Structural basis for DNA bending

The authors report proton NMR studies on DNA oligonucleotides that contain A tracts of lengths known to produce various degrees of bending. Spectra of duplexes in the series 5'-(GGCAnCGG)·(CCGTnGCC) (n = 3,4,5,7,9) reveal substantial structural changes within the An·Tn tract as its length is increased. Chemical-shift comparisons show that A tracts with fewer than about seven members do not contain regions of uniform structure. Throughout the series, there is a striking monotonic relationship between the location of an A·T pair in the A tract and the relative position of its ThyH3 resonance. The direction of this chemical-shift dispersion is opposite to that expected from consideration of ring-current effects alone. This model features a substantial negative base-pair tilt, which has been suggested previously as the source of A-tract bending. In contrast, the nuclear Overhauser effect distances are inconsistent with at least one known crystallographic A-tract structure which lacks appreciable base-pair tilt