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At least 235 records · Page 13Linked to original sources
PubMed1987

[Amino acids as catalysts of the binding reaction of formaldehyde with adenine residue in polyadenylic acid].

Binding of formaldehyde and amino acids (Gly, Lys and Leu) with poly(A), poly(G), and poly(C) has been investigated in comparison with treatment with formaldehyde alone. It was found that in the case of poly(A) amino acids were found to catalyze the N-hydroxymethylation reaction on exocyclic amino groups of adenine. For example, at 20 degrees C and pH 6.0 the rate of this reaction increased about 10 fold in the presence of glycine.

Adenine↗
PubMed1984

Characterization of the calf uterine progesterone receptor and its stabilization by nucleic acids.

The molecular and steroid hormone-binding properties of the calf uterine progesterone receptor and its interaction with nucleic acids were investigated. A positive cooperative binding interaction of [3H]progesterone with the receptor was evident from a nonlinear Scatchard plot and a Hill coefficient of 1.22 +/- 0.02. The range of progesterone receptor concentrations was 0.73-1.04 pmol/mg protein, approximately twice that of the estrogen receptor. Competitive binding assays revealed a high specificity for progesterone: R5020 greater than or equal to progesterone greater than deoxycorticosterone greater than 5 alpha-pregnane-3,20-dione much greater than 17 alpha-hydroxyprogesterone greater than or equal to 20 alpha-dihydroprogesterone greater than or equal to testosterone greater than or equal to estradiol greater than cortisol. Thus, a progesterone-specific receptor of high affinity and concentration is obtainable from calf uterus in large quantities without estrogen pretreatment. Thermal inactivation of the unoccupied progesterone receptor is inhibited by 10 mM sodium molybdate, whereas thermal inactivation of the ammonium sulfate-purified progesterone receptor is not. Thermal inactivation of the ammonium sulfate-purified receptor is inhibited by nucleic acids and polynucleotides; polyguanylate (poly G) is the most effective. DNA and poly G also effectively restore the progesterone-binding ability of the ammonium sulfate-purified receptor which had been lost due to heat inactivation. After incubation of the unoccupied receptor from 5-30 min at 25 C, the addition of poly G restored the receptor's [3H]progesterone-binding ability to control levels. These data suggest that the progesterone receptor's steroid-binding site is more readily inactivated by heat than is the DNA-binding site, and that nucleic acid binding induces a conformational change, which consequently restores the receptor's progesterone-binding site to functional activity.

Animals↗
PubMed2005

Complete nucleotide sequence of the hirame rhabdovirus, a pathogen of marine fish.

Reverse transcription-polymerase chain reaction (RT-PCR) derived clones were constructed for the hirame rhabdovirus (HIRRV) CA-9703 strain from Korea, and the DNA was sequenced. The 3'-end of genomic RNA was cloned by poly(A)-tailing of the genomic RNA before reverse transcription, and the 5'-end of the genome was cloned by poly(G)- or poly(C)-tailing of the first strand, followed by PCR. The remainder of the genomic DNA was cloned by reverse transcription-polymerase chain reaction using primers that were based on the published rhabdovirus sequences. The complete genome of HIRRV CA-9703 strain comprises 11,034 nucleotides and encodes six genes in the order of: 3'-leader, N, P, M, G, NV, L, and 5'-trailer. These genes are separated by conserved sequences or gene junctions, with one-nucleotide gene spacers. The first 16 of the 19 nucleotides at the ends of the HIRRV genome are complementary, and the first four nucleotides at the 3'-ends of the HIRRV, infectious hematopoietic necrosis virus (IHNV), viral hemorrhagic septicemia virus (VHSV), and snakehead rhabdovirus (SHRV) genomes are identical. The HIRRV proteins share the highest amino acid sequence homology (ranging from 72% to 92%) with the proteins of IHNV, of all the known fish rhabdoviruses, and the highest sequence homology with respect to the L protein was shared among HIRRV, IHNV, VHSV, and SHRV. Although there were differences in the degrees of relatedness, phylogenetic trees that were derived from multiple sequence alignments of the rhabdovirus proteins showed similar patterns of relationship among these viruses, in which fish Novirhabdoviruses formed a separate clade from spring viremia of carp virus (SVCV), unassigned fish rhabdovirus that was closer to mammalian rhabdoviruses.

Amino Acid Sequence↗
PubMed1994

Characterization of a new monoclonal antibody to triplex DNA and immunofluorescent staining of mammalian chromosomes.

A monoclonal antibody, Jel 466, was prepared from mice immunized with poly[d(Tm5C)].poly[d(GA)]. The binding of Jel 466 to nucleic acids was characterized by solid phase radioimmunoassays and competition experiments. There was no binding to single-stranded DNAs or to duplexes which could not form triplexes. In addition, the antibody preferred the triplex form of poly[d(TC)].poly[d(GA)]; it bound weakly to the triplex derived from poly[d(G)].poly[d(C)], but there was no interaction with poly[d(T)].poly[d(A)].poly[d(T)]. This pattern of specificity is very different from that of Jel 318, a triplex-specific antibody that will bind to poly[d(T)].poly[d(A)].poly[d(T)]. The amino acid sequence of Jel 466 also showed very little homology with Jel 318, although both contain many positively charged amino acids. The immunofluorescent staining of mouse and human chromosomes with Jel 466 was studied. In all cases, there was a marked reciprocal relationship between the pattern of Jel 466 on the one hand and that of Hoechst 33258 and Jel 318 on the other. Jel 466 was negative for C-band and G-band but positive for R-band, whereas the opposite was found for Hoechst and Jel 318. Since C and G-bands are AT-rich and R-bands are GC-rich, these staining patterns match the sequence preferences of the two antibodies. Thus the base composition of triplex-forming DNA differs from domain to domain.

Amino Acid Sequence↗
PubMed2001

Isolation and characterization of an endonuclease synthesized by barley (Hordeum vulgare L.) uninucleate microspores.

Few biochemical and molecular details are available on microspore growth and development. In this work, a nuclease was partially purified from diffusates of barley (Hordeum vulgare L.) microspores by using concanavalin-A as ligand. The chromatographic preparation contained a 34-kDa protein with nucleolytic activity; the enzyme (called BMN: barley microspore nuclease) was very stable at pH > 8.0 and temperatures below 50 degrees C. Activity was highest at pH 5.6 and increased almost exponentially with temperature until a breakpoint between activity and stability was reached at 70 degrees C. Although BMN was able to cleave RNA, the enzyme showed a remarkable preference for DNA, especially in the single-stranded form. The best homopolymeric substrates were poly(dA) and poly(A), whereas poly(dC), poly(G) and poly(I) were almost completely uncleaved. When incubated with intact nuclei, BMN caused a nucleosomal DNA ladder of approximately 200 bp. On the basis of DNA laddering, substrate specificity, Mg2+ -dependence and best performance at apoplastic pH, BMN can be referred to as a putative apoptotic nuclease involved in pollen development.

Apoptosis↗
PubMed1984

In vivo and in vitro binding of epichlorohydrin to nucleic acids.

Epichlorohydrin (EC) binds to macromolecules of biological relevance in vivo: DNA is less labelled than RNA and proteins, rat organs interact more than mouse organs, stomach is the most labelled organ with liver, kidney and lung involved in decreasing order. Based on the Covalent Binding Index (CBI), EC is a weak-moderate oncogen, just as other chlorinated hydrocarbons such as 1,2-dichloroethane and carbon tetrachloride. An interaction of EC with nucleic acids (DNA and polyribonucleotides) occurs also in vitro. It is mediated either by chemical reactivity per se of the molecule (near-UV (NUV) irradiation does not photoactivate EC) and by enzymatic (microsomal and/or cytosolic) fractions, whose relative effectiveness is variable in relation to the organ tested. The best substrates for interaction are poly(G) and poly(A) when using microsomal and cytosolic fractions, respectively, whereas the labelling of double-stranded DNA is always lower. On the whole, the picture of enzyme (microsome + cytosol)-mediated in vitro interaction is similar to the pattern of in vivo binding, with the exception of rat stomach enzymes which are inactive in vitro.

Animals↗
PubMed1985

The covalent binding of bromobenzene with nucleic acids.

The hepatotoxic compound bromobenzene binds to DNA, RNA, and proteins of rat and mouse liver in vivo. Binding to a significant extent is also detected in mouse kidney. The covalent binding index (CBI) of bromobenzene is comparable to CBI values of moderately oncogenic substances. The enzyme-mediated in vitro interaction of bromobenzene with calf thyumus DNA and synthetic polyribonucleotides is effected only by microsomes, especially those from mouse and rat liver. Microsomes from mouse lung are also efficient in bioactivating bromobenzene to interact with DNA. Among polyribonucleotides, poly(G) and poly(A) are the most labeled substrates. The suppression of binding to DNA by SKF 525-A and the induction of microsomal activity by a pretreatment with phenobarbitone in vivo confirm that bromobenzene is bioactivated by a P-450 dependent-microsomal mixed function oxidase system. The covalent binding can be the main event to determine the possible carcinogenicity by genotoxic mechanisms. Bromobenzene is photoactivated by ultraviolet light (lambda = 254 nm) to forms capable of interacting with DNA in vitro; the binding is linear up to time.

Animals↗
PubMed1976

Renaturation of a multisubunit multiactivity enzyme complex: recovery of phage Qbeta RNA replicase, EF-Tu, and EF-Ts activities after denaturation in urea.

Phage Qbeta RNA replicase consists of four nonidentical subunits three of which are required for poly(C)-directed synthesis of poly(G): a phage-coded polypeptide and the two host-supplied protein biosynthesis elongation factors EF-Tu and EF-Ts. After denaturation of the enzyme in 8 M urea, poly(G) polymerase activity can be renaturated by dilution of the denatured subunits into a high ionic strength buffer with glycerol. The renaturation reaction has a broad temperature optimum between 11 and 21 degrees. The extent of renaturation is dependent on enzyme concentration: at low enzyme concentrations and 21 degrees renaturation proceeds for more than 3 h with greater than 40% recovery of activity, whereas at high enzyme concentrations the reaction is complete by 1 h with less than 10% of the poly(G) polymerase activity regained. Activities catalyzed by the elongation factors can be measured while they are part of the replicase complex. Study of rates of renaturation of EF-Tu and EF-Ts dependent activities alone and in the replicase complex revealed that virtually 100% of the EF-Ts activity was recovered more rapidly than could be assayed at temperatures as low as 2 degrees, while the rate of recovery of EF-Tu activity was comparable to that of the poly(G) polymerase activity and was independent of either EF-Tu concentration or the presence of other enzyme subunits. The rate of recovery of the poly(G) polymerase activity was found to be limited by the renaturation of EF-Tu, since the rate was dramatically increased by the addition of undenatured EF-Tu.

Binding Sites↗
PubMed2006

Physical interaction of apoptosis-inducing factor with DNA and RNA.

Apoptosis-inducing factor (AIF) is a mitochondrial flavoprotein, which upon apoptosis induction translocates to the nucleus where it interacts with DNA by virtue of positive charges clustered on the AIF surface. Here we show that the AIF interactome, as determined by mass spectroscopy, contains a large panel of ribonucleoproteins, which apparently bind to AIF through the RNA moiety. However, AIF is devoid of any detectable RNAse activity both in vitro and in vivo. Recombinant AIF can directly bind to DNA as well as to RNA. This binding can be visualized by electron microscopy, revealing that AIF can condense DNA, showing a preferential binding to single-stranded over double-stranded DNA. AIF also binds and aggregates single-stranded and structured RNA in vitro. Single-stranded poly A, poly G and poly C, as well double-stranded A/T and G/C RNA competed with DNA for AIF binding with a similar efficiency, thus corroborating a computer-calculated molecular model in which the binding site within AIF is the same for distinct nucleic acid species, without a clear sequence specificity. Among the preferred electron donors and acceptors of AIF, nicotine adenine dinucleotide phosphate (NADP) was particularly efficient in enhancing the generation of higher-order AIF/DNA and AIF/RNA complexes. Altogether, these data support a model in which a direct interaction of AIF contributes to the compaction of nucleic acids within apoptotic cells.

Amino Acid Sequence↗
PubMed1984

Interaction of rat prostate androgen receptors with polynucleotides, RNA, DNA and cloned DNA fragments.

Androgen receptors were partially purified from prostates of mature (non-castrated) rats by chromatography on 2',5'-ADP-Sepharose and labelled by exchange with 5 alpha-[3H]dihydrotestosterone. The partially purified receptor preparation was free of DNAase activity and sedimented at approx. 3 S. The specificity of the interaction of this androgen receptor with nucleotides was investigated in a competitive binding assay using inhibition of binding of the steroid receptor complex to ADP-Sepharose. Certain polyribonucleotides were strongly bound (e.g., poly(UG), poly(AU), poly(G) and poly(U] and competed more effectively for the receptor binding sites than prostate RNA. Restriction fragments of genomic clones from the genes which code for prostatic binding protein showed only moderate affinity for the 3 S receptor form. These data suggest that the 3 S form of the androgen receptor lacks the specific domain or conformation necessary for specific interaction with DNA, but retains a high affinity for certain forms of RNA. Some potent inhibitors of proteolysis (diisopropylfluorophosphate, leupeptin) did not have any effect on the form of the receptor isolated from mature intact animals. A possible function of the 3 S form in post-transcriptional processing is discussed.

Adenosine Diphosphate↗
PubMed1993

The human hnRNP M proteins: identification of a methionine/arginine-rich repeat motif in ribonucleoproteins.

Recent reports indicate that proteins which directly bind to nascent RNA polymerase II transcripts, the heterogeneous nuclear ribonucleoproteins (hnRNPs), play an important role in both transcript-specific packaging and alternative splicing of pre-mRNAs. Here we describe the isolation and characterization of a group of abundant hnRNPs, the M1-M4 proteins, which appear as a cluster of four proteins of 64,000-68,000 daltons by two-dimensional electrophoresis. The M proteins are pre-mRNA binding proteins in vivo, and they bind avidly to poly(G) and poly(U) RNA homopolymers in vitro. Covalently associated polyadenylated RNA-protein complexes, generated by irradiating living HeLa cells with UV light, were purified and used to elicit antibodies in mice. The resulting antisera were then employed to isolate cDNA clones for the largest M protein, M4, by immunological screening. The deduced amino acid sequence of M4 indicates that the M proteins are members of the ribonucleoprotein consensus sequence family of RNA-binding proteins with greatest similarity to a hypothetical RNA-binding protein from Saccharomyces cerevisiae. The M proteins also possess an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif) that resembles a repeat in the 64,000 dalton subunit of cleavage stimulation factor, which is involved in 3'-end maturation of pre-mRNAs. Proteins immunologically related to M exist in divergent eukaryotes ranging from human to yeast.

3T3 Cells↗
PubMed1996

An eight-nucleotide sequence in the potato virus X 3' untranslated region is required for both host protein binding and viral multiplication.

Gel retardation and UV-cross-linking techniques were used to demonstrate that two tobacco proteins, with approximate molecular masses of 28 and 32 kDa, bind to a site within the 3' region of potato virus X (PVX) genomic RNA. The protein binding is specific, in that a 50-fold excess of unlabeled probe prevents formation of the complexes but no reduction is observed with a 2,000-fold molar excess of yeast tRNA. Complex formation is inhibited by poly(U) but is relatively unaffected by poly(A), poly(G), or poly(C-I). PVX RNA-host protein complex formation occurs in vitro at salt concentrations up to 400 mM. Deletion mapping indicates that the proteins bind within the 3' untranslated region (UTR) of PVX genomic RNA and that an 8-nucleotide U-rich sequence (5'-UAUUUUCU) is required for the binding. Deletion of the 8-nucleotide U-rich region from the 3' UTR of a sensitive PVX reporter virus that carries the luciferase gene in place of the PVX coat protein gene results in a more than 70,000-fold reduction in luciferase expression in tobacco protoplasts. RNA probes carrying the sequence GCGC in place of the central four contiguous uridines of the 8-nucleotide U-rich motif fail to bind host protein at detectable levels, and the same mutation, when introduced into the PVX reporter virus, eliminates viral multiplication. Mutations of 1 or 2 nucleotides within the same four uridines reduced both binding of host proteins and replication of reporter virus. These results indicate that the 8-nucleotide U-rich motif within the PVX 3' UTR is important for some aspect of viral multiplication and suggest that host protein binding plays a role in the process.

Gene Deletion↗
PubMed1990

Limited proteolysis as a probe of the conformation and nucleic acid binding regions of nucleolin.

Nucleolin, also called protein C23, is a RNA-associated protein implicated in the early stages of ribosome assembly. To study the general conformation and map the nucleic acid binding regions, rat nucleolin was subjected to limited proteolysis using trypsin and chymotrypsin in the presence or absence of poly(G). The cleavage sites were classified according to their locations in the three putative domains: the highly polar amino-terminal domain, the central nucleic acid binding domain, which contains four 90-residue repeats, and the carboxyl-terminal domain, which is rich is glycine, dimethylarginine, and phenylalanine. The most labile sites were found in basic segments of the amino-terminal domain. This region was stabilized by Mg2+. At low enzyme concentrations, cleavage by trypsin or chymotrypsin in the amino-terminal domain was enhanced by poly(G). Trypsin produced a relatively stable 48-kDa fragment containing the central and carboxyl-terminal domains. The enhanced cleavage suggests that binding of nucleic acid by the central domain alters the conformation of the amino-terminal domain, exposing sites to proteolytic cleavage. At moderate enzyme concentrations, the 48-kDa fragment was protected by poly(G) against tryptic digestion. At the highest enzyme concentrations, both enzymes cleaved near the boundaries between repeats 2, 3, and 4 with some sites protected by poly(G), suggesting that the repeats themselves form compact units. The carboxyl-terminal domain was resistant to trypsin but was cleaved by chymotrypsin either in the presence or in the absence of poly(G), indicating exposure of some phenylalanines in this region. These studies provide a general picture of the topology of nucleolin and suggest that the nucleic acid binding region communicates with the amino-terminal domain.

Carrier Proteins↗
PubMed1994

Characterization of a cDNA encoding a novel type of RNA-binding protein in tobacco: its expression and nucleic acid-binding properties.

A cDNA encoding an RNA-binding protein (ribonucleoprotein or RNP) was isolated from a tobacco (Nicotiana sylvestris) cDNA library. The predicted protein (termed RGP-2) is 259 amino acids in length and consists of an N-terminal sequence of 39 amino acids, a consensus sequence type RNA-binding domain of 82 amino acids, a glycine-rich domain of 83 amino acids and an acidic C-terminal domain of 46 amino acids. It is distinct from the RGP-1 proteins previously reported, which consist of an RNA-binding domain in the N-terminal half and a glycine-rich domain in the C-terminal half. Homology searches revealed that RGP-2 is a novel consensus sequence-type RNA-binding protein. Its RNA-binding domain is structurally related to those of some chloroplast RNPs, while the amino acid composition of its glycine-rich domain (rich in glycine and asparagine) is similar to those in animal heterogeneous nuclear RNPs (hnRNP) A1 and A2/B1. The RGP-2 gene seems to be a single-copy gene, and its transcripts accumulate mainly in cultured cells and roots. A nucleic acid-binding assay using RGP-2 protein synthesized in vitro confirmed that it is an RNA-binding protein. Based on its greater affinity for total tobacco RNA than for poly(G) and poly(U), RGP-2 is suggested to bind to specific RNA sequences, probably G/U-rich regions. Quantitative analysis of the nucleic acid-binding properties of RGP-2 and RGP-1b indicates that they bind differently to nucleic acids. A possible role for RGP-2 is discussed in relation to known functions of animal hnRNP proteins.

Amino Acid Sequence↗
PubMed2000

A novel nucleic acid-binding protein in the cyanobacterium Synechococcus sp. PCC6301: a soluble 33-kDa polypeptide with high sequence similarity to ribosomal protein S1.

Cyanobacteria are prokaryotes that carry out plant-type photosynthesis and contain several eukaryotic-type RNA-binding proteins. Using a single-stranded DNA column, a 33-kDa protein was isolated and characterized from Synechococcus sp. PCC6301. This protein of 293 amino acids is similar in overall structure to the ribosomal protein S1 found in the same species, and contains three repeated units that are highly similar to the S1 motif originally found in the ribosomal protein S1 of Escherichia coli. However, the 33-kDa protein was found not to be associated with ribosomes and its nucleic acid binding specificity is distinct from that of the ribosomal protein S1. As this protein has high affinity for both single- and double-stranded DNA, as well as for poly(G) and poly(A), we tentatively named it nucleic acid-binding protein 1 (Nbp1).

Amino Acid Sequence↗
PubMed1991

Nucleolin promotes secondary structure in ribosomal RNA.

The effect of nucleolin on the secondary structure of RNA was studied using circular dichroism (CD). Nucleolin caused decreases in the main positive bands and shifts to higher wavelengths in the CD spectra of synthetic polynucleotides such as poly(G) and poly(A) indicating helix destabilizing activity. In contrast, nucleolin effected increases in signal and shifts to lower wavelengths of the peaks of CD spectra of ribosomal RNA, suggesting enhancement of secondary structure. Another major nucleolar RNA binding protein, B23, had helix destabilizing activity but did not enhance RNA secondary structure. It is proposed that nucleolin promotes formation of secondary structure in preribosomal RNA during the early stages of ribosome biogenesis.

Animals↗
PubMed1980

The effects of tetraalkylammonium salts on helix-coil transition parameters in natural and synthetic ribo- and deoxyribo-polynucleotides.

Thermal transition profiles were recorded for a variety of natural and synthetic DNA and double-stranded RNA preparations in the presence of tetramethylammonium (TMA+) and tetraethylammonium (TEA+) cations. Double-stranded RNAs of natural origin, with GC contents of 50% exhibited the same profiles and Tm values as native DNA containing normal bases. Hence the tetraalkylammonium cations liquidate not only the effects of base composition, and the difference in stability between A-T and A-U base pairs (further confirmed by measurements with uracil-containing DNA from phage PBS-2), but also that of the 2'OH. In the presence of TMA+ cations, there is very marked enhancement of the stability of U-U base pairs in poly(rU) and poly(Um). In 2.4 M TEA, the 1:1 complex of poly(G) with poly (C) formed readily and melted reversibly with a Tm as low as 87 degrees C. At concentrations of TMA and TEA for which dTm/dXGC = 0, the Tm values for various phage DNA preparations containing atypical bases (phages T2, T4, phi e, phi W-14, PBS-2) differ appreciably from those with 'normal bases'. Analysis of these findings indicates that the selective interaction of TMA and TEA cations with A-T base pairs occurs in the minor groove of the DNA helix. The overall results show that the action of these quaternary ammonium cations is not due exclusively to preferential binding to A-T base pairs, but must involve other factors, including modifications of solvent structure. They also underline the utility of TMA and TEA solvent systems for placing in evidence transition profiles not accessible in other solvent systems.

DNA↗
PubMed1980

Binding of quinoline to nucleic acid in a subcellular microsomal system.

Quinoline, a hepatocarcinogen in rats and mutagen in Salmonella typhimurium, binds to RNA, DNA and certain polyribonucleotides in the presence of NADPH and rat liver microsomes. The binding was pronounced with the help of liver microsome preparations made from the rats pretreated with some inducers of the microsomal monooxygenase system. The binding reaction required NADPH and was inhibited by carbon monoxide or aniline, and also by 7,8-benzoflavone, methyrapone or SKF 525A. These results suggested that the cytochrome P-450-linked monooxygenase system is involved in this binding process. Quinoline bound preferably to poly(A), poly(C), poly(G) and poly(X), but negligibly to poly(U) and poly(I). Most of the quinoline residues of the adducts, regardless of the kind of polynucleotides used, were released by acid or alkali at 100 degrees C in the form of 3-hydroxyquinoline. This suggests that 2,3- or 3,4-epoxy derivative of quinoline is the reactive intermediate for nucleic acid modification.

Animals↗