Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles.

Abstract

The principal sequence feature responsible for intrinsic DNA curvature is generally assumed to be runs of adenines. However, according to the wedge model of DNA curvature, each dinucleotide step is associated with a characteristic deflection of the local helix axis. Thus, an important test of a more general view of sequence-dependent DNA curvature is whether sequence elements other than A-A cause the DNA axis to deflect. To address this question, we have applied the wedge model to a large body of experimental data. The axial path of DNA can be described at each step by three Eulerian angles: the helical twist, the deflection angle (wedge angle), and the direction of the deflection. Circularization and gel electrophoretic mobility data on 54 synthetic DNA fragments, both from other laboratories and from our own, were used to compare the theoretical predictions of the wedge model with experiment. By minimizing misfit between calculated and observed DNA curvature, we have found that the stacks AG/CT, CG/CG, GA/TC, and GC/GC, in addition to AA/TT, have large wedge values. We have also synthesized seven sequences without AA/TT elements but with these other wedges correctly phased to cause appreciable predicted curvature. All appear curved as demonstrated by anomalous gel mobilities. The full set of 16 roll and tilt wedge angles is estimated and, together with the known 10 helical twists, these allow prediction of the general sequence-dependent trajectory of the DNA axis.

Interaction between a DNA oligonucleotide and a dinuclear iron(II) supramolecular cylinder; an NMR and molecular dynamics study

“…For example, a large upfield shift of H2' in a cis-platinated duplex was attributed to shielding by the destacked adenine base of the kinked structure [46]. It is now well established that Y-R steps (Y= pyrimidine, R= purine) like CpG are geometrically flexible [47] and several studies have shown that CpG steps are involved in DNA bending [48,49]. Since linear dichroism shows that very low loading of [Fe 2 L 3 ] 4+ have a dramatic bending effect on the DNA [1] and atomic force microscopy images show that this is an intramolecular effect resulting in coils of DNA [1] it is interesting to look for similar bending pattern in the NMR data.…”

Compositional Changes in RNA, DNA and Proteins for Bacterial Adaptation to Higher and Lower Temperatures

“…The dinucleotide composition is known to account for the curvature (18) and therefore the supercoiling of double-stranded DNA. For examination of this physicochemical aspect of DNA regarding thermostability, the following index has been introduced:…”

Distribution of bending propensity in DNA sequences

“…(AT)n and poly(dA)). An example is the central 'aaaaatatata' motif in synl (Table 2 [6,22]). Comparing the extreme values in Tables 2 and 3 one can see that the high helical asymmetry values characteristic of strong intrinsic curvature are conspicuously missing from the genomes analyzed so far.…”