Separation of purine derivatives by polymer-bound nucleic acid bases

Separation of a variety of purine bases, which include 7-methyl derivatives, was studied by using polyethyleneimine-coated silicagel which bound hypoxanthine, cytosine or guanine moieties. The separation behavior seems to be related to the interaction of imidazole part of purine derivatives with the resins through hydrogen bonding.     

Reaction of nucleic acid bases with the mercury electrode: Determination of purine derivatives at submicromolar concentrations by means of cathodic stripping voltammetry

It was found that adenine, guanine, hypoxanthine, 8-hydroxyadenine, and a number of further purine derivatives react in alkaline media with mercury of the electrode charged to potentials close to zero V (against the saturated calomel electrode) and form sparingly soluble compounds. Formation of these compounds with mercury is manifested on the polarographic (voltammetric) curves by characteristic anodic waves (peaks) which can be exploited for analytical purposes. Differential pulse polarography renders it possible to determine bases at concentrations of 10^?5–10^?6m. Substantially higher sensitivity can be reached by cathodic stripping voltammetry (CSV). This method is based on a slow accumulation of the sparingly soluble compound at the electrode surface and its subsequent rapid cathodic stripping. A number of purine derivatives can be determined by CSV at concentrations as low as 10^?8m (the limit of adenine detection is about 2 × 10^?9m). As compared with sulphur-containing substances CSV analysis of the purine derivatives is limited to a narrower range of deposition potentials. It was shown that the presence of an excess of proteins or DNA does not interfere with determination of purine bases.     

Analysis of nucleic acid bases by high-performance liquid ion chromatography

Optimal conditions for the high-speed chromatography of nucleic acid bases using cation exchangers are described. Bases are resolved on Aminex A-7 with 1 m phosphate in 20% ethanol at pH 3.4 and 70°C and with 1 m phosphate at pH 2.75 and 50°C. The optimal conditions for the same analysis on the anion exchanger Aminex A-28 are by elution with 0.4 m phosphate-borate, pH 8.25, at 45°C. The dependence of the charge of various analogs of the nucleic acid bases on the pH of the solution is tabulated.     

Raman diagnosis of nucleic acid structure: sugar-puckering and glycosidic conformation in the guanosine moiety.

Observations of Raman spectra of various nucleic acids indicate that the guanine ring breathing frequency is sensitive to the internal rotation angle around the glycosidic bond and to the conformation of the five-membered ring of the ribose residue that is directly connected with the guanine residue in question. It is found that 682 cm-1 for C2'-endo-anti, at 665 cm-1 for C3'-endo-anti, and at 625 cm-1 for C3'-endo-syn. A DNA octamer d(GpGpApApTpTpCpC) shows, in its aqueous solution, a broad Raman band at 680 cm-1 with a tail at 670 cm-1. This fact suggests that the guanosine residues in this oligomer take primarily C2'-endo-anti conformation but an appreciable amount of fluctuation of the ribose ring structure towards C3'-endo is involved.     

Recognition of nucleic acid bases and base-pairs by hydrogen bonding to amino acid side-chains

Sequence-specific protein-nucleic acid recognition is determined, in part, by hydrogen bonding interactions between amino acid side-chains and nucleotide bases. To examine the repertoire of possible interactions, we have calculated geometrically plausible arrangements in which amino acids hydrogen bond to unpaired bases, such as those found in RNA bulges and loops, or to the 53 possible RNA base-pairs. We find 32 possible interactions that involve two or more hydrogen bonds to the six unpaired bases (including protonated A and C), 17 of which have been observed. We find 186 "spanning" interactions to base-pairs in which the amino acid hydrogen bonds to both bases, in principle allowing particular base-pairs to be selectively targeted, and nine of these have been observed. Four calculated interactions span the Watson-Crick pairs and 15 span the G:U wobble pair, including two interesting arrangements with three hydrogen bonds to the Arg guanidinum group that have not yet been observed. The inherent donor-acceptor arrangements of the bases support many possible interactions to Asn (or Gln) and Ser (or Thr or Tyr), few interactions to Asp (or Glu) even though several already have been observed, and interactions to U (or T) only if the base is in an unpaired context, as also observed in several cases. This study highlights how complementary arrangements of donors and acceptors can contribute to base-specific recognition of RNA, predicts interactions not yet observed, and provides tools to analyze proposed contacts or design novel interactions.     

Simulation of interactions between nucleic acid bases by refined atom-atom potential functions

Energy of interaction between nitrogen bases of nucleic acid has been calculated as a function of parameters determining the mutual position of two bases. Refined atom-atom potential functions are suggested. These functions contain terms proportional to the first (electrostatics), sixth (or tenth for the atoms forming a hydrogen bond) and twelfth (repulsion of all atoms) powers of interatomic distance. Calculations have shown that there are two groups of minima of the base interaction energy. The minima of the first group correspond to coplanar arrangement of the base pairs and hydrogen bond formation. The minima of the second group correspond to the position of bases one above the other in almost parallel planes. There are 28 energy minima corresponding to the formation of coplanar pairs with two (three for the G:C pair) almost linear N-H . . . O and (or) N-H . . . N hydrogen bonds. The position of nitrogen bases paired by two such H-bonds in any crystal of nucleic acid component in polynucleotide complexes and in tRNA is close to the position in one of these minima. Besides, for each pair there are energy minima corresponding to the formation of a single N-H . . . O or N-H . . . N and one C-H . . . O or C-H . . . N hydrogen bond. The form of potential surface in the vicinity of minima has been characterized. The results of calculations agree with the experimental data and with more rigorous calculations based on quantum-mechanical approach.     

Solvation free energies of nucleic acid bases in ionic liquids

The solvation free energies of five nucleic acid bases in [C_nbim]Br (where n = 2, 4, 6) ionic liquids (ILs) were computed using the Bennett acceptance ratio (BAR) method employing molecular dynamics simulations. The computed free energies using BAR were in agreement with other methods. The large and negative predicted free energies of the bases in ILs indicated that the bases were better solvated in the ILs rather than in water. Hydrogen bonding interactions between polar sites of the bases and ILs’ ions significantly contributed to the solvation mechanism.     

Nature of the stacking of nucleic acid bases in water: a Monte Carlo simulation

The results of a Monte Carlo simulation of the hydration of uracil and thymine molecules, their stacked dimers and hydrogen-bonded base pairs are presented. Simulations have been performed in a cluster approximation. The semiempirical atom-atom potential functions have been used (cluster consisting of 200 water molecules). It has been shown that the stacking interactions of uracil and thymine molecules in water arise mainly due to the increase in the water-water interaction during the transition from monomers to dimer. It has been found out that stacked base associates are more preferable than base pairs in water. This preference is mainly due to the energetically more favourable structure of water around the stack.     

Analysis of conformational parameters in nucleic acid fragments. II. Co-crystal complexes of nucleic acid bases.

Studies have been made of conformational parameters in co-crystal complexes and compounds of nucleic acid bases in which there is the possibility of formation of hetero-base-pairs. Using published data extracted from the Cambridge structural database, a total of 37 base-pairs were found, of which 25 were hetero-pairs and 12 homo-pairs. These base-pairs were subject to analysis to reveal hydrogen bond parameters, propeller twist, buckle and C1'-C1' separation (or a similar parameter if C1' atoms were not present). Hetero-pairs were found to show larger twists than homo-pairs, the magnitude of twist being unrelated to hydrogen bond parameters or buckle value. The propeller twisting is less pronounced in these nucleic acid bases than in nucleosides, but still has a significant magnitude. Propeller twisting in hetero-pairs is found to be larger than in homo-pairs. Hetero-pairs appear to be formed preferentially in competitive situations.