Contextual Equilibrium Effects in DNA Molecules

Abstract

The thermodynamic parameters of DNA triplex formation between oligonucleotides and double-stranded DNA segments containing adenine runs (A-tracts) were investigated to explore equilibrium structural effects exerted by flanking segments upon the A-tracts. Results obtained from isothermal titration calorimetry, temperature-dependent circular dichroism (CD), and UV melting experiments indicate that A-tracts, considered as a uniquely robust and inflexible DNA motif, can be structurally perturbed by neighboring sequences in a way that significantly affects the propensity of this motif to interact with triplex-forming oligonucleotides. These contextual equilibrium effects, which depend upon the composition and location of the flanking sequences, are likely to apply not only to the interaction of A-tracts with single-stranded DNA molecules but also to interactions with drugs and proteins. As such, the current results refine the guidelines for the design of triplexforming oligonucleotides used for antigene strategies. More generally, they substantiate the notion that significant data might be encoded by structural DNA parameters.The demonstrated in vivo existence of non-B-DNA morphologies and the potential involvement of such altered structures in the regulation and fine-tuning of cellular processes (1, 2) elicited intensive studies on the factors that affect and modulate DNA conformational transitions. It is well established that the physical chemistry of these transitions is determined by an intricate array of environmental conditions and intrinsic factors, including the ionic strength, relative humidity, pH, and torsional strain. The actual structure exhibited by a given DNA segment is, however, generally considered to be dictated by the particular composition and sequential order of the base pairs within this segment. Indeed, left-handed DNA conformations, cruciforms, intramolecular triplexes, as well as bent or macroscopically curved motifs are detected predominantly in nonrandom DNA sequences such as alternating purine-pyrimidine segments, direct or inverted repeats, and purine-rich tracts (2). Several studies have indicated, however, that the kinetics of a conformational change, as well as the features of the resulting DNA structure, may be influenced or even dominated by sequences that are removed from those directly participating in the transition.The first evidence that structural information can be transmitted along the DNA molecule was provided by the observation that the melting of a DNA segment can be strongly affected by the base composition of a contiguous region (3). The kinetics of cruciform extrusion (4), as well as of the formation of intramolecular triple-stranded DNA motifs (5), were found to be dominated by sequences flanking the region that undergoes the transition. The effects were shown to operate over relatively long distances and to be independent of polarity. Right-to-lefthanded transitions of alternating d(G-C) n and d(A-T) n segments were also found to be significantly modulated by regions...

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