Bonding interactions nucleic acids

In all these events, the hydrogen-bonded Watson-Crick base pair is operative and is responsible for DNA reduplication, transcription, and translation. Since mispairing can occur, all these processes are checked for fidelity by several enzymes which can correct for errors [6521. At this and all other levels of DNA reduplication and protein biosynthesis, intermolecular hydrogen bonds between nucleic acids and between nucleic acids and proteins are responsible for recognition, interaction, and, finally, for information transfer. 

Poly(vinyl alcohols) bonded with nucleic acid bases through phosphate linkages were prepared. Contents of uracil, thymine and hypoxanthine in the polymers were about 50 to 60 mol-%, and that of adenine was about 10%. Interactions of these polymers with DNA in aqueous solution were studied. The apparent hypochromidty was 6.5% for adenine substituted poly(vinyl alcohol) - DNA and 3% for the corresponding uracil substituted derivative83. ... 

OPTS (Optim i/.ed Potentials for Liquid Simulations) is based on a force field developed by the research group of Bill Jorgensen now at Yale University and previously at Purdue University. Like AMBER, the OPLS force field is designed for calculations on proteins an d nucleic acids. It in troduces non bonded in leraclion parameters that have been carefully developed from extensive Monte Carlo liquid sim u lation s of small molecules. These n on-bonded interactions have been added to the bonding interactions of AMBER to produce a new force field that is expected to be better than AMBER at describing simulations w here the solvent isexplic-... 

OPLS is designed for calculations on proteins and nucleic acids the non-bonded interactions have been carefully developed from liquid simulations on small molecules. There are many more force fields in the literature, but the ones given above are representative. 

When thinking about chemical reactivity, chemists usually focus their attention on bonds, the covalent interactions between atoms within individual molecules. Also important, hotvever, particularly in large biomolecules like proteins and nucleic acids, are a variety of interactions between molecules that strongly affect molecular properties. Collectively called either intermolecular forces, van der Waals forces, or noncovalent interactions, they are of several different types dipole-dipole forces, dispersion forces, and hydrogen bonds. 

Three classes of nucleic acid triple helices have been described for oligonucleotides containing only natural units. They differ according to the base sequences and the relative orientation of the phosphate-deoxyribose backbone of the third strand. All the three classes involve Hoogsteen or reverse Hoogsteen-like hydrogen bonding interaction between the triple helix form-... 

P2j Z = 2 DX = 1.43 R = 0.067 for 1269 intensities. The uracil residue is in the anti (63.4°) disposition. The conformation of the D-ribosyl group is 2T3 (176.8°, 37.5°). The orientation about the exocyclic, C-4 -C-5 bond is t (—174.2°). The phenyl and uracil ringsofthe same molecule lie in almost parallel planes, 120 pm apart. The phenyl group is disordered. The uracil ring is sandwiched by the phenyl rings, and vice versa. The 0-1 and N-a atoms of the peptide backbone are hydrogen-bonded to 0-4 and N-3 of atranslationally related uracil to form cyclic dimers. Such interactions serve as models for nucleic acid-protein interactions. [Coordinate errors H(02 ) x should be —1574, instead of —1474 H(Na)2 z should be —145 instead of— 645.]... 

What is the importance of this enzyme family for the biogenesis problem These enzymes form the link between the protein world and the nucleic acid world . They catalyse the reaction between amino acids and transfer RNA molecules, which includes an activation step involving ATR The formation of the peptide bond, i.e., the actual polycondensation reaction, takes place at the ribosome and involves mRNA participation and process control via codon-anticodon interaction. 

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