Conformation of polynucleotides

NUCLEOTIDES AND NUCLEIC ACIDS Abbreviations and symbols for nucleic acids, polynucleotides and their constituents /. Biol. Chem. (1970) 245, 5171-5176 Corrections, J. Biol Chem. (1971) 246, 4894 Abbreviations and symbols for the description of conformations of polynucleotide chains Eur. J. Biochem. (1983) 131, 9-15 Nomenclature for incompletely specified bases in nucleic acid sequences... 

Abbreviations and Symbols for Nucleic Adds, Polynucleotides and their Constituents http //www.chem.qmul.ac.uk/iupajc/misc7naabb.html Abbreviations and Symbols for the Description of the Conformation of Polypeptide Chains http //www.cheni.qinul.ac.uk/iiipac/misc/ppepl.hiinl Abbreviations and Symbols for the Description of Conformations of Polynucleotide Chains http //www.chem.qmul.ac.uk/iupac/misc/pnucl.htni]... 

For many years, different spectroscopic methods were used to study conformations of polynucleotides in different environments [64, 65], Spectroscopy offers most developed techniques for studying structural and functional properties of varieties of molecules. Absorption spectroscopy is one of the oldest and most common methods used in chemical science to elucidate molecular structures. Since... 

IUPAC-IUB Joint Commission on Biochemical Nomenclature (1983). Abbreviations and symbols for the description of conformations of polynucleotide chains. Eur J Biochem 131 9-15... 

Biomacromolecules are considered as single molecules when they are present in a well-defined stoichiometry and when they display little tendency to dissociate spontaneously under physiological conditions. This text deals specifically with covalent bio-macromolecnles in which monomer units are linked together by covalent bonds to form giant biomolecules. They include nucleic acids, proteins and polysaccharides (under this defiifition, biomembranes are excluded). The Web site of the International Union of Bio-chenfistry and Molecular Biology (lUBMB) at http //www.chem.qmw.ac.uk/iubmb/ provides useful information for the nomenclature and conformations of polynucleotides, polypeptides and polysaccharides (Figure 1.1). 

Metal Ions can produce a large variety of other effects on nucleic acids that could be deleterious if they occur during genetic information transfer. Metal ions can bring about the degradation of RNA (17, 18, 19), changes in the specificity of enzymes that act on DNA (20), changes in the conformation of polynucleotides and nucleic acid - protein complexes (21). 

The most fundamental level of modeling of any chemical system employs quantum mechanics. Quantum mechanical (QM) treatments are required to understand many important chemical and biological properties of nucleic acids. Moreover, empirical force-field methods, employed to study the conformations of polynucleotides, rely on quantum calculations to obtain crucial parameters that are difficult to measure experimentally, such as atom-centered charges for calculating electrostatic interactions. The obtain a description of a chemical system using QM one solves the time-independent Schrodinger equation with or without the use of empirical parameters. 

J. Brahms Optical activity and the conformation of polynucleotide models of... 

Polozov, R. V., Poltev, V. L, Sukhorukov, B. I. (1973). Relation of the interactions of nucleic acid bases to the helical conformations of polynucleotides. Studia Biophysica, 40,13. 

The lUBMB Commission on Nomenclature has issued a number of recommendations dealing with areas of a more biochemical nature (72), such as peptide hormones (86), conformation of polypeptide chains (87), abbreviations for nucleic acids and polynucleotides (88), iron—sulfur proteins (89), enzyme units (90), etc. The Commission has also produced rules and recommendations for naming enzymes (91,92). 

The illustration opposite shows selected nucleic acid molecules. Fig. A shows various conformations of DNA, and Fig. B shows the spatial structures of two small RNA molecules. In both, the van der Waals models (see p. 6) are accompanied by ribbon diagrams that make the course of the chains clear. In all of the models, the polynucleotide backbone of the molecule is shown in a darker color, while the bases are lighter. 

An additional five torsion angles are needed to specify the backbone conformation of a polynucleotide. According to the convention adopted by the IUB the six angles are desig-... 

While these "energies" are necessarily approximate, they afford a basis for clear discrimination between sterically allowed and sterically forbidden structures. The "energy" approach also offers a means to extrapolate experimental studies (nmr, X-ray, etc.) on the conformation of small model compounds to the polynucleotide level and to test the relevance of the data in a helical complex. In addition, the method provides a starting point for a refined potential energy analysis of double helical conformation and stability. 

Figure 5.1. Notation for torsion angles of biopolymer chains. Torsion angles ( and ift) that affect the main chain conformations of biopolymers are shown for polysaccharide (a), polypeptide (b), and polynucleotide (c) chains according to the IUBMB notation. The two torsion angles, and ij>, specified around the phosphodiesteric bonds of nucleic acids correspond to a and respectively. Reproduced from IUBMB at http //www.chem.gmw. ac.uk/iubmb.

One of the most exciting biological discoveries is the recognition of DNA as a double helix (Watson and Crick, 1953) of two antiparallel polynucleotide chains with the base pairings between A and T, and between G and C (Watson and Crick s DNA structure). Thus, the nucleotide sequence in one chain is complementary to, but not identical to, that in the other chain. The diameter of the double helix measured between phosphorus atoms is 2.0 nm. The pitch is 3.4 nm. There are 10 base pairs per turn. Thus the rise per base pair is 0.34 nm, and bases are stacked in the center of the helix. This form (B form), whose base pairs lie almost normal to the helix axis, is stable under high humidity and is thought to approximate the conformation of most DNA in cells. However, the base pairs in another form (A form) of DNA, which likely occurs in complex with histone, are inclined to the helix axis by about 20° with 11 base pairs per turn. While DNA molecules may exist as straight rods, the two ends bacterial DNA are often covalently joined to form circular DNA molecules, which are frequently supercoiled. 

For polynucleotide, choose various options such as either DNA or RNA, Form (a, b, c, d, e, t, or z forms), Build (5 to 3 or 3 to 5 ), single strand/double strand, and conformation of pentofuranose ring. Add bases (pairs) in the specified direction to build polynucleotide chain. 

The stability of polynucleotide systems and the conformational variability of nucleic acids are governed, inter alia, by noncovalent interactions [1], They lead to the... 

Laurent, T. C., Preston, B. N., and Carlsson, B. (1974). Interaction between polysaccharides and other macromolecules. Conformational transitions of polynucleotides in polymeric media. Eur. J. Biochem. 43 231-235. 

In 1953, James D. Watson and Francis C. Crick used X-ray diffraction patterns of DNA fibers to determine the molecular structure and conformation of DNA. They found that DNA contains two complementary polynucleotide chains held together by hydrogen... 

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