Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Homopolymers”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 523 records · Page 29Linked to original sources
PubMed1984

Sequence specific binding of tetraols of benzo[a]pyrene-diol-epoxide to DNA in neutral and acidic solutions.

Comparative binding studies of tetraols (anti- BPTs ) derived from trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetra- hydrobenzo [a]py rene (anti-BPDE) with native DNA in neutral and acidic solutions reveal that 4-5 times stronger intercalative binding occurs in the protonated duplex DNA than in the unprotonated one. Spectroscopic (absorption and circular dichroism) investigations with synthetic polynucleotides indicate that in neutral pH, anti- BPTs intercalate significantly in poly(dA-dT):poly(dA-dT), only slightly in guanine containing alternating polynucleotides poly(dG-dC): poly(dG-dC) and poly(dA-dC):poly(dG-dT), and hardly in homopolymers poly(dG):poly(dC) and poly(dA):poly(dT). In acidic solutions, on the other hand, all three alternating polynucleotides, poly(dG-dC):poly(dG-dC) in particular, exhibit strong intercalative binding to anti- BPTs although the homopolymers still lack such capability. These results are very similar to those of corresponding pyrene studies suggesting that pyrene can be a useful model compound for the DNA binding studies of benzo[a]pyrene metabolites. The observed enhanced binding of anti- BPTs in the acidic natural DNA solution is seen as the consequence of changes in base sequence preference upon base protonation.

Animals↗
PubMed2003

Fragile X Mental Retardation protein determinants required for its association with polyribosomal mRNPs.

Fragile X Mental Retardation protein (FMRP) is an RNA-binding protein that contains multiple domains with apparently differential affinity to mRNA and to the ribonucleotide homopolymer poly(G). Attempts have been made to map the RNA-binding sites along the protein sequence with a view to determining which of the KH1, KH2 and RGG domains are required to recognize and bind to RNA. While these studies have greatly contributed to the delineation of domains that bind homopolymers or mRNA in vitro, little is known concerning their implications in FMRP function(s) in vivo. To address this question, we have prepared a series of FMRP versions, in which each known in vitro functional domain has been individually deleted, leaving the rest of the protein intact. Constructs with deletions in the protein-protein interaction and RNA-binding as well as in the phosphorylation domains were expressed in STEK-KO cells lacking FMRP and their recruitment into polyribosomal mRNPs and their intra-cellular localization were determined. Our results indicate that the KH RNA-binding domains and the Protein-Protein Interacting domain are essential for FMRP to associate with polyribosomal mRNPs, while the RGG box and the phosphorylated domains are dispensable.

Animals↗
PubMed1983

Poly(2-methylthio-7-deazainosinic acid)--hydrophobic stabilization of polynucleotide secondary structure by the 2-methylthio group.

Poly(2-methylthio-7-deazainosinic acid) [poly(ms2c7I)] was enzymatically synthesized by polymerization of 2-methylthio-7-deazainosine 5'-diphosphate with polynucleotide phosphorylase from Micrococcus luteus in high yield. The homopolymer shows much higher thermal stability than its parent polynucleotides poly(7-deazainosinic acid) [poly(c7I)] and poly(I). Its sigmoidal melting curve and pronounced hypochromicity imply a rigid, ordered structure. Poly(ms2c7I), like poly(2-methylthio-inosinic acid) [poly(ms2I)], does not form a complex with poly(C) because of the bulky 2-methylthio substituent. On the other hand, two poly(ms2c7I) strands form very rigid triple strands with poly(A). Different from poly(I) and poly(c7I) the homopolymer poly(ms2c7I) is very stable against cleavage by nuclease S1 and ribonuclease T2 as expected from its rigid secondary structure.

Circular Dichroism↗
PubMed1988

Nuclear proteins from Drosophila melanogaster embryos which specifically bind to simple homopolymeric sequences poly [(dT-dG).(dC-dA)].

The binding of nuclear proteins from Drosophila melanogaster embryos to simple homopolymeric DNA sequences was studied. Nuclear proteins were electrophoresed, transferred onto nitrocellulose and incubated with labelled synthetic homopolymers or natural fragment containing simple sequences. Several protein bands were found in the 65-72 KDa region, which specifically bind both poly [(dG-dT).(dA-dC)] and a natural fragment containing 40 bp of this sequence. These proteins do not bind to homopolymers poly [(dA).(dT)] and poly [(dG-dA).(dC-dT)], or other foreign DNAs.

Animals↗
PubMed1989

Molecular dynamics of spermine-DNA interactions: sequence specificity and DNA bending for a simple ligand.

We used molecular dynamics to model interactions between the physiologically important polyamine spermine and two B-DNA oligomers, the homopolymer (dG)10-(dC)10 and the heteropolymer (dGdC)5-(dGdC)5. Water and counterions were included in the simulation. Starting coordinates for spermine-DNA complexes were structures obtained by molecular mechanics modeling of spermine with the two oligomers; in these models, spermine binding induced a bend in the heteropolymer but not in the homopolymer. During approximately 40 psec of molecular dynamics simulation, spermine moves away from the floor of the major groove and interacts nospecifically with d(G)10-d(C)10. In contrast, a spermine-induced bend in the helix of (dGdC)5-(dGdC)5 is maintained throughout the simulation and spermine remains closely associated with the major groove. These results provide further evidence that the binding of spermine to nucleic acids can be sequence specific and that bending of alternating purine-pyrimidine sequences may be a physiologically important result of spermine binding.

Base Sequence↗
PubMed1991

Nucleic acid-binding specificities of tobacco chloroplast ribonucleoproteins.

Many ribonucleoproteins (RNPs) are involved in the regulation of gene expression at the post-transcriptional level. We previously isolated three nuclear-encoded RNPs from tobacco chloroplasts. Here we report their binding specificities for various nucleic acids. The three RNPs synthesized in vitro were subjected to binding assays using ssDNA, dsDNA and four ribonucleotide homopolymers. The affinities for ribonucleotide homopolymers are higher than those for ssDNA and dsDNA, suggesting that they bind preferentially to RNA in vivo. All three RNPs show high specificities for poly(G) and poly(U) in the presence of 1.2-1.8 M NaCl, providing additional evidence for the similarity to HeLa hnRNP proteins. Possible involvement of these RNPs in the post-transcriptional regulation of chloroplast gene expression is discussed.

Base Sequence↗
PubMed1992

Bleomycin mediated degradation of DNA-RNA hybrids does not involve C-1' chemistry.

Incubation of Fe(II) bleomycin and O2 with a number of 'A'-like DNA-RNA hybrid homopolymers at 4 atm O2 results in formation of base propenal and base in a ratio of approximately 1.0:1.0. This ratio differs dramatically from the corresponding ratio of approximately 10:1.0 observed when activated BLM degrades 'B'-like DNA homopolymers. Experiments were undertaken to determine if the shift to enhanced base production observed in the A-like hybrids is the result of C-1' chemistry in addition to the C-4' chemistry normally observed with B-like DNA under identical conditions. Increased accessibility of the 1'-hydrogen might be anticipated due to widening of the minor groove in the A-like conformers. Experiments using poly([1'-3H]dA) poly(rU) and poly([U-14C]dA) poly(rU) indicated that neither 3H2O nor deoxyribonolactone accompanied adenine release. In addition, studies using poly([4'-2H]dA) poly(rU) and poly([1'-2H]dA) poly(rU) unambiguously establish that the altered base to base propenal ratio is not the result of C-1' chemistry, but a direct consequence of C-4' chemistry.

Bleomycin↗
PubMed1999

RNA binding characteristics and overall topology of the vaccinia poly(A) polymerase-processivity factor-primer complex.

The vaccinia virus-encoded heterodimer responsible for poly(A) tail elongation comprises a polyadenylylation catalytic subunit (VP55) and associated processivity factor (VP39). We show that monomeric VP39's affinity for RNA homopolymers follows the hierarchy poly(I) >poly(U) >>poly(G) >poly(A) >poly(C), that the heterodimer interacts stably with 40-45 nucleotide nucleic acid segments, and that its homopolymer preference for polyadenylylation priming is comparable to the VP39 affinity hierarchy (above). For oligonucleotide ligands possessing the previously-identified (rU)2-(N)25-rU heterodimer-binding motif, the heterodimer's affinity and base-type preference are mediated via both the (rU)2and rU portions, with the greater contribution coming from (rU)2. VP39's R107 sidechain contributes to specificity at the downstream rU. Substitution of each ribouridylate of the motif with either ribothymidine or 4-thiodeoxythymidine indicated that the downstream rU interacts with both heterodimer subunits, whereas the upstream (rU)2interacts only with VP55. A 'crosslinking SELEX' approach indicated VP39-base proximity around position -10 of a 4-thioribouridine/deoxycytidine ligand pool. Upon incubating the heterodimer with a panel of identical-sequence oligonucleotides derivatized with azidophenacyl bromide at various phosphate positions, those derivatized at positions -11 to -21 photocrosslinked to both subunits in a coordinated manner. This region may therefore pass through a 'cleft' or enclosed 'channel' at the subunit interface.

Binding Sites↗
PubMed2001

Improved hybridisation potential of oligonucleotides comprising O-methylated anhydrohexitol nucleoside congeners.

The hybridising potential of anhydrohexitol nucleoside analogues (HNAs) is well documented, but tedious synthesis of the monomers hampers their development. In a search for better analogues, the synthesis of two new methylated anhydrohexitol congeners 1 and 2 was accomplished and the physico-chemical properties of their respective oligomers were evaluated. Generally, oligonucleotides (ONs) containing the 3'-O-methyl derivative 1 showed a small increase in thermal stability towards complementary sequences as compared to HNA. Compared to the altritol modification, 3'-O-methylation seems to cause a small decrease in thermal stability of duplexes, especially when targeting RNA. These results suggest the possibility of derivatisation of the 3'-hydroxyl group of altritol-containing congeners without significantly affecting the thermal stability of the duplexes. The methyl glycosidic analogues 2 likewise increased the affinity for RNA in comparison with well-known HNA, while at the same time being economically more favorable monomers. However, homopolymers of 2 displayed self-pairing, but not so homopolymers of 1. Upon incorporation of the hexitols within RNA sequences in an effort to induce a beneficial pre-organised structure, the positive effect of the 3'-O-methyl derivative 1 proved larger than that of 2.

Methylation↗
PubMed1978

Protonated polynucleotides structures - 22.CD study of the acid-base titration of poly(dG).poly(dC).

The acid-base titration (pH 8 --> pH 2.5 --> pH 8) of eleven mixing curve samples of the poly(dG) plus poly(dC) system has been performed in 0.15 M NaCl. Upon protonation, poly(dG).poly(dC) gives rise to an acid complex, in various amounts according to the origin of the sample. We have established that the hysteresis of the acid-base titration is due to the non-reversible formation of an acid complex, and the liberation of the homopolymers at the end of the acid titration and during the base titration: the homopolymer mixtures remain stable up to pH 7. A 1G:1C stoichiometry appears to be the most probable for the acid complex, a 1G:2C stoichiometry, as found in poly(C(+)).poly(I).poly(C) or poly(C(+)).poly(G).poly(C), cannot be rejected. In the course of this study, evidence has been found that the structural consequences of protonation could be similar for both double stranded poly(dG).poly(dC) and G-C rich DNA's: 1) protonation starts near pH 6, dissociation of the acid complex of poly(dG).poly(dC) and of protonated DNA take place at pH 3; 2) the CD spectrum computed for the acid polymer complex displays a positive peak at 255 nm as found in the acid spectra of DNA's; 3) double stranded poly(dG).poly(dC) embedded in triple-stranded poly(dG).poly(dG).poly(dC) should be in the A-form and appears to be prevented from the proton induced conformational change. The neutral triple stranded poly(dG).poly(dG).poly(dC) appears therefore responsible, although indirectly, for the complexity and variability of the acid titration of poly(dG).poly(dC) samples.

Circular Dichroism↗
PubMed1980

Repeating oligonucleosomal units. A new element of chromatin structure.

Supranucleosomal chromatin structure has been analysed by the use of histone H1 polymers crosslinked in nuclei and extended chromatin with bifunctional reagents methyl-4-mercaptobutyrimidate (MMB) and dimethyl suberimidate dihydrochloride. Almost pure H1 homopolymers were obtained in milligram amounts and examined for the distribution in molecular weights. The H1 homopolymer molecules both from nuclei and chromatin have been found to be integer multiples of an elementary structure (called "clisone") consisting of 12 histone H1 molecules. This finding strongly suggests that nucleosomal chains of chromatin are not uniform but rather organized as repeating oligonucleosomal units each consisting of 12 nucleosomes. Correlation between oligonucleosomal structures in nuclei and chromatin implies that a linearized nucleosomal chain retains the information on chromatin superstructure. The relation of the disclosed 12-nucleosome units to superbeads (nucleomeres) and other structures is discussed.

Animals↗
PubMed1981

Nucleosomes will not form on double-stranded RNa or over poly(dA).poly(dT) tracts in recombinant DNA.

We have been unable to "force" double-stranded RNA to fold into nucleosome-like structures using several different histone-RNA "reconstitution" procedures. Even if the histones are first stabilized in octameric form by dimethylsuberimidate cross-linking they are still unable to form specific complexes with the RNA. Moreover double-stranded RNA is unable to induce histones to assemble into octamers although we confirm that the non-nucleic acid homopolymer, polyglutamic acid, has this ability. We have also determined, using pyrimidine tract analysis, that nucleosomes will not form over a sufficiently long segment of poly(dA).poly(dT) in a recombinant DNA molecule. Thus nucleosomes cannot fold DNA containing an 80 base pair poly(dA).poly(dT) segment but a 20 base pair segment can be accommodated in nucleosomes fairly well. Segments of intermediate length can be accommodated but are clearly selected against. Poly(dA).poly(dT) differs only slightly from natural DNA in helix structure. Therefore either this homopolymer resists folding, or nucleosomes are very exacting in the nucleic acid steroid parameters they will tolerate. Such constraints may be relevant to nucleosome positioning in chromatin.

Animals↗
PubMed1997

Specific interaction between erythrocytes and a glucose-carrying polymer mediated by the type-1 glucose transporter (GLUT-1) on the cell membrane.

A reducing glucose-carrying polymer, called poly [3-O-(4'-vinylbenzyl)-D-glucose] (PVG), interacted with erythrocytes carrying the type-1 glucose transporter (GLUT-1) on the cell membrane. The cooperative interaction between a number of GLUT-1s and a number of reducing 3-O-methyl-D-glucose moieties on a PVG polymer chain is responsible for the increase in the interaction with erythrocytes. In contrast to the PVG homopolymer, other sugar-carrying polymers showed lower interaction with erythrocytes. The affinity of erythrocytes and PVG was studied using FITC-labeled glycopolymers. The fluorescence intensity significantly changed, whereas a small change in fluorescence intensity was observed for other homopolymers. The specific interaction between GLUT-1 on erythrocytes and the PVG polymer carrying reducing glucose was suppressed by the inhibitors, phloretin, phloridzin, and cytochalasin B, and a monoclonal antibody to GLUT-1. Direct observation by confocal laser microscopy with the use of FITC-labeled PVG demonstrated that erythrocytes interacted with the soluble form of the PVG polymer via GLUT-1, while fluorescence labeling of the cell surface was prevented on pretreatment with the monoclonal antibody to GLUT-1.

Animals↗
PubMed1998

Synthesis of artificial glycoconjugate polymers starting from enzymatically synthesized oligosaccharides and their interactions with lectins.

Styrene derivatives substituted with N-linked beta-anomeric oligosaccharides were synthesized via a simple two-step procedure starting from three enzymatically prepared oligosaccharides: N-acetyllactosamine (Galbeta1-4GlcNAc), N-acetylisolactosamine (Galbeta1-6GlcNAc), and 4'-galactosyllactose (Galbeta1-4Galbeta1-4Glc). Their homo- and copolymerization with acrylamide using 2,2'-azobisisobutyronitrile as an initiator in dimethyl sulfoxide at 60 degreesC gave the corresponding glycopolymers. Binding between glycopolymers and lectins was investigated by means of hemagglutination inhibition experiments. The inhibition of RCA120 lectin-induced hemagglutination by N-acetyllactosamine-carrying homopolymer was about 10(3) times stronger than that of the oligosaccharide itself. The enhanced binding capacity with lectins can be explained in terms of a multivalent or cluster effect along the polymeric chain. In some combinations between lectins and polymers, the copolymers inhibited hemagglutination more strongly than the homopolymers did. N-Acetyllactosamine-carrying glycopolymer showed about 3 x 10(3) times weaker inhibition of DSA lectin-induced hemagglutination than the different type of N-acetyllactosamine-carrying glycopolymer which has an O-linked beta-anomeric phenyl aglycon of each repeating unit along a polyacrylamide backbone.

Biopolymers↗
PubMed1976

Effects of polyamines on in vitro dna synthesis by DNA polymerases from calf thymus.

DNA synthesizing reactions catalyzed both large and small species of calf thymus DNA polymerase (DNA polymerase-alpha and -beta) [EC 2.7.7.7] were stimulated to comparable extents by the presence of spermidine or spermine, and it was not possible to differentiate these two species in terms of their sensitivities to polyamines. Optimal concentrations for stimulation were 0.5-1.0 mM for spermidine and 2-10 mjM for spermine. Excess polyamines strongly inhibited the reactions. The modes of stimulation were as follows: 1) Stimulation was observed with templates bearing long single-stranded sections when either natural DNA or synthetic homopolymer-oligomer duplex was used. 2) The nautral DNA-dependent reaction was stimulated by polyamines at suboptimal concentrations of Mg2+; the apparent Km value for Mg2+ was lowered on adding polyamines, while the Vmax value was unchanged. When synthetic homopolymer-oligomer duplex was used as a template, the reaction was stimulated spermidine even at the optimal concentration of Mn2+. 3) Polyamines markedly influenced the salt requirements of the reactions of DNA polymerase. Spermidine could replace salts such as KC1 or NaC1 at concentrations less than 1/100 of those of salts.

Animals↗
PubMed1983

Isolation and characterization of nucleases from a clinical isolate of Serratia marcescens kums 3958.

Two new extracellular nucleases, nucleases SM1 and SM2, were purified from the culture fluid of S. marcescens kums 3958, a fresh clinical isolate. The purification was carried out by the following steps; ammonium sulfate precipitation, and DEAE-cellulose and Sephadex G-100 column chromatography. At the final step, nucleases SM1 and SM2 were purified about 3,700- and 1,000-fold, respectively. They were free from phosphomonoesterase and phosphodiesterase activities. The pIs were 8.1 and 7.5 for nucleases SM1 and SM2, respectively. The molecular weight was estimated to be 35,000 for both enzymes by SDS-polyacrylamide disc gel electrophoresis. The results of amino acid analyses showed that both the threonine and serine contents were higher in nuclease SM2 than in SM1. Furthermore, nuclease SM1 was more stable than nuclease SM2 at 4 degrees C. The other properties of the two enzymes were similar; pH optimum (8.0), Mg2+ or Mn2+ for activation, and inhibition by chemical reagents such as EDTA and pyrophosphate. No significant difference was found in base specificity between nucleases SM1 and SM2. Both enzymes specifically degraded double-stranded homopolymers, especially poly(I). poly(C), as well as yeast RNA and calf thymus DNA. They hardly degraded, however, single-stranded homopolymers such as poly(dA), poly(G), and poly(U).

Amino Acids↗
PubMed2002

Investigating the relationship between genome structure, composition, and ecology in prokaryotes.

Our thesis is that the DNA composition and structure of genomes are selected in part by mutation bias (GC pressure) and in part by ecology. To illustrate this point, we compare and contrast the oligonucleotide composition and the mosaic structure in 36 complete genomes and in 27 long genomic sequences from archaea and eubacteria. We report the following findings (1) High-GC-content genomes show a large underrepresentation of short distances between G(n) and C(n) homopolymers with respect to distances between A(n) and T(n) homopolymers; we discuss selection versus mutation bias hypotheses. (2) The oligonucleotide compositions of the genomes of Neisseria (meningitidis and gonorrhoea), Helicobacter pylori and Rhodobacter capsulatus are more biased than the other sequenced genomes. (3) The genomes of free-living species or nonchronic pathogens show more mosaic-like structure than genomes of chronic pathogens or intracellular symbionts. (4) Genome mosaicity of intracellular parasites has a maximum corresponding to the average gene length; in the genomes of free-living and nonchronic pathogens the maximum occurs at larger length scales. This suggests that free-living species can incorporate large pieces of DNA from the environment, whereas for intracellular parasites there are recombination events between homologous genes. We discuss the consequences in terms of evolution of genome size. (5) Intracellular symbionts and obligate pathogens show small, but not zero, amount of chromosome mosaicity, suggesting that recombination events occur in these species.

AT Rich Sequence↗
PubMed2007

Dendritic keratitis caused by an acyclovir-resistant herpes simplex virus with frameshift mutation.

PURPOSE: To report a case of acyclovir-resistant herpes simplex virus (HSV) keratitis after long-term, inconsistent use of topical acyclovir and fluorometholone. METHODS: A 70-year-old man with dendritic keratitis caused by an acyclovir-resistant HSV strain was examined. The 50% inhibitory concentration of different antiviral agents against the isolated virus and the DNA sequence of viral thymidine kinase were determined. RESULTS: The 50% inhibitory concentration of acyclovir and trifluorothymidine for the isolated HSV strain was 13.75 and 0.28 microg/mL, respectively, indicating that the virus was resistant to acyclovir. DNA sequencing of the viral thymidine kinase revealed that this virus had a frameshift mutant with a G insertion in the 7Gs homopolymer. Topical trifluorothymidine was effective, and the epithelial lesion was completely resolved within 2 weeks. CONCLUSION: A typical form of dendritic keratitis was caused by an acyclovir-resistant HSV with frameshift mutation in a 7Gs homopolymer region.

Acyclovir↗