Shift, nucleic acid conformation

The question of identifying model compounds to provide reference shifts for nucleic acids has been a vexing one. For proteins, short, disordered peptides can be used, whose shifts are reasonably independent of the exact sequence or solution conditions (at least for protons bonded to carbons) (3-5). This is much less true for nucleic acids (1), presumably because the conformations and electrostatic... 

Because conformational changes in RNA or short DNAs typically cause small changes in electrophoretic mobility, analysis of nucleic acid folding requires careful optimization of electrophoresis conditions. By contrast, protein—nucleic acid interactions are typically easier to analyze by native PAGE because the molecular weight and positive charge of the protein produces a relatively large shift in gel mobility. 

It is well known that the conformations and stabilities of nucleic acids are sensitive to the concentrations and identities of salts that are present. With regard to RNAs, the strongly stabilizing effect of Mg2"1" ion on tertiary structures has been of particular interest (Stein and Crothers, 1976), but virtually any RNA conformational equilibrium may shift in response to changes in either mono- or divalent ion concentrations. 

Hoechst 33258 binds to the minor groove of double-stranded DNA with a preference for the A-T sequence (Pjura et al. 1987). Interaction between DNA and proteins very often induces structural modifications in both interacting molecules. Such modifications in DNA can be characterized with 2-aminopurine (2AP), which is a highly fluorescent isomer of adenine. 2AP does not alter the DNA structure. It forms a base pair with thymine and can be selectively excited, since its absorption is red-shifted compared to that of nucleic acids and aromatic amino acids. In addition, its fluorescence is sensitive to the conformational change that occurs within the DNA (Rachofsky et al. 2001). 

A conformational study of nucleic acid phosphate esters has been carried out using n.m.r. and the temperature-dependent chemical shifts used to give information about the geometry of the phosphodiester linkage. Compounds studied were 3 - and 5-O-methyl phosphates of uridine and adenosine, and the 3-0-methyl phosphate of 6-A-dimethyladenosine. It has been reported that the n.m.r. of myo-inositol hexakisphosphate has four resonances that shift and broaden as a function of pH. ° Reference to the use of P n.m.r. in the configurational determination of cyanomethyl-branched phosphonates is made in Chapter 16. 

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