Nucleotides, base-pairing structure

The human genome contains approximately 3 billion nucleotide bases, which code for approximately 30,000 genes. Two purine nucleotide bases, adenine (A) and guanine (G), and two pyrimidine nucleotide bases, cytosine (C) and thymidine (T), are present in DNA, with purines and pyrimidines always pairing together as A-T and C-G in the two strands that make up the DNA structure. Most nucleotide base pairs are identical from person to person, with only 0.1% contributing to individual differences. 

Scheme 10.8 Structure of the enclathrated nucleotide base pair 24.25 23...

The 7i TC interactions occur in all areas of chemistry and for chemically diverse molecules. The stacking of 7t-delocalized molecules favors cooperative phenomena. such as electron conduction. The n-stacking motifs are key components of the design of molecular materials with ensemble properties. Nucleotide base-pair stacking is fundamental to molecular biology, and aromatic interactions between amino-acid side chains influence protein structure. 

Recent reviews from this Laboratory provide an overview of the literature of MD simulations on DNA oligomers through 1993 (27) and theoretical and computational aspects of DNA hydration (28) and counterion atmosphere (29). References to the most recent literature can be found in (30). Experimental data for comparison with MD results are available for crystal structures in the Nucleic acids Data Bank (NDB) (31), and for NMR structure in a review by Ulyanov and James (52). The research described in this article is directed towards understanding the dynamical structure of the various right-handed helical forms of DNA, their deformations and interconversions. The canonical A and B structures of DNA are shown for reference in Figure 1. The A and B forms are distinguishable in three major ways the displacement of nucleotide base pairs from the helix axis, the inclination of base pairs with respect to the helix axis, and sugar puckers. Details on these and other structural features of DNA relevant to MD analysis is readily available (33). 

The DNA isolated from different cells and viruses characteristically consists of two polynucleotide strands wound together to form a long, slender, helical molecule, the DNA double helix. The strands run in opposite directions that is, they are antiparallel and are held together in the double helical structure through interchain hydrogen bonds (Eigure 11.19). These H bonds pair the bases of nucleotides in one chain to complementary bases in the other, a phenomenon called base pairing. 

FIGURE 12.39 The proposed secondary structure for E. coli 16S rRNA, based on comparative sequence analysis in which the folding pattern is assumed to be conserved across different species. The molecule can be subdivided into four domains—I, II, III, and IV—on the basis of contiguous stretches of the chain that are closed by long-range base-pairing interactions. I, the 5 -domain, includes nucleotides 27 through 556. II, the central domain, runs from nucleotide 564 to 912. Two domains comprise the 3 -end of the molecule. Ill, the major one, comprises nucleotides 923 to 1391. IV, the 3 -terminal domain, covers residues 1392 to 1541. 

DNA is made up ot two intertwined strands. A sugar-phosphate chain makes up the backbone of each, and the two strands are joined by way of hydrogen bonds betwen parrs of nucleotide bases, adenine, thymine, guanine and cytosine. Adenine may only pair with thymine and guanine with cytosine. The molecule adopts a helical structure (actually, a double helical stnrcture or double helix ). 

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