Geometry nucleic acids

A significant advantage of computational studies on nucleic acids is that reasonable guesses of the starting geometries can be made. When studying duplexes, these are typi-... 

Gorin has extended this analysis to include (1) the effects of the finite size of the counterions in the double layer of spherical particles [137], and (2) the effects of geometry, i.e. for cylindrical particles [2]. The former is known as the Debye-Huckel-Henry-Gorin (DHHG) model. Stigter and coworkers [348,369-374] considered the electrophoretic mobility of polyelectrolytes with applications to the determination of the mobility of nucleic acids. 

Several complexes that involve intercalation of an acridine in a portion of a nucleic acid have been studied by X-ray crystallographic techniques. These include complexes of dinucleoside phosphates with ethidium bromide, 9-aminoacridine, acridine orange, proflavine and ellipticine (65-69). A representation of the geometry of an intercalated proflavine molecule is illustrated in Figure 6 (b) this is a view of the crystal structure of proflavine intercalated in a dinucleoside phosphate, cytidylyl- -S ) guano-sine (CpG) (70, TV). For comparison an example of the situation before such intercalation is also illustrated in Figure 6 (a) by three adjacent base pairs found in the crystal structure of a polynucleotide (72, 73). In this latter structure the vertical distance (parallel to the helix axis) between the bases is approximately... 

The lack of long-range restraints has hindered the precise and accurate structure determination of nucleic acids for a long time. The isotopic enrichment mostly improved the accuracy of local geometry without a pronounced influence on the overall shape. However,... 

For molecular sizes that are amenable by NMR techniques, nucleic acids usually lack a tertiary fold. This fact, together with the characteristic low proton density, complicates NMR structural analysis of nucleic acids. As a result, local geometries and overall shapes of nucleic acids, whose structures have been determined by NMR, usually are poorly defined. Dipolar couplings provide the necessary long-range information to improve the quality of nucleic acid structures substantially [72]. Some examples can be found already in the literature where the successful application of dipolar couplings into structure calculation and structure refinement of DNA and RNA are reported [73-77]. 

Comparisons of the measured coupling constants to the geometry of the H-bond are hampered by the limited availability of very high-resolution diffraction data. Especially, no crystallographic data are available for most of the nucleic acids for which H-bond cou-... 

Nature is also selective in the geometry involved in nucleic acid synthesis. This specificity involves both the base order and the particular sugar employed. For DNA the employed sugar is (3-2-deoxy-D-ribose, deoxyribose (below left). Deoxyribose has three chiral centers but only one of them is employed in the synthesis of nucleic acids. Ribose, the sugar employed in the synthesis of RNA, has four geometric sites (below right). 

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