Nucleic acid helices

Lomant AJ, Fresco JR (1975) Structural and energetic consequences of noncomplementary base opposition in nucleic acid helices. Prog Nucl Acid Res Mol Biol 15 185-218... 

The chemically synthesized L-d(CGCGCG) was co-crystallized with equimolar D-enantiomer. The enantiomers of nucleic acid helices, e.g. 

Reagent 206 has been prepared that allows disulfide cross-links to be introduced into nucleic acids during solid-phase synthesis. The disulfide is formed between thioalkyl tethers at the N-3-position of thymidines and stabilises the termini of nucleic acid helices. Disulfide linked triplexes have been studied. ... 

The most common element of secondary structure in proteins is the helix. Helices are enriched at protein/protein interfaces, where a helixxleft motif is often employed to recognize hot spot residues at the protein/protein interface. Helices are also enriched in protein/nucleic acid interactions, where the helical motif facilitates molecular recognition by projecting residues into the grooves of nucleic acid helices. 

It fits nicely into the picture of dual structure-phase views of biomesogenic organizations that objects of rod-like appearance , for instance the little world of the tobacco mosaic virus (which - its overall design reduced to a simple rod-like entity - became the starting point of Onsager s theory [37]), as well as much simpler protein and nucleic acid helices are typical mesophase formers in the classical liquid-crystal phase... 

Dolinnaya NG, Fresco JR (1992) Single stranded nucleic acid helical secondary structure stabilized by ionic bonds d(A -G)10. Proc Natl Acad Sci USA 89 9242-9246... 

E. J. Gabbay Topography of Nucleic acid helices in solutions I. Nonidentity... 

The helical form may be left- or right-handed Gust like an a-helix in a protein (p. 35), but of course unlike protein or nucleic acid helices, it is not made of asymmetric units, so has no preference for one handedness over the other). This form is called chiral from... 

Amino Acids, Peptides, Proteins, Enzymes, and Nucleic Acids helix about 20 A in diameter. The arrangement is shown schematically in 12 ... 

Tan, Z., and Chen, S. (2006). Nucleic acid helix stability Effects of salt concentration, cation valence and size, and chain length. Biophys.J. 90(4), 1175-1190. 

Tan, Z. J., and Chen, S. J. (2006b). Ion-mediated nucleic acid helix-helix interactions. Biophys.J. 91, 518-536. 

Nucleoproteins are at the core of cellular processes utilizing genetic information. Most proteins in the nucleoprotein assemblies are basic and small, having molecular weights of 10-25 kDa. Many of these proteins associate with a single nucleic acid and generally with a single stretch of nucleic acid helix. 

Dolinnaya NG, Braswell EH, Fosella JA, Klump H, Fresco JR (1993) Molecular and thermodynamic properties of d(A -G)10, a single-stranded nucleic acid helix without paired or stacked bases. Biochemistry 32 10263-10270... 

A further step in quantum-chemical studies of base pairing and stacking should be inclusion of solvent effects [44,45]. In a polar solvent the stacked pairs are formed, i.e., the stability order is reversed. The base - base interactions within a nucleic acid helix further differ from the pure solvent. Base pairs embedded between two very polar GC base pairs experience a different electric field than in the case when they are surrounded by two rather nonpolar AT base pairs. 

Herrick, G., and Alberts, B., 1976a, Purification and physical characterization of nucleic acid helix-unwinding proteins from calf thymus, /. Biol. Chem. 251 2124. 

Porschke D. Elementary steps of base recognition and helix-coil transitions in nucleic acids. Mol. Biol. Biochem. Biophys. 24 (1977) 191-218... 

H bonding also vitally influences the conformation and detailed structure of the polypeptide chains of protein molecules and the complementary intertwined polynucleotide chains which form the double helix in nucleic acids.Thus, proteins are built up from polypeptide chains of the type shown at the top of the next column. 

F. H. C. Crick. J. B. Watson and M. H. F. Wilkins (with Rosalind Franklin) establish the double helix structure of nucleic acids (Nobel Pnze 1962). 

WiTTUNG P., Nielsen P. E., Buchardt O., Egholm M., Norden B. DNA-like double helix formed by peptide nucleic acid. Nature 1994, 368 561-563. 

N. T., Lhomme J., Helene C. Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an oligo-[alpha]-thymidylate covalently linked to an azidoproflavine derivative. Nucleic Acids Res. 1987 15 7749-7760. 

The amino acid sequence of our first aPNA (which we termed backbone 1 or bl) was designed based on this amphipathic hehx sequence (Fig. 5.3 B). Specifically, this aPNA backbone included hydrophobic amino acids (Ala and Aib), internal salt bridges (Glu-(aa)3-Lys-(aa)3-Glu), a macrodipole (Asp-(aa)i5-Lys), and an N-ace-tyl cap to favor a-helix formation. The C-termini of these aPNA modules end in a carboxamide function to preclude any potential intramolecular end effects. Each aPNA module incorporates five nucleobases for Watson-Crick base pairing to a target nucleic acid sequence. 

Some virus particles have their protein subunits symmetrically packed in a helical array, forming hollow cylinders. The tobacco mosaic virus (TMV) is the classic example. X-ray diffraction data and electron micrographs have revealed that 16 subunits per turn of the helix project from a central axial hole that runs the length of the particle. The nucleic acid does not lie in this hole, but is embedded into ridges on the inside of each subunit and describes its own helix from one end of the particle to the other. 

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-... 

A typical virus with helical symmetry is the tobacco mosaic virus (TMV). This is an RNA virus in which the 2130 identical protein subunits (each 158 amino acids in length) are arranged in a helix. In TMV, the helix has 16 1/2 subunits per turn and the overall dimensions of the virus particle are 18 X 300 nm. The lengths of helical viruses are determined by the length of the nucleic acid, but the width of the helical virus particle is determined by the size and packing of the protein subunits. 

The term peptide nucleic acids was chosen because of the peptide bond in the polymer (see Sect. 5.2). The bond between the polyamide strand and the organic bases involves an acetyl group. The formation of DNA-like double helix structures by PNAs was described by Pernilla Wittung et al. (1994). The question arises as to whether peptide nucleic acids can in fact be synthesized under prebiotic conditions. 

Base pair (bp) The four nucleotides in the DNA contain the bases adenine (A), guanine (G), cytosine (C), and thymine (T). Two bases (adenine and thymine or guanine and cytosine) are held together by weak bonds to form base pairs. The two strands of human DNA are held together in the shape of a double helix by those bonds between base pairs. For example, the complementary nucleic acid base sequence to G-T-A-C that forms a double-stranded structure with the matching bases is C-A-T-G. 

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