-
Science (New York, N.Y.) Nov 1969The nucleotide sequence of a 3'-terminal fragment obtained by ribonuclease T(1) hydrolysis of the ribonucleic acid from bacteriophage Qbeta has been determined by an...
The nucleotide sequence of a 3'-terminal fragment obtained by ribonuclease T(1) hydrolysis of the ribonucleic acid from bacteriophage Qbeta has been determined by an improved method of sequence analysis which involves sequential removal of bases by periodate oxidation and beta-elimination. The results obtained from ten such oxidation-elimination cycles and from the alkaline hydrolysis of the remaining oligonucleotide indicate that the first 16 nucleotides at the 3'-terminus of this ribonucleic acid have the sequence: -G-C-C-C-U-C-U-C-U-C-C-U-C-C-C-A.
Topics: Bacteriophages; Chromatography, Ion Exchange; Edetic Acid; Methods; Nucleotides; Oxidation-Reduction; Polynucleotides; RNA, Viral; Ribonucleases
PubMed: 4981494
DOI: 10.1126/science.166.3908.1004 -
Nucleic Acids Research Feb 1982Details of polynucleotide flexibility may be probed through a combination of semiempirical potential energy calculations and statistical mechanical analyses. The...
Details of polynucleotide flexibility may be probed through a combination of semiempirical potential energy calculations and statistical mechanical analyses. The pseudorotational motions of the furanose and the long-range correlated rotations of the chain backbone are described briefly here.
Topics: Computers; Mathematics; Nucleic Acid Conformation; Polynucleotides; X-Ray Diffraction
PubMed: 7063420
DOI: 10.1093/nar/10.3.777 -
Biophysical Chemistry Dec 1982A model for polynucleotide replication is presented and analyzed by means of perturbation theory. Two basic assumptions allow handling of sequences up to a chain length...
A model for polynucleotide replication is presented and analyzed by means of perturbation theory. Two basic assumptions allow handling of sequences up to a chain length of v approximately 80 explicitly: point mutations are restricted to a two-digit model and individual sequences are subsumed into mutant classes. Perturbation theory is in excellent agreement with the exact results for long enough sequences (v greater than 20).
Topics: DNA Replication; Mathematics; Models, Genetic; Mutation; Polynucleotides; Transcription, Genetic
PubMed: 7159681
DOI: 10.1016/0301-4622(82)87037-3 -
Journal of Biomolecular Structure &... Apr 2020The binding of proflavine, an acriflavine derivative, with the RNA polynucletodide polyadenylic acid-polyuridylic acid is investigated here to understand the structural...
The binding of proflavine, an acriflavine derivative, with the RNA polynucletodide polyadenylic acid-polyuridylic acid is investigated here to understand the structural and thermodynamic basis of the binding process. Such binding data are crucial for designing viable theraperutic agents. Spectroscopic studies clearly suggest a strong binding interaction between proflavine and polyadenylic acid-polyuridylic acid leading to efficient energy transfer between the poly AU base pairs and proflavine. The stoichiometry of proflavine polyadenylic acid-polyuridylic acid binding was independently estimated by continuous variation analysis of Job. An intercalative binding model is envisaged for the binding from hydrodynamic studies. Circular dichroism experiments revealed that the binding induced conformational changes in the RNA, and also led to induction of optical activity in the bound dye molecules. The binding affinity of the complex was deduced to be (6.57 ± 0.75) 10 M at (298.15 ± 0.10) K from isothermal titration calorimetry experiment. Positive entropy and negative enthalpy changes characterized the complexation. The binding was observed to be weaker both at higher temperatures and increased [Na]. The affinity of binding decreased with increasing [Na]. When the Gibbs energy was parsed between polyelectrolytic and nonpolyelectropytic components, it surprisingly revealed a higher role for the non-polyelectrolytic forces. These results present new data for developing RNA targeted ligands.Communicated by Ramaswamy H. Sarma.
Topics: Calorimetry; Circular Dichroism; Nucleic Acid Conformation; Poly A; Polynucleotides; Proflavine; RNA; Thermodynamics
PubMed: 31057051
DOI: 10.1080/07391102.2019.1615001 -
Biochemistry Jun 1981We report equilibrium dialysis studies of the binding of ethidium to a variety of double-helical synthetic polynucleotides containing A.U (or T) and I.C base pairs. The...
We report equilibrium dialysis studies of the binding of ethidium to a variety of double-helical synthetic polynucleotides containing A.U (or T) and I.C base pairs. The results are interpreted in terms of the neighbor exclusion model of drug binding, with allowance both for cooperativity of binding and for a structural switch of the helix to a different form which binds the drug more effectively. Both DNA and the alternating copolymers examined [poly[d(A-T)] and poly[d(I-C)]] showed high affinity (10(4)--10(5) M-1) in 1 M salt. Homopolynucleotides showed a more complicated pattern of affinities: poly(rA).poly(rU), poly(rA).poly(dT), and poly(dA).poly(rU) showed high affinity, whereas poly(dA).poly(dT), poly(rI).poly(rC), and poly(dI).poly(dC) showed low affinity (less than or equal to 10(3) M-1). The neighbor exclusion range was inferred to be two base pairs for DNA or B family helices and three for RNA or A family helices. Generally, polynucleotides showed some cooperativity in their ethidium binding. The data reveal a switch of poly[d(I-C)] to a form able to bind ethidium more effectively.
Topics: Animals; Cattle; Chemical Phenomena; Chemistry; DNA; Dialysis; Ethidium; Kinetics; Mathematics; Polydeoxyribonucleotides; Polyribonucleotides; Structure-Activity Relationship; Thymus Gland
PubMed: 7260057
DOI: 10.1021/bi00515a038 -
Nature Jun 1960
Topics: Nucleosides; Nucleotides; Poly I-C; Polynucleotides
PubMed: 13814388
DOI: 10.1038/1861030a0 -
The Journal of Biological Chemistry Jan 1975The kinetics of the phosphorolysis of polynucleotide (as differentiated from oligonucleotide) by polynucleotide phosphorylase of Micrococcus luteus has been...
The kinetics of the phosphorolysis of polynucleotide (as differentiated from oligonucleotide) by polynucleotide phosphorylase of Micrococcus luteus has been investigated. Double reciprocal plots of initial velocity against either inorganic phosphate or polynucleotide concentration are linear, and furthermore, the affinity of the enzyme for either substrate is unaffected by the presence of the other. dADP, an analogue of ADP product, is a competitive inhibitor with respect to Pi and polynucleotidy. (Ap)tA-cyclic-p is a competitive inhibitor with respect to Pi. The results are almost identical with both primer-independent (Form-I) and primer-dependent (Form-T) enzymes, although the various kinetic constants differ. On the vasis of these data a rapid equilibrium random Bi Bi mechanism is proposed. The demonstration of two different inhibitor constants for dADP and the difference between the Michaelis and the inhibitor constant for polyadenylic acid in polynucleotide phosphorolysis indicate at least two binding sites for polyadenylic acid and dADP on M. luteus polynucleotide phosphorylase. Its is suggested that in the phosphorolysis of long chain polymers the second binding site permits the polynucleotide to snap right back into position after removal of I mononucleotide unit and thus leads to the observed processive degradation. A general discussion of oligonucleotide and polynucleotide phosphorolysis and the differences between Form-I and Form-T enzymes in de novo synthesis and degradation of polynucleotides is presented.
Topics: Binding Sites; Binding, Competitive; Deoxyadenosines; Deoxyribonucleotides; Enzyme Activation; Kinetics; Magnesium; Micrococcus; Oligonucleotides; Polynucleotides; Polyribonucleotide Nucleotidyltransferase; Spectrophotometry, Ultraviolet
PubMed: 1078670
DOI: No ID Found -
Science (New York, N.Y.) Jul 1966The formation of cyclobutane-type dimers between adjacent pyrimidine residues in model polynucleotides or DNA may be represented by the general scheme See pdf 379.pdf... (Review)
Review
The formation of cyclobutane-type dimers between adjacent pyrimidine residues in model polynucleotides or DNA may be represented by the general scheme See pdf 379.pdf Whereas the formation of all other known photoproducts follows the irreversible path See pdf 379.pdf Thus dimers are distinguished from other photoproducts by the fact that they can be monomerized, as well as formed, by ultraviolet irradiation. At large incident fluxes of photons the steady-state value of dimers depends on wavelength and pH, as well as on other characteristics of the surrounding medium. The number of dimers in an irradiated polynucleotide may be decreased by purely photochemical means, whereas this is not true for most other photoproducts, for which continued irradiation, irrespective of wavelength, always results in the formation of more photoproduct (37). The wavelength dependence of the steady-state for dimers is also reflected in the biological activity of irradiated transforming DNA. This experiment and the fact that photoreactivating enzyme plus visible light monomerizes dimers (and has not been demonstrated to have any effect on other photoproducts) are the strongest lines of experimental evidence that pyrimidine dimers of the cyclobutane type are biologically important lesions and can account for a large fraction of the effects of ultraviolet light on DNA in solution. Insofar as DNA is one of the more important biological structures, such dimers, when formed, account for a large part of the effects of ultraviolet radiation on biological systems.
Topics: Chemical Phenomena; Chemistry; Polynucleotides; Pyrimidines; Ultraviolet Rays
PubMed: 5328566
DOI: 10.1126/science.153.3734.379 -
Biochemistry Nov 1966
Topics: Adenine Nucleotides; Centrifugation, Zonal; Electrophoresis; Escherichia coli; Nucleotidyltransferases; Polynucleotides; RNA, Bacterial
PubMed: 5339595
DOI: 10.1021/bi00875a041 -
Analytical Biochemistry Jan 1997A synthetic polynucleotide sequence was developed and cloned to serve as a target in footprinting and other assays designed to characterize the sequence-selective...
A synthetic polynucleotide sequence was developed and cloned to serve as a target in footprinting and other assays designed to characterize the sequence-selective binding of drugs and other small molecules to various forms of nucleic acids. The target sequence comprehensively represents all base quartet recognition sites in a minimal length sequence. Minimal length target sequences were found to be 144 nt long. One such target sequence was divided into two parts. One strand of each part was chemically synthesized and the complementary strands were generated using a DNA polymerase. Double-stranded sequences were then cloned into pGEM-3Zf(+/-) vectors (Promega, Inc.). The cloned target sequence can be used directly in double-stranded DNA form. Alternatively, features of the plasmid vector allow expression of the target sequences as single-stranded DNA or RNA or as RNA/DNA or RNA/RNA duplexes. These cloned target sequences designed for high information content overcome limitations to the use of natural DNA sequences for footprinting and related experiments arising from the unequal representation of base quartets and the potential for secondary structure formation in single-stranded forms.
Topics: Base Sequence; Cloning, Molecular; DNA; DNA Footprinting; Genetic Vectors; Molecular Sequence Data; Polynucleotides
PubMed: 9025910
DOI: 10.1006/abio.1996.9824