Intrinsic flexibility of B-DNA: the experimental TRX scale

Abstract

B-DNA flexibility, crucial for DNA–protein recognition, is sequence dependent. Free DNA in solution would in principle be the best reference state to uncover the relation between base sequences and their intrinsic flexibility; however, this has long been hampered by a lack of suitable experimental data. We investigated this relationship by compiling and analyzing a large dataset of NMR 31P chemical shifts in solution. These measurements reflect the BI ↔ BII equilibrium in DNA, intimately correlated to helicoidal descriptors of the curvature, winding and groove dimensions. Comparing the ten complementary DNA dinucleotide steps indicates that some steps are much more flexible than others. This malleability is primarily controlled at the dinucleotide level, modulated by the tetranucleotide environment. Our analyses provide an experimental scale called TRX that quantifies the intrinsic flexibility of the ten dinucleotide steps in terms of Twist, Roll, and X-disp (base pair displacement). Applying the TRX scale to DNA sequences optimized for nucleosome formation reveals a 10 base-pair periodic alternation of stiff and flexible regions. Thus, DNA flexibility captured by the TRX scale is relevant to nucleosome formation, suggesting that this scale may be of general interest to better understand protein-DNA recognition.

The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA

“…In addition, both experimental sources of BII values suffer from a sequence bias due to the limited number of tetranucleotide represented in the limited set of sequence available 20,22,29 .…”

“…Equivalent results were obtained for YpR and YpY steps (Table S2 and Figure S4). It should be noted that in spite of the extended set of structures used in this work, BII propensities from crystal structures still seems underestimated when compared with NMR and MD results (Table S2) [4][5][6]12,20,21 . The reasons for the apparent discrepancies between the methods, which are beyond the scope of the present work, are complex, of diverse sources, and have been partially addressed recently 21 .…”

DNA information: from digital code to analogue structure

“…Concomitant with this narrowing is a change in the structure of the phosphate backbone favouring the BII rather than the BI conformation [41]. The propensity to adopt the BII conformation is sequence dependent such that, in solution, it is freely adopted by G/C-containing, but not A/T-containing, steps [41]. This sequence preference is apparent in the formation of extreme distortions, in the form of DNA kinks into the minor groove [4,42].…”

“…The base steps are grouped according to the type and base composition. Beneath each base step are listed successively the stacking energy, the melting energy (in red) (both in kJ mol −1 from [77]), the range of conformations adopted by the base step from El Hassan & Calladine [78] as shown in figure 7, the twist, roll and X-disp (base-pair displacement) index (a measure of the percentage probability of one of two phosphates in the base step assuming a BII conformation) [41], and the preferred minor groove orientation of the step in chicken nucleosomal DNA (I = in, O = out, i = in as a minor preference, np = no preference [18,79]). The terms 'flexible' and 'rigid' beneath the YR and RY steps are taken from [80]).…”

“…towards the minor or major groove. For base steps, including G-C base pairs, important factors include the presence of the 2-amino group (of guanine) in the minor groove, the pronounced dipole moment associated with the base pair and the ability to adopt both BI and BII phosphate conformations, correlating, respectively, with wide and narrower minor grooves [41]. The 2-amino group limits compression of the minor groove while in base steps containing only G-C base pairs, the dipole moment by shifting the relative alignments of successive base pair results in the displacement of the central axis of the base pair away from the double-helical axis.…”