Nucleic acid sugar pucker

The "rigid nucleotide as building block in the nucleic adds. In this discussion, which is primarily concerned with aspects of hydrogen bonding, the simplified rigid nucleotide concept will be sufficient in the description of nucleotide and nucleic acid conformation. Accord- ing to this concept [545], there are two basic nucleotide units which differ mainly in sugar pucker ... 

NMR structure of a 2 -deoxy-2 -fluoro-D-arabinose (aF) nucleic acid duplex has been reported. The structure is a hybrid hairpin duplex containing a ribose-aF stem duplex and a four-residue DNA loop (177). The RNA strand adopted the classical A-form structure with endo sugar puckers, whilst the aF strand contained O -endo puckers and was intermediate between A- and B-form, similar to that found in DNA-RNA structures. 

Ikeda H, Fernandez R, WiUc A, Barchi JJ Jr, Huang X, Marquez VE (1998) The effect of two antipodal fluorine-induced sugar puckers on the conformation and stability of the Dickerson-Drew dodecamer duplex[d(CGCGAATTCGCG)]2. Nucleic Acids Res 26 2237-2244... 

Swama Latha Y, Yathindra N (1992) Stereochemical studies on nucleic acid analogs. I. Conformations of a-nucleosides and a-nucleotides interconversion of sugar puckers via 04 -exo. Biopolymers 32 249-269... 

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). 

Ground-state properties of nucleic acid constituents smdied by density functional calculations. 3. Role of sugar puckering and base orientation on the energetics and geometry of 2 -deoxyribonucleosides and ribonucleosides ... 

Nucleosides are linked through a phosphodiester bond via the 3 and 5 oxygens to give the primary structure of the nucleic acids, which is ubiquitous and, without exception, the same (Fig. 3.7). The differences between DNA and RNA will be evoked in connection with the corresponding model compounds (Chapter 6, Section 6.2.3). It is essentially due to differences in the sugar pucker DNA shows the 3 -exo conformation, RNA the 3 -endo conformation. 

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