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PubMed1979

The molecular electrostatic potential of the B-DNA helix. VI. The regions of the base pairs in poly (dG.dC) and poly (dA.dT).

The evaluation of the electrostatic molecular potential at important nucleophilic sites of the purine and pyrimidine bases in poly (dG.dC) and poly (dA.dT) and of the evolution of the potential through the series free bases-nucleosides-nucleotides-single polynucleotide helices-double helices enables the interpretation of the evolution of the corresponding reactivity of the bases towards a series of electrophilic carcinogenic and mutagenic reactants.

Base Composition↗
PubMed1979

The effect of antibiotics on the T4 polynucleotide ligase catalyzed template dependent polymerization of oligodeoxythymidylates.

The poly(dA) dependent T4 polynucleotide ligase catalyzed polymerization of oligodeoxythymidylates is dependent upon duplex stability. The antibiotics ethidium bromide, netropsin and Hoechst 33258 stabilize the duplex poly(dA) . P(dT)n (n = 6-10) to thermal denaturation. Ethidium bromide to DNA ratio of 1.25 and netropsin or Hoechst 33258 to DNA ratio of 0.1 the Tm of d(pT) 10 . poly (dA) was increased by 10 degrees and 25 degrees C respectively. The T4 polynucleotide ligase activity was not inhibited under these conditions and temperature optimum of joining of d(pT) 10 . poly(dA) was increased 5 degrees to 10 degrees by the binding of the antibiotics. Duplexes containing shorter oligodeoxythymidylates required lower concentrations of the antibiotics netropsin or Hoechst 33258 to show no inhibition of T4 polynucleotide ligase. The temperature optima of joining the duplexes d(pT)6 . POLY(DA) and d(pT) 8 . poly(dA) were increased by 5 degrees C upon binding of the antibiotics. Polyacrylamide gel analysis of the T4 polynucleotide ligase catalyzed joining of the oligodeoxythymidylates showed that the presence of antibiotics affected the product distribution of the polymerized oligomers.

Anti-Bacterial Agents↗
PubMed1979

Evidence that populations of Dictyostelium single-copy mRNA transcripts carry common repeat sequences.

Two recombinant plasmids, M4 and KH10, carrying Dictyostelium DNA inserted into the Eco RI restriction endonuclease site of pMB9 by poly(dA)-poly(dT) tailing, were selected for study because they are complementary to abundant mRNA populations from Dictyostelium. Both plasmids have been shown to hybridize a heterogeneous size class of mRNAs which, in the case of KH10, comprise 5-10% of the pulse-labeled poly(A)+ RNA from vegetative cells. Analysis of the sequence organization of the two pieces of Dictyostelium DNA shows that they consist mostly of single-copy sequences with a short DNA sequence which is repeated in the genome and interspersed with single-copy DNA. These and other results suggest that the majority of the hybridization of pulse-labeled mRNA to M4 and KH10 is to the short "repeated" DNA sequences. In the genome, members of these repeat families appear to be transcribed onto a population of different single-copy mRNAs. Additional results show that M4 DNA contains a sequence which is entirely complementary to a discrete mRNA.

Base Sequence↗
PubMed1979

Studies on gene control regions X. The effect of specific adenine-thymine transversions on the lac repressor-lac operator interaction.

Chemical and enzymatic methods were used to synthesize a transition (AT to GC) and a transversion (AT to TA) at a lac operator site known to interact with lac repressor through the thymine 5 methyl group. These operators also contained a poly(dA) . poly(dT) tail 8 to 12 base pairs in length at one end. Results suggest that the steric constraints of lac repressor relative to the position of the 5 methyl group are quite critical. For example a seven fold reduction in stability was observed for the transversion. Results also suggest that the operator spans at least 21 base pairs.

Adenine↗
PubMed1979

Conformation of DNA in chromatin core particles containing poly(dAdT)-poly(dAdT) studied by 31 P NMR spectroscopy.

We have prepared semi-synthetic chromatin core particles from a complex of chicken erythrocyte inner histones (H2A, H2B, H3 and H4) with double-stranded poly(dAdT).poly(dAdT) and studied the conformation of the phosphodiester backbone using 31P NMR at 109.3 MHz. At 20 degrees C, the core particle spectrum is fit well by a single Lorenzian distribution with a line width of 110 Hz. This signal is significantly broader than that for the 145 base pair poly(dAdT).poly(dAdT) alone; the latter consists of two resonances, approximately equal in intensity, with average line width 41 Hz. Major changes in the spectrum ensue on heating the core particle preparation. In conjunction with other results (1) these data suggest four states for the core particle at increasing temperatures. Additionally, analysis of the spectrum of the unmelted core particle and its differences from protein-free DNA of the same length suggests that the conformation of the phosphodiester backbone and/or its interactions with histones along the length of the core particle DNA segment may not be uniform.

Animals↗
PubMed1979

Aspects of specific protein-DNA interaction; multi-mode binding of the oligopeptide antibiotic netropsin to (A.T)-rich DNA segments.

By means of titration viscometry a number of distinct modes could be resolved for the interaction between the antibiotic netropsin and DNA species of 50, 58, and 69 mole + (A+T) below r = 0.04 netropsin molecules bound per DNA phosphate group. The number of corresponding binding sites increases with a high power of the (A+T) content. The apparent association constants are very high (greater than 10(6) M-1, some perhaps greater than 10(6) M-1) and also rather different for most of the binding sites. It is suggested that some of these interaction modes differ in the number of hydrogen bonds formed between donors of the ligand and acceptors of the binding sites. The interaction modes were characterized quantitatively by their (species-independent) changes of DNA contour length and by the percentage of local DNA stiffening.

Animals↗
PubMed1977

Studies on the transcription complex of Escherichia coli RNA polymerase.

To study the chain elongation phase of enzymatic RNA synthesis ternary transcription complexes with T7 DNA or poly[dA) - (dT)] as template were isolated by gel exclusion chromatography. The DNA in these complexes contains single-stranded regions which are recognized by a single-strand-specific nuclease from Neurospora crassa. The non-codogenic DNA strand in the poly[(dA) - (dT)] ternary complex is preferentially hydrolysed by the nuclease. The polymerase protects predominantly the codogenic strand in this complex from digestion by DNAse I. In the T7 DNA ternary complex a DNA fragment with a chain length of approximately 26 nucleotides and an RNA fragment of about 22 nucleotides are protected by polymerase from digestion by DNAse and RNAse.

Coliphages↗
PubMed1978

Studies on the purification and properties of a 6.8-S DNA polymerase activity found in calf-thymus DNA polymerase-alpha fraction.

The heterogeneity of calf thymus DNA polymerase-alpha has been further investigated. In particular, an enzyme (enzyme D) which exhibits higher activity on poly(dA) . (dT)10 (A:T = 20:1) compared with that on activated DNA, has been further purified and its properties compared with two other activities of the DNA polymerase-alpha fraction (enzymes A1 and C) which do not show a preference for poly(dA) . (dT)10 over activated DNA. As with A1 and C, enzyme D was shown to have many of the characteristic properties of DNA polymerase-alpha in that it is an acidic protein as judged by its binding to DEAE-cellulose, has a molecular weight of about 140000, does not use a poly (A) . (dT)10 template-initiator complex and is inhibited by N-ethylmaleimide. It exhibits anomalous gel filtration behaviour on Sepharose 6B and it binds relatively weakly to DNA-cellulose compared with DNA polymerase-beta. The extreme sensitivity of enzyme D to inhibtion by N-ethylmaleimide distinguishes it from A1 and C, as does its elution position from a DEAE-cellulose column. On the other hand enzymes C and D are readily inactivated by heating at 45 degrees C unlike enzyme A1. The possible interrelationships of the multiple activities of calf thymus DNA polymerase-alpha are discussed.

Animals↗
PubMed1978

A study of unwinding of DNA and shielding of the DNA grooves by RNA polymerase by using methylation with dimethylsulphate.

The dimethylsulphate method has been used to study the complexes of RNA polymerase (Escherichia coli) with DNA of T7 phage, poly[d(A--T)] and fragments of calf thymus DNA protected against DNase digestion by RNA polymerase. The binding of RNA polymerase to DNA significantly increases the formation of 1-methyl-adenine produced by methylation of the single-stranded DNA region, diminishes by about 10% the formation of 3-methyl-adenine by methylation within the minor groove and does not affect the formation of 7-methyl-guanine by methylation within the major DNA groove. The presence of nascent RNA decreases the formation of 1-methyl-adenine in DNA of the complex by about 30%. The initiation of RNA synthesis or RNA synthesis itself does not influence the methylation of the major groove but shielding of the minor groove increases by about twice as much. These results suggest that RNA polymerase, upon binding, breaks Watson-Crick base-pairing in a DNA region of about 15-base-pairs long, that nascent RNA forms a duplex with DNA of about 10-base-pairs long; and that the enzyme weakly interacts with DNA along its grooves and preferentially makes contacts with the minor groove.

Adenine↗
PubMed1977

Lipiarmycin-resistant ribonucleic acid polymerase mutants of Bacillus subtilis.

Lipiarmycin inhibited the activity of deoxyribonucleic acid-dependent ribonucleic acid (RNA) polymerase in vitro. We showed that inhibition was due to interference by lipiarmycin with the activity of sigma-containing molecules of RNA polymerase. Transcription by core enzyme was relatively resistant to the drug, but addition of sigma led to highly drug-sensitive RNA synthesis. We isolated lipiarmycin-resistant mutants of Bacillus subtilis and characterized them genetically and biochemically. Drug-resistant mutants contained an altered RNA polymerase that was resistant to the drug in vitro. By separation and mixed reconstitution of core and sigma fractions of mutant and wild-type RNA polymerase, we showed that lipiarmycin resistance in one mutant strain was a property of the core fraction. Genetic mapping experiments indicated that at least two lpm mutants are located between loci determining rifampin resistance and streptolydigin resistance.

Anti-Bacterial Agents↗
PubMed1978

A deoxyribonucleic acid unwinding protein isolated from regenerating rat liver. Physical and functional properties.

A DNA-unwinding protein has been purified from regenerating rat liver cytosol to apparent homogeneity. The protein is present in about 10(6) copies per cell. It is a tetramer, composed of 25,000-dalton subunits which does not exhibit enzymatic activity for ATPase, DNA polymerase, or DNase. The protein is able to unwind the double helix of poly[d(A-T)], depressing the melting point of this synthetic polymer by about 40 degrees. It also binds to supercoiled SV40 DNA, probably by melting A-T-rich regions in the genome. The fully saturated complex of protein and SV40 DNA sediments at 30 S. Homologous DNA polymerases-alpha and -beta are stimulated by the protein at a different level depending on the templates used. This result argues in favor of the intervention of the unwinding protein in replication processes.

Animals↗
PubMed1977

Novel properties of Escherichia coli exonuclease III.

The specificity of hydrolysis of polynucleotide termini by Escherichia coli exonuclease III was studied with the use of oligothymidylate annealed to polydeoxyadenylate. The size of the products after 3' leads to 5'-hydrolysis of 5'-labeled substrate is temperature-dependent. At 25 degrees the enzyme can hydrolyze a polynucleotide chain up to the last 5'-terminal dinucleotide. A gradation of higher 5'-terminal oligonucleotides of defined chain lengths is produced after limit digestion by the enzyme when the temperature is raised between 25 degrees to 60 degrees. When the oligothymidylate was labeled at the 3'-ends with ribonucleotides, it was observed that exonuclease III can cleave a single or two consecutive ribonucleotides regardless of whether the ribonucleotides are base-paired or mismatched.

Deoxyribonucleases↗