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PubMed1989

Polynucleotide cross-linking by aluminum.

The observations that there was an increased concentration of Al in the brains of Alzheimer's, Guam-Parkinson, and amyotrophic lateral sclerosis disease patients and that there was an apparent localization of the Al in chromatin led to a study of the interaction of Al(III) with DNA. We have previously shown that Al cross-links calf thymus DNA at low pH (S. J. Karlik, G. L. Eichhorn, P. N. Lewis, and D. R. Crapper, Biochemistry 19, 5991 [1980]). Extended studies indicate that cross-linking occurs in DNAs of all base ratios, including polydAdT and polydGdC. Since Al cross-links prevent renaturation in polydAdT, the decrease in the amount of polymer renatured in the presence of Al becomes a quantitative appraisal of the extent of cross-linking. Saturation of cross-linking occurs at a 0.4 ratio of Al to nucleotide phosphate, indicating that potentially 80% of the base pairs are Al bound. Cross-links are broken at elevated pH and by EDTA.

Aluminum↗
PubMed1986

Preferential secretion of a common anti-DNA idiotype (16/6 Id) and anti-polynucleotide antibodies by normal mononuclear cells following stimulation with Klebsiella pneumoniae.

Peripheral blood mononuclear cells derived from 6 normal subjects were incubated with 5 polyclonal activators (pokeweed mitogen, Epstein-Barr virus, group-A Streptococcus, Staphylococcus aureus and Klebsiella pneumoniae. After 7 days of incubation, the supernatants were examined for immunoglobulin (IgG and IgM) production, the level of a common anti-DNA idiotype (16/6 Id) and autoantibody activity against ssDNA, dsDNA, poly(I), poly(dT) and cardiolipin. Significantly increased levels of the 16/6 Id were recorded only with the Klebsiella stimulated MNC. Increased immunoglobulin levels and autoantibody reactivity were noted with all 5 polyclonal activators. The Klebsiella cell membrane preparation induced the highest values. No correlation was found between the 16/6 levels, autoantibody activity and the absolute concentrations of IgG or IgM. This study, together with previous reports, suggests a role for Klebsiella in the etiology of autoimmune diseases. We suggest that Klebsiella can induce anti-DNA-like autoantibodies not only by polyclonal activation, but also by a more specific stimulus.

Autoantibodies↗
PubMed1982

Natural self-organization of polynucleotides and polypeptides in protobiogenesis: appearance of a protohypercycle.

Basic thermal polyamino acids or proteinoids have been reported to be catalytic for both self-instructing polymerization of amino acids and internucleotide synthesis. We show theoretically that a complex suspension of thermal proteinoids, free amino acids, nucleotides and ATP as an energy source can exhibit an evolutionary character. The suspension can produce a prototype of Eigen's hypercycle, or protohypercycle, for which translation proceeds from amino acid to nucleotide. The protohypercycle is suggested to be an evolutionary precursor of the hypercycle, in which translation is from nucleotide to amino acid. The possibility that the Fox-Nakashima microsphere containing both lysine-rich and acidic proteinoids may work as a model of a protohypercycle is considered.

Adenosine Triphosphate↗
PubMed1989

Extent of formation of a dimeric adenine photoproduct in polynucleotides and DNA.

Quantum yields are reported for the formation of a dimeric adenine photoproduct, A = A, in adenine homopolymers and DNA irradiated at 254 nm. The A = A content of irradiated samples was assayed by using reversed-phase HPLC to isolate the 4,6-diamino-5-guanidinopyrimidine (DGPY) which is produced from A = A on acid hydrolysis. Acid hydrolysates derived from DNA radiolabelled with [14C] 2'-deoxyadenosine were spiked with unlabelled DGPY before fractionation on HPLC and the recovered material was further purified by chromatography on Sephadex G-10 followed by co-crystallization with DGPY sulphate. Although A = A is formed with a relatively high quantum yield of 1.6 X 10(-3) mol einstein-1 in single-stranded poly(dA) the photoaddition reaction is strongly quenched in base-paired poly(dA).poly(dT) and undetectable in poly(rA).poly(dT). Respective quantum yields of 6 X 10(-5) and 9 X 10(-6) were estimated for the formation of A = A in single- and double-stranded E. coli DNA implying that the photoproduct has very limited biological significance. From studies with d(ApG), d(GpA), ApG, GpA, d(A)20 and d(A4G)4 it is concluded that adjacent guanine and adenine bases do not form a photoadduct analogous to A = A and also that guanine residues have no local or long-range quenching effect on photodimerization within A-A doublets.

Adenine↗
PubMed2006

Insight into the CSA tensors of nucleobase carbons in RNA polynucleotides from solution measurements of residual CSA: towards new long-range orientational constraints.

Using residual chemical shift anisotropies (RCSAs) measured in a weakly aligned stem-loop RNA, we examined the carbon chemical shift anisotropy (CSA) tensors of nucleobase adenine C2, pyrimidine C5 and C6, and purine C8. The differences between the measured RCSAs and the values back-calculated using three nucleobase carbon CSA sets [D. Stueber, D.M. Grant, 13C and 15N chemical shift tensors in adenosine, guanosine dihydrate, 2'-deoxythymidine, and cytidine, J. Am. Chem. Soc. 124 (2002) 10539-10551; D. Sitkoff, D.A. Case, Theories of chemical shift anisotropies in proteins and nucleic acids, Prog. NMR Spectrosc. 32 (1998) 165-190; R. Fiala, J. Czernek, V. Sklenar, Transverse relaxation optimized triple-resonance NMR experiments for nucleic acids, J. Biomol. NMR 16 (2000) 291-302] reported previously for mononucleotides (1.4 Hz) is significantly smaller than the predicted RCSA range (-10-10 Hz) but remains larger than the RCSA measurement uncertainty (0.8 Hz). Fitting of the traceless principal CSA values to the measured RCSAs using a grid search procedure yields a cytosine C5 CSA magnitude (CSAa=(3/2.(delta11(2)+delta22(2)+delta33(2)))1/2=173+/-21 ppm), which is significantly higher than the reported mononucleotide values (131-138 ppm) and a guanine C8 CSAa (148+/-13 ppm) that is in very good agreement with the mononucleotide value reported by solid-state NMR [134 ppm, D. Stueber, D.M. Grant, 13C and (15)N chemical shift tensors in adenosine, guanosine dihydrate, 2'-deoxythymidine, and cytidine, J. Am. Chem. Soc. 124 (2002) 10539-10551]. Owing to a unique sensitivity to directions normal to the base plane, the RCSAs can be translated into useful long-range orientational constraints for RNA structure determination even after allowing for substantial uncertainty in the nucleobase carbon CSA tensors.

Adenine↗
PubMed1972

Proton dispersion forces. Secondary-structure stabilizing forces between the hydrogen bonds of the polynucleotides.

In the double helix formed by the semiprotonated polycytidylic acid (poly C), both strands are linked via NH(+)...N hydrogen bonds. It is a known fact that such symmetrical hydrogen bonds with a double minimum potential well are extremely polarizable. This polarizability causes interaction effects, in particular the proton dispersion forces between such hydrogen bonds. These forces result in a shift of the energy levels and a continuum is observed in the infrared (IR) spectra of solutions in which such hydrogen bonds are present. The continuum occurs in the IR spectrum of the semiprotonated poly C, when the former is present in coiled state. If the double helix forms, an extremely broad band of the NH stretching vibration is observed instead of the continuum, since in the double helix all hydrogen bonds are oriented equally to one another and polarize each other mutually to a strong degree. The proton dispersion forces between the hydrogen bonds balance a considerable part of the electrostatic repulsion of the protons and hence enable the double helix to form. It is conceivable that an unsymmetrical double minimum potential well is present in the NH...N bonds in the DNA and RNA. Such bonds may likewise be considerably more polarizable than electron systems and thus, in this case too, proton dispersion forces would contribute to helix stabilization.

Cytosine Nucleotides↗
PubMed1973

Polarography of polynucleotides. 3. Polyadenylic acid: the electrode process and interaction with polyamines.

Polyadenylic acid (poly A) was studied under various conditions using both DC polarography and phase sensitive AC polarography and by measuring the time-course of the current during the lifetime of a single drop of the dropping mercury electrode. Under certain conditions the current at potentials of the limiting portion of the DC polarographic wave does not reach its limiting value and in extreme situations peak-shaped curves are observed. This phenomenon is explained in terms of desorption and repulsion from the electrode of neutral poly A due to its polyanionic character. Consequently, the suppression of the current can be enhanced by increasing negative potential of the electrode and by exposing the negative charges of phosphate groups, e.g., by increasing pH and temperature and by decreasing ionic strength and buffer capacity; vice versa, the current suppression can be at least partially eliminated by reversing these conditions. Polyamines which seem to shield the phosphate groups through specific interactions are very effective in eliminating the current suppression. The effectiveness of a polyamine is determined by its chain length and by the density of its amino groups and the geometry of their distribution.

Adenine Nucleotides↗