Slow motions in A•T rich DNA sequence

In free B-DNA, slow (microsecond-to-millisecond) motions that involve equilibrium between Watson-Crick (WC) and Hoogsteen (HG) base-pairing expand the DNA dynamic repertoire that could mediate DNA-protein assemblies. R-1 rho relaxation dispersion NMR methods are powerful tools to capture such slow conformational exchanges in solution using C-13/N-15 labelled DNA. Here, these approaches were applied to a dodecamer containing a TTAAA element that was assumed to facilitate nucleosome formation. NMR data and inferred exchange parameters assign HG base pairs as the minor, transient conformers specifically observed in three successive A center dot T base pairs forming the TAA center dot TTA segment. The abundance of these HG A center dot T base pairs can be up to 1.2% which is high compared to what has previously been observed. Data analyses support a scenario in which the three adenines undergo non-simultaneous motions despite their spatial proximity, thus optimising the probability of having one HG base pair in the TAA center dot TTA segment. Finally, revisiting previous NMR data on H2 resonance linewidths on the basis of our results promotes the idea of there being a special propensity of A center dot T base pairs in TAA center dot TTA tracts to adopt HG pairing. In summary, this study provides an example of a DNA functional element submitted to slow conformational exchange. More generally, it strengthens the importance of the role of the DNA sequence in modulating its dynamics, over a nano- to milli-second time scale.