ... | 1995 | 8673006 |
| inheritance of rapd markers in the guppy fish, poecilia reticulata. | random amplified polymorphic dna (rapd) fingerprinting offers a rapid and efficient method for generating a new series of dna markers in fishes. three oligonucleotide primers (two 10-mers and one 9-mer) and their paired combinations were found to generate different but reproducible rapd fingerprints in the guppy. of these, a 10-mer primer (designated s3d2) was used to detect dna polymorphisms in two guppy varieties, green snakeskin (gss) and 3/4black (3/4b). high genetic similarity (si) was foun ... | 1995 | 8590830 |
| impact of local and non-local interactions on thermodynamics and kinetics of protein folding. | to address the question of how the geometry of a protein's native conformation affects its folding and stability, we studied three model 36-mers on a cubic lattice. the native structure of one of these model 36-mers consisted mostly of local contacts, while that of a second consisted mostly of non-local contacts. the third native structure had a typical compact native conformation, and served as our reference. for each protein, the amino acid sequence was designed to have a pronounced energy min ... | 1995 | 7563065 |
| analysis of modified oligonucleotides by matrix-assisted laser desorption/ionization fourier transform mass spectrometry. | matrix-assisted laser desorption/ionization (maldi) fourier transform ion cyclotron resonance mass spectrometry (ftms) has been applied to the structural characterization of modified oligodeoxyribonucleotide 4-, 6-, and 11-mers. each oligonucleotide contained one modified base, either an o6-methyl-substituted guanine, an n6-(10r)-trans-opened benzo[a]pyrenediol epoxide adduct of adenine, or an n2-(r)-styrene oxide adduct of guanine. 3-hydroxypicolinic acid was used as the maldi matrix for molecu ... | 1995 | 8779417 |
| d-enantiomers of 15-residue cecropin a-melittin hybrids. | the all-d enantiomers of six 15-residue hybrids of cecropin a and melittin were synthesized. they contained the seven n-terminal residues of cecropin a, followed by eight residues from the n-terminal region of melittin. they were pure and of the correct composition and structure. the peptides were compared with their all-l enantiomers. the l and d isomer pairs were each exact mirror images by circular dichroism at several concentrations of hexafluoroisopropanol, and at 12 or 20% were highly heli ... | 2008 | 8537174 |
| differential display rt-pcr for identifying novel gene expression in the lung. | the unique identity of each cell is the result of differential gene expression. a new strategy for differential cdna screening introduced by liang and pardee utilizes anchored oligo-dt primers and random 5' oligonucleotide 10-mers to carry out polymerase chain reaction (pcr) on reverse-transcribed rna from different cell populations. the amplified cdnas are displayed on a standard sequencing gel as 100-500 bands per lane on the resulting autoradiograms and comparisons are drawn between the diffe ... | 1995 | 7573459 |
| an automated multiplex oligonucleotide synthesizer: development of high-throughput, low-cost dna synthesis. | an automated oligonucleotide synthesizer has been developed that can simultaneously and rapidly synthesize up to 96 different oligonucleotides in a 96-well microtiter format using phosphoramidite synthesis chemistry. a modified 96-well plate is positioned under reagent valve banks, and appropriate reagents are delivered into individual wells containing the growing oligonucleotide chain, which is bound to a solid support. each well has a filter bottom that enables the removal of spent reagents wh ... | 1995 | 7644513 |
| on the mechanism of the modular primer effect. | modular primers are strings of three contiguously annealed unligated oligonucleotides (modules) as short as 5- or 6-mers, selected from a presynthesized library. it was previously found that such strings can prime dna sequencing reactions specifically, thus eliminating the need for the primer synthesis step in dna sequencing by primer walking. it has remained largely a mystery why modular primers prime uniquely, while a single module, used alone in the same conditions, often shows alternative pr ... | 1995 | 7659510 |
| stability measurements of antisense oligonucleotides by capillary gel electrophoresis. | the approach of using antisense oligonucleotides as potential drugs is based on hybridization of a short chemically-modified oligonucleotide with complementary cellular dna or rna sequences. a critical question is the stability of chemically modified antisense oligonucleotides in cellular environments. in a model system, resistance against various nucleases was evaluated by capillary gel electrophoresis (cge). for some of the samples, matrix assisted laser desorption and ionization mass spectrom ... | 1995 | 7581844 |
| improved amplitude of myogenic motor evoked responses after paired transcranial electrical stimulation during sufentanil/nitrous oxide anesthesia. | measurement of motor evoked responses to transcranial stimulation (tc-mer) is a technique for intraoperative monitoring of motor pathways in the brain and spinal cord. however, clinical application of tc-mer monitoring is hampered because most anesthetic techniques severely depress the amplitude of motor evoked responses. because paired electrical stimuli increase tc-mer responses in awake subjects, we examined their effects in anesthetized patients undergoing surgery. methods. eleven patients w ... | 1995 | 7631948 |
| measurement of bile salt aggregation equilibria using kinetic dialysis and spreadsheet modeling. | bile salts initially self-associate into small aggregates such as dimers and trimers before forming micelles at higher concentrations. the very size of these small aggregates hampers quantitation of their formation. we have devised a method using kinetic dialysis measurements to quantitatively examine aggregation of bile salt at concentrations below 10 mm. data for rate of dialysis versus concentration were fitted to hypothetical models of aggregation using a personal computer spreadsheet. for s ... | 1995 | 8533889 |
| contrasting structural impacts induced by cis-syn cyclobutane dimer and (6-4) adduct in dna duplex decamers: implication in mutagenesis and repair activity. | the relative biological importance of cis--syn cyclobutane dimer and pyrimidine(6-4)pyrimidone photoadduct ([6-4] photoadduct) appears to be dependent on the biological species, dipyrimidine sites and local conformational variation induced at the damaged sites. the single-strained deoxynucleotide 10-mers containing the site-specific (6-4) adduct or cis--syn cyclobutane dimer of thymidylyl(3'-->5')-thymidine were generated by direct photolysis of d(cgcattacgc) with uvc (220-260 nm) irradiation or ... | 1995 | 7638271 |
| syk protein-tyrosine kinase is regulated by tyrosine-phosphorylated ig alpha/ig beta immunoreceptor tyrosine activation motif binding and autophosphorylation. | syk is a cytoplasmic protein-tyrosine kinase containing two amino-terminal src homology 2 domains that is activated following ligation of the b cell antigen receptor. syk activation in b cells correlates with syk tyrosine phosphorylation as well as with syk sh2-mediated association with the tyrosine-phosphorylated ig alpha and ig beta b cell antigen receptor subunits. tyrosine-phosphorylated peptide 20-mers representing ig alpha and ig beta immunoreceptor tyrosine activation motifs were synthesi ... | 1995 | 7538118 |
| detailed motifs for peptide binding to hla-a*0201 derived from large random sets of peptides using a cellular binding assay. | extensive sets of in total about 2000 synthetic peptides were investigated for their binding affinities to hla-a*0201. comparisons of the amino acid compositions of binding to nonbinding sets of peptides provided new information concerning the rules for 9-, 10-, and 11-mer peptide binding at the amino acid level. preferred primary anchors were shown to depend on peptide length, longer peptides being more demanding in this respect. a clear preference exists for certain amino acids at several nona ... | 1995 | 7558923 |
| high hydrostatic pressure induces the dissociation of cpn60 tetradecamers and reveals a plasticity of the monomers. | hydrostatic pressures up to 2 kbar have been used to form monomers from the 14-subunit oligomer of the chaperonin, cpn60. the fluorescence of 1,1'-bi(4-anilino) naphthalene-5,5'-disulfonic acid (bisans), followed at high pressure, demonstrated an increase in hydrophobic exposure on dissociation. cpn60 dissociated with first order kinetics. the transition occurred between 1.3 and 2 kbar (p50 = 1.75 kbar), and it was facilitated by mgatp (p50 = 1.1 kbar). with mgatp, the fluorescence showed a rapi ... | 1995 | 7836434 |
| a test of lattice protein folding algorithms. | we report a blind test of lattice-model-based search strategies for finding global minima of model protein chains. one of us (e.i.s.) selected 10 compact conformations of 48-mer chains on the three-dimensional cubic lattice and used their inverse folding algorithm to design hp (h, hydrophobic; p, polar) sequences that should fold to those "target" structures. the sequences, but not the structures, were sent to the ucsf group (k.y., k.m.f., p.d.t., h.s.c., and k.a.d.), who used two methods to att ... | 1995 | 7816842 |
| forces of tertiary structural organization in globular proteins. | the tertiary structures of globular proteins have remarkable and complex symmetries. what forces cause them? we find that a very simple model reproduces some of those symmetries. proteins are modeled as copolymers of specific sequences of hydrophobic (h) and polar (p) monomers (hp model) configured as self-avoiding flights on simple three-dimensional cubic lattices. the model has no parameters; we just seek the conformations that have the global maximum number of hh contacts for any given sequen ... | 1995 | 7816806 |
| interaction of oligonucleotides containing anthraquinone at the 2'-sugar position with complementary nucleic acids. | oligonucleotide 15-mers containing 2-anthraquinonylmethyl substituents at the different 2'-sugar residues have been synthesized. these oligomers exhibit increased stability in formation of hybrids with complementary dna and rna without loss of sequence specificity. | 1995 | 8841539 |
| synthesis and evaluation of oligodeoxynucleotides containing acyclic nucleosides: introduction of three novel analogues and a summary. | novel flexible oligodeoxynucleotides containing (s)-1-(2,3-dihydroxypropyl)thymine or 2',3'-seco-thymidine nucleoside analogues were synthesized on an automated dna-synthesizer. oligodeoxynucleotides with one, two or three acyclic nucleosides incorporated in the middle or in the ends of 17-mers have been evaluated. 3'-end-modified oligomers were significantly stabilized towards 3'-exonucleolytic degradation compared to unmodified analogues and showed acceptable hybridization properties as measur ... | 1995 | 8612043 |
| nicorandil suppressed myocardial purine metabolism during exercise in patients with angina pectoris. | to elucidate the effect of nicorandil on myocardial energy metabolism and myocardial sympathetic activity, we administered nicorandil orally to eight patients with angina pectoris prior to exercise testing. arterial and coronary sinus levels of lactate, ammonia, hypoxanthine (hx), adrenaline and noradrenaline were measured during exercise in order to determine the irrespective myocardial extraction ratios (mer). compared to placebo, nicorandil increased the time to development of significant st ... | 1995 | 7589040 |
| rheumatoid-factor-reactive sites on ch3 established by overlapping 7-mer peptide epitope analysis. | polyclonal igm rheumatoid factors (rf) from ten patients with rheumatoid arthritis and six monoclonal igm rf were isolated from monomeric igg affinity columns and studied for their reactivity with the entire ch3 domain of igg synthesized as overlapping 7-mers using a pin-elisa assay. all ten polyclonal igm rf showed similar profiles of reactivity which included peptides with solvent accessible residues prepqvy (residues 343-349), pqvytlp (residues 346-352), tlpprse (350-356), dgsffly (401-407), ... | 1995 | 7532785 |
| thermodynamic characterization of the cooperativity of 40s complex formation during the initiation of eukaryotic protein synthesis. | the first step in mammalian protein synthesis is the formation of the 40s initiation complex, composed of the 40s ribosomal subunit (r), mrna (m, here, a 10-mer oligoribonucleotide analogue containing the initiation codon), and the quaternary complex (q, composed of eif-2, gtp, met-trna(fmet), and the ancillary protein factor co-eif-2c). the interdependence of the binding of r, m, and q in forming the 40s complex is currently unclear. we have determined the thermodynamic parameters that characte ... | 1994 | 7999777 |
| assembly of synthetic laminin peptides into a triple-stranded coiled-coil structure. | laminin, a large multidomain glycoprotein specific to basement membranes, is a heterotrimer with alpha, beta, and gamma chains held together in an alpha-helical coiled-coil structure. synthetic peptides comprising two 51-mers (b1 and b2) from the beta 1 and gamma 1 subunits and a 55-mer (m) from alpha 2 were used to study the molecular mechanisms in laminin chain assembly. using the synthetic peptides in various mixing experiments, the heterotrimer (b1-b2-m) was preferentially produced. the ther ... | 1994 | 7982952 |
| effects of droperidol, pentobarbital, and ketamine on myogenic transcranial magnetic motor-evoked responses in humans. | myogenic motor-evoked responses to transcranial magnetic stimulation of the motor cortex (tcmag-mers) may become clinically useful for the noninvasive assessment of motor pathway conduction during surgery. however, application is hindered because most anesthetic regimens result in severe depression of tcmag-mer amplitudes. as part of our systematic attempts to identify anesthetic agents and supplements suitable for use during tcmag-mer recording, we studied the effect of bolus doses of pentobarb ... | 1994 | 7885550 |
| formation and stability of acetaldehyde-induced crosslinks between poly-lysine and poly-deoxyguanosine. | the amino acid residue and nucleoside specificity of acetaldehyde-induced dna-protein crosslinks (dpxls) were studied using a modified filter binding assay. a 40% inhibition of acetaldehyde-induced puc13 plasmid dna-calf thymus histone crosslink formation was achieved by addition of 50 mm lysine (free base), while arginine was unable to affect crosslink formation at concentrations to 150 mm. polymers (5-mers) of lysine (poly-lys5) were able to substitute for histones in acetaldehyde-induced plas ... | 1994 | 7526174 |
| accumulation and storage of ionized duplex dna molecules in a quadrupole ion trap. | evidence for the accumulation and storage of ionized duplex dna molecules in a quadrupole ion trap is presented. aqueous solutions of complementary single-strand molecules of dna were annealed to form duplexes in solution and subjected to electrospray ionization. the ions liberated in this process were transported through an atmosphere/vacuum interface and injected into a quadrupole ion trap operated with a bath gas present at a pressure of 1 mtorr. despite the roughly 2 order of magnitude poore ... | 1994 | 7978315 |
| translesional synthesis on dna templates containing site-specifically placed deoxyadenosine and deoxyguanosine adducts formed by the plant carcinogen aristolochic acid. | synthetic oligonucleotides (18-mers) containing either a single deoxyadenosine residue or a single deoxyguanosine residue were treated with aristolochic acid i (aai) or aristolochic acid ii (aaii), the main components of the plant carcinogen aristolochic acid (aa). these reactions resulted in the formation of site-specifically adducted oligonucleotides containing the two known aai-dna adducts (da-aai, dg-aai) or the two known aaii-dna adducts (da-aaii, dg-aaii) at position 15 from the 3' end. us ... | 1994 | 7955074 |
| analysis of protein s c4b-binding protein interactions by homology modeling and inhibitory antibodies. | a monoclonal antibody (mab 6f6) directed against the beta-chain of c4b-binding protein (c4bp) was previously shown to inhibit the binding of protein s to c4bp. to localize the epitope of this antibody, 23 overlapping synthetic peptides (15-mers) covering the entire sequence (1-235) of the beta-chain of c4bp were used. when the immobilized peptides were screened for their ability to bind mab 6f6, only peptide beta(51-65) showed high-affinity binding. the apparent affinity of mab 6f6 for immobiliz ... | 1994 | 7727359 |
| a small family of elements with long inverted repeats is located near sites of developmentally regulated dna rearrangement in tetrahymena thermophila. | extensive dna rearrangement occurs during the development of the somatic macronucleus from the germ line micronucleus in ciliated protozoans. the micronuclear junctions and the macronuclear product of a developmentally regulated dna rearrangement in tetrahymena thermophila, tlr1, have been cloned. the intrachromosomal rearrangement joins sequences that are separated by more than 13 kb in the micronucleus with the elimination of moderately repeated micronucleus-specific dna sequences. there is a ... | 1994 | 8065327 |
| parallel-stranded duplex dna containing blocks of trans purine-purine and purine-pyrimidine base pairs. | a 30 base pair parallel-stranded (ps) duplex ps-l1.l2 composed of two adjoined purine-purine and purine-pyrimidine sequence blocks has been characterized thermodynamically and spectroscopically. the 5'-terminal 15 residues in both strands ('left-half') consisted of the alternating d(ga)7g sequence that forms a ps homoduplex secondary structure stabilized by d(g.g) and d(a.a) base pairs. the 3'-terminal 15 positions of the sequence ('right-half') were combinations of a and t with complementary re ... | 1994 | 8078763 |
| unfolding of a branched double-helical dna three-way junction with triple-helical ends. | we have designed three oligonucleotides (33 mers) which when mixed in a 1:1:1 ratio form double-helical dna three-way junctions with triple helical ends in the ph interval ph 4 to 5.5. the triplex to coil transition is initiated by raising the temperature and was recorded by temperature gradient gel electrophoresis, uv melting, and differential scanning calorimetry. the transitions can be deconvoluted into three subtransitions representing the independent thermal denaturation of each of the arms ... | 1994 | 8053683 |
| synthetic polyamines stimulate in vitro transcription by t7 rna polymerase. | the influence of nine synthetic polyamines on in vitro transcription with t7 rna polymerase has been studied. the compounds used were linear or macrocyclic tetra- and hexaamine, varying in their size, shape and number of protonated groups. their effect was tested on different types of templates, all presenting the t7 rna promoter in a double-stranded form followed by sequences encoding short transcripts (25 to 35-mers) either on single- or double-stranded synthetic oligodeoxyribonucleotides. all ... | 1994 | 8052534 |
| sequence-dependent effects on dna stability resulting from guanosine replacements by inosine. | the effect of replacing a g.c base-pair with an i.c base-pair on dna stability was investigated for a related set of 14-mers. dna melting analysis of the 14-mers was used to determine delta hzero, delta szero and delta g(zero)37 of the double to single stranded transition. all 14mers were shown to have b-dna character by circular dichroism analysis. 14mers substituted with a single inosine in place of guanosine at different positions showed that consequences on dna stability are sequence-depende ... | 1994 | 8029016 |
| short antisense oligonucleotide-mediated inhibition is strongly dependent on oligo length and concentration but almost independent of location of the target sequence. | the inhibitory effect of short antisense oligodeoxynucleotides (aodns) on crna expression in xenopus oocytes was measured using an electrophysiological assay based on subunit-specific block of cloned alpha-amino-3-hydroxy-5-methyl-4-isoxazole-propionate receptors. the effect of both phosphorothioate-modified (ps) and phosphodiester (po) aodns was strongly length dependent with a half-maximal inhibition calculated for an oligo length of 7.6 nucleotides (nt) and 9.9 nt, respectively. more than 95% ... | 1994 | 8206920 |
| matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of chemically modified oligonucleotides. | a variety of chemically modified oligonucleotides have been studied by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (maldi-tofms) in the negative ion mode. these include oligonucleotides containing modified bases, such as uracil glycol, bromoguanine, o6-butylguanine, as well as oligonucleotides in which the phosphodiester groups had been replaced by other functional groups, such as phosphorothioates. with the linear tof mass spectrometer, there is no or very littl ... | 1994 | 8030793 |
| the role of the l-chain in ferritin iron incorporation. studies of homo and heteropolymers. | mammalian ferritins are 24-meric proteins composed of variable proportions of h and l-subunits. the l-chain, in contrast to the h-chain, lacks detectable ferroxidase activity, and its role in ferritin iron incorporation is unclear. in this study, apoferritins were subjected to iron loading with large iron increments to favour spontaneous iron hydrolysis. the homopolymers of the wild-type h-chain, and of a mutant h-chain with an inactivated ferroxidase centre, formed massive protein aggregates, w ... | 1994 | 8182740 |
| synthesis of oligodeoxynucleotides containing 2-thiopyrimidine residues--a new protection scheme. | a method is described for the incorporation of 2'-deoxy-2-thiouridine (ds2u) and 2'-deoxy-2-thiothymidine (ds2t) into oligodeoxynucleotides at predetermined positions. this requires n3 or o4-acylation of ds2u and ds2t with toluoyl chloride. these base-protected thiopyrimidines are completely stable toward the aqueous iodine oxidation reagent used in the phosphoramidite dna synthesis method. the toluoyl protecting group is removed during the standard post-synthetic ammonia treatment. this novel p ... | 1994 | 8190635 |
| incorporation of (r)- and (s)-3',4'-seco-thymidine into oligodeoxynucleotides: hybridization properties and enzymatic stability. | novel flexible oligodeoxynucleotide analogues containing (r)- and (s)-3',4'-seco-thymidine were synthesized on an automated dna-synthesizer using the phosphoramidite approach. oligodeoxynucleotide analogues (17-mers) having one or three modifications in the middle or one or two modifications in the ends were evaluated with respect to hybridization properties and enzymatic stability. 3'-end-modified oligomers were stable towards 3'-exonuclease degradation and displayed acceptable hybridization pr ... | 1994 | 8139908 |
| interaction of the restriction endonuclease ecorv with the deoxyguanosine and deoxycytidine bases in its recognition sequence. | the interaction of the ecorv restriction endonuclease with the dg and dc bases in its recognition sequence (gatatc) has been studied using base analogues. these modified dg and dc bases each have a single potential protein contact removed. the analogues have been incorporated into the self-complementary dodecamer d(pgacgatatcgtc) at the appropriate positions (underlined). many of the analogues caused no change in the tm of the duplex or else lowered the tm by a small amount such that a duplex wa ... | 1994 | 8110783 |
| oligonucleotides as short as 7-mers can be used for pcr amplification. | amplification of dna sequences using the polymerase chain reaction (pcr) requires as primers two oligonucleotides, which are carefully designed for length and g/c content. such primers are generally between 18 and 30 bases long so that the primer sequences can amplify a unique sequence in the target genome; they should possess a minimal degree of secondary structure. we have tested the minimum length of g/c-rich and palindromic oligonucleotides to be used as primers in pcr. oligonucleotides with ... | 1994 | 8286042 |
| evidence for plant ribosomal 5s rna involvement in elongation of polypeptide chain biosynthesis. | a series of short oligo-dna probes (8-10-mers) complementary to various regions of the plant ribosomal 5s ribonucleic acid (5s rrna) have been synthesized. the results of their hybridization to free 5s rrna and to ribosomes pointed to the availability of nucleotides in loop "c" for complexation. we found a correlation between hybridization of selected oligonucleotides and their inhibitory effect on enzymatic binding of phe-trna and poly(phe) synthesis on wheat germ 80s ribosomes. evidence was ob ... | 1994 | 8030375 |
| unmodified phosphodiester antisense oligodeoxynucleotides to the bcr-abl junction do not suppress philadelphia-positive clonogenic cells. | the bcr-abl fusion gene is directly involved in the pathogenesis of chronic myeloid leukemia (cml). specific inhibition of the bcr-abl gene expression with antisense oligodeoxynucleotides has been shown to have profound effects on cell growth in vitro. we examined antisense phosphodiester oligonucleotides (16-mers at a concentration of 60 micrograms/ml) spanning the two possible junction sites k28 (b3a2) and l6 (b2a2) in a clonogenic assay. single colonies from 9 patients with cml and from patie ... | 1994 | 7701917 |
| multichannel magnetoencephalographic mapping of sensorimotor cortex for epilepsy surgery. | preliminary reports have shown a close correlation between the anatomic location of evoked magnetic somatosensory fields and intraoperative evoked somatosensory potentials in patients with mass lesions. we have performed magnetic source imaging (msi) of sensory and motor (mer) evoked responses or fields on 4 patients with frontal convexity epileptic foci. the method involves (1) graphic overlaying of magnetoencephalography evoked field data and three-dimensional (3d) phase contrast magnetic reso ... | 1994 | 7631076 |
| polyamine-linked oligonucleotides for dna triple helix formation. | the concept of antigene therapy of disease is based on the ability of an oligonucleotide (the therapeutic agent) to bind to double-stranded genomic dna (the target associated with the disease). examples are herein given of the linkage of a series of polyamines to a 21-mer homopyrimidine oligonucleotide. these conjugated 21-mers can each form a triple helix with an appropriate double-stranded homopurine-homopyrimidine dna according to hoogsteen base-pairing rules. no triple helix was found when u ... | 1993 | 8265366 |
| dipentafluorophenyl carbonate--a reagent for the synthesis of oligonucleotides and their conjugates. | dipentafluorophenyl carbonate has been successfully used as condensing agent for the internucleotide bond formation in the synthesis of oligonucleotides via h-phosphonate approach. the mechanism of a nucleotide component activation with this reagent has been investigated with the help of 31p nmr spectroscopy. it was shown that preactivation of deoxynucleoside h-phosphonate with dipentafluorophenyl carbonate has no influence on the efficiency of the synthesis. this reagent is highly reactive, non ... | 1993 | 8265346 |
| comparative spectroscopic, calorimetric, and computational studies of nucleic acid complexes with 2',5"-versus 3',5"-phosphodiester linkages. | we have used a combination of spectroscopic, calorimetric, and computational techniques to characterize the properties of nucleic acid complexes with 2',5''- and 3',5''-phosphodiester linkages. specifically, we have compared the properties of complexes formed by the association of 3',5'' single-stranded 16-mers of adenylic acid (a16) and thymidylic acid (t16) with the complexes formed by the corresponding single-stranded 16-mers with 2',5''-phosphodiester linkages (a*16 and t*16). our results re ... | 1993 | 8248146 |
| mobility at the tpa cleavage site in the t3a3-containing ahaiii and pmei restriction sequences. | lefevre et al. originally observed conformational transitions at the tpa step in the ttaa pribnow box sequence of the trp promoter [lefevre, j.-f., lane, a. n., & jardetzky, o. (1985) febs lett. 190, 37-40]. in 500-mhz 1h nmr studies on the tna(n)-containing dna oligonucleotides [d(cgaggtttaaacctcg)]2, [d(gctcctttaaaggagc)]2, and [d(gccgttaacggc)]2, we observe that, in addition to the h2 proton (which resides in the minor groove of dna), the h8 proton of the first adenine (which resides in the m ... | 1993 | 8347604 |
| the trans-syn-i thymine dimer bends dna by approximately 22 degrees and unwinds dna by approximately 15 degrees. | irradiation of dna with ultraviolet light leads to the formation of two classes of cyclobutane dimers at adjacent thymines sites, of which the cis-syn is the major class and the trans-syn is the minor class. while the structure and properties of dna containing cis-syn thymine dimers have been extensively studied, virtually nothing is known about dna containing trans-syn thymine dimers. to investigate the bending and unwinding of dna induced by the trans-syn-i thymine dimer, the electrophoretic p ... | 2007 | 8374051 |
| identification of gremmeniella abietina races with random amplified polymorphic dna markers. | seven random amplified polymorphic dna (rapd) markers amplified from four oligonucleotides (10-mers) by the polymerase chain reaction were used to distinguish between the north american and european races of gremmeniella abietina, the causal agent of scleroderris canker of conifers. forty-three isolates of the pathogen from 11 different host species originating from 11 countries, states, and provinces were tested; race designation was consistent with results from immunogenic and soluble-protein ... | 1993 | 16348951 |
| oligodeoxynucleotides capable of binding to gc-rich regions in dna are inappropriately synthesized during random hexanucleotide-primed labeling reactions. | random hexanucleotide labeling is a commonly used and powerful technique for preparing radiolabeled nucleic acid probes. because of the dependence of dna polymerase upon single-stranded dna as a template, the technique should theoretically also be useful for detecting small amounts of single-stranded dna in the presence of a larger amount of double-stranded dna. in the course of such an experiment, we identified an unexpected reaction that could contribute to background problems often encountere ... | 1993 | 8471165 |
| spectroscopic characterization of heterochiral dnas. | we have synthesized heterochiral dodecadeoxynucleotides having an unnatural l-nucleotide residue, and have investigated their structures by ultraviolet (uv) absorption, circular dichroism (cd) measurements and nuclear magnetic resonance (nmr) spectroscopy. it was clearly shown that the overall structures of the heterochiral 12-mers are a right-handed b-conformation and the unnatural l-nucleotide residue in the heterochiral 12-mer (l-4) forms stable watson-crick type base-pairing with the natural ... | 1993 | 8247797 |
| preparation and physical properties of conjugates of oligodeoxynucleotides with poly(delta)ornithine peptides. | oligodeoxynucleotides (12-mers) having either a 3' aminolinker or both 3' and 5' aminolinker groups were synthesized and then reacted with n-iodoacetoxysuccinimide. separately, a series of peptides, consisting of cysteine carboxyamide and a varying number of residues of ornithine coupled through their side-chain amino groups, was prepared, leaving on the final fmoc protecting group. reaction of each fmoc-peptide with an activated oligodeoxynucleotide yielded the desired conjugates, which were pu ... | 1993 | 8155976 |
| photomodification of rna and dna fragments by oligonucleotide reagents bearing arylazide groups. | photomodification of ribo- and deoxyribo-octanucleotides by oligonucleotide reagents (6- and 7-mers) bearing p-azidotetrafluorobenzamido and 2-nitro-5-azidobenzamido groups has been investigated. it is shown that the oligonucleotides with a perfluoroarylazide group were effective modifiers both of deoxyribo- and ribo-targets. maximum extent of cross-linked product formation (70%) was obtained when the deoxyribo-octanucleotide was modified by a heptanucleotide reagent with a perfluoroarylazide gr ... | 1993 | 7684935 |
| sequencing by hybridization: towards an automated sequencing of one million m13 clones arrayed on membranes. | an immediately applicable variant of the sequencing by hybridization (sbh) method is under development with the capacity to determine up to 100 million base pairs per year. the proposed method comprises six steps: (i) arraying genomic or cdna m13 clones in 864-well plates (wells of 2 mm); (ii) preparation of dna samples for spotting by growth of the m13 clones or by polymerase chain reaction (pcr) of the inserts using standard 96-well plates, or plates having as many as 864 correspondingly small ... | 1992 | 1451694 |
| use of the multipin peptide synthesis technique for the generation of antipeptide sera. | the multipin peptide synthesis technique has been used to map antigenic sites of proteins (1,2). antibodies raised to the whole protein are screened on pin-synthesized overlapping octapeptides homologous with the protein of interest, and the peptides that bind antibodies clearly identify the epitopes. what is described in this study is a method using pin-synthesized peptides to generate specific antibodies to many peptides. cleavable linkers have been developed (3) that, used together with the m ... | 2003 | 1285329 |
| microtubule-associated protein tau is required for axonal neurite elaboration by neuroblastoma cells. | nb2a/d1 neuroblastoma cells constitutively express multiple isoforms of the microtubule-associated protein tau and incorporate this protein into the axonal neurites elaborated during serum deprivation. to examine whether or not tau played an essential role in axonal outgrowth, cells cultured in serum-free medium were treated at 24 h intervals with antisense- and sense-oriented cdna oligonucleotides (25 or 36 mers that span or are upstream of tau initiation codon) and were simultaneously serum de ... | 1992 | 1433385 |
| uranyl photofootprinting of triple helical dna. | two triple helix structures (15-mers containing only t.a-t triplets or containing mixed t.a-t and c.g-c triplets) have been studied by uranyl mediated dna photocleavage to probe the accessibility of the phosphates of the dna backbone. whereas the phosphates of the pyrimidine strand are at least as accessible as in double stranded dna, in the phosphates of the purine strand are partly shielded and more so at the 5'-end of the strand. with the homo a/t target increased cleavage is observed towards ... | 1992 | 1614860 |
| the immobiline family: from "vacuum" to "plenum" chemistry. | we list here a total of 17 acrylamido acids and bases as potential buffers and titrants for isoelectric focusing separations in immobilized ph gradients. the chemistry of these compounds is reviewed and general guidelines are given for their proper use. in particular, it is shown that the most delicate compounds are the basic species, since they can undergo several degradation pathways, including: (i) spontaneous hydrolysis to acrylic acid and a diamine; (ii) spontaneous autopolymerization to ol ... | 1992 | 1628597 |
| random sequential adsorption of different-sized k-mers on a line. | | 1992 | 9907391 |
| co-operative autoregulation of a replication protein gene. | in this work we present the localization and characterization of the repl promoter (prepl) and show aspects of the regulation. comparison of prepl with other autoregulated replication protein gene promoters revealed similarities, but prepl differs from some of these characterized promoters in not being regulated by the heat-shock rna polymerase. primer extension analysis showed that prepl is contained within five helically aligned 18 base pair repeats, or 18-mers of the previously defined minima ... | 1991 | 1809840 |
| solid phase synthesis of oligodeoxyribonucleoside phosphorodithioates from thiophosphoramidites. | oligonucleoside phosphorodithioates 1 are modified dna sequences with potential use as antisense oligonucleotides. the preparation of up to 20-mers containing all four bases by solid phase synthesis is described, with details on the preparation of the four monomer units (protected nucleoside thiophosphoramidites 2), the conditions used for the assembly of the strands with up to 19 phosphorodithioate linkages, and the purification and characterisation of the products. full-length homogeneity of h ... | 1991 | 1945874 |
| retention behaviour of a template-assembled synthetic protein and its amphiphilic building blocks on reversed-phase columns. | the retention behaviour of a six-helix bundle template-assembled synthetic protein (tasp) molecule and its amphiphilic building blocks was investigated. the tasp consists of a circular template, cyclo(1-12)[kg]6, and six identical potentially alpha-helical peptides of the sequence klalklalkalklalkla. as an alpha-helix, this peptide is amphiliphilic along the axis of its helix. based on this sequence, the retention times of a set of acetylated peptides containing from seven to twenty amino acids ... | 1991 | 1806554 |
| mechanism of cellular uptake of modified oligodeoxynucleotides containing methylphosphonate linkages. | the cellular uptake and intracellular distribution of methylphosphonate oligonucleotides (15 mers) has been examined using both 32p labeled and fluorescent labeled oligonucleotides. the cellular uptake process for methylphosphonate oligonucleotides is highly temperature dependent, with a major increase in uptake occurring between 15 and 20 degrees c. most of the label which becomes cell associated at 37 degrees c cannot be removed by acid washing or trypsinization and thus seems to be within the ... | 1991 | 1658734 |
| low concentrations of isoflurane abolish motor evoked responses to transcranial electrical stimulation during nitrous oxide/opioid anesthesia in humans. | to study the feasibility of noninvasive monitoring of motor pathways in anesthetized patients, we evaluated the effect of isoflurane on motor evoked responses to constant-voltage transcranial electrical stimulation (tce-mers). reproducible tce-mers were recordable from the tibialis anterior muscle during nitrous oxide/opioid anesthesia in 11 patients. before the introduction of isoflurane, tce-mer onset latency was 30.8 +/- 1.9 ms, and amplitude ranged from 19 microv to 2.6 mv (median, 209 micro ... | 1991 | 1832825 |
| hybridization methods for dna sequencing. | i have conducted a general analysis of the practicability of using oligonucleotide hybridization to sequence dna. any dna sequence may be sequenced by hybridization with a complete panel of oligonucleotides. however, sequencing dna segments over 2 kb long requires an unrealistic number of hybridization reactions. the optimal protocol is to hybridize 7-mer or 8-mer mixed oligonucleotide probes to immobilized dna fragments 80 bp long: should this prove impractical, hybridization of labeled 270-bp ... | 1991 | 1769648 |
| site-specific interaction of the antitumor antibiotic dynemicin with branched dna molecules. | a specific interaction of stable branched dna molecules with the antitumor antibiotic dynemicin is reported. dynemicin contains an anthraquinone and an enediyne unit, and belongs to the family of enediyne antitumor agents. dna strand scission by dynemicin appears to involve interaction of the anthraquinone core with dna and release of a phenyl diradical from the enediyne core that can abstract hydrogen atoms from the sugar phosphate backbone of dna. the cleavage patterns of each labeled strand i ... | 1991 | 1741963 |
| dna sequence dependence of guanine-o6 alkylation by the n-nitroso carcinogens n-methyl- and n-ethyl-n-nitrosourea. | after intracellular in vitro exposure to the mutagenic and carcinogenic n-nitroso compounds n-methyl-n-nitrosourea (menu) or n-ethyl-n-nitrosourea (etnu), respectively, the average relative amounts of the premutational lesion o6-alkylguanine represent about 6% and 8% of all alkylation products formed in genomic dna. at the level of individual dna molecules guanine-o6 alkylation does not occur at random; rather, the probability of a substitution reaction at the nucleophilic o6 atom is influenced ... | 2013 | 1944330 |
| [oncogene-directed mutagenesis in vivo. polyalkylating derivatives of short single-stranded polynucleotides, complementary e1-adeno-oncogene, in the normalization of adenovirus-transformed rodent cell lines]. | polyalkylating derivatives of single-stranded polynucleotides (30-200-mers) complementary to the long e1 oncogene sequences of simian adenovirus sa7 cause inherited normalization of sh2 and g11 cells transformed with adenovirus sa7; certain deletions in the integrated proviral e1a oncogene were observed in several cases during this process. the transformed cells are indifferent to reagents noncomplementary to the e1 region. thus polyalkylating derivatives of single-stranded 30-200-mers act as ad ... | 2006 | 1795710 |
| duplex stabilities of phosphorothioate, methylphosphonate, and rna analogs of two dna 14-mers. | the duplex stabilities of various phosphorothioate, methylphosphonate, rna and 2'-och3 rna analogs of two self-complementary dna 14-mers are compared. phosphorothioate and/or methylphosphonate analogs of the two sequences d(taattaattaatta) [d1] and d(tagctaattagcta) [d2] differ in the number, position, or chirality (at the 5' terminal linkage) of the modified phosphates. phosphorothioate derivatives of d1 are found to be less destabilized when the linkage modified is between adenines rather than ... | 1991 | 1711677 |
| effects of 2-chloroadenine substitution in dna on restriction endonuclease cleavage reactions. | the purine analog, 2-chloro-2'-deoxyadenosine triphosphate (cldatp), was incorporated enzymatically in place of datp into the minus strand of m13mp18 duplex dna. its effect on protein-dna interactions was assessed by determining the amount of dna cleavage by type ii restriction endonucleases. substitution of chloroadenine (ciade) for adenine (ade) in dna appreciably decreased the amount and rate of dna cleavage of the minus strand when the analog was situated within the appropriate endonuclease ... | 1991 | 1647525 |
| influence of the incorporation of (s)-9-(3,4-dihydroxybutyl)adenine on the enzymatic stability and base-pairing properties of oligodeoxynucleotides. | (s)-9-(3,4-dihydroxybutyl)adenine was used at several positions as nucleoside substitute in the synthesis of dimers and 13-mers. therefore we used the phosporamidite and the h-phosphonate chemistry. the nuclease susceptibilities and the base-pairing properties of these oligomers have been evaluated. | 1991 | 2041735 |