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. 2009 Sep;37(17):5917-29.
doi: 10.1093/nar/gkp608. Epub 2009 Jul 22.

Conformational analysis of nucleic acids revisited: Curves+

R Lavery  1 , M Moakher, J H Maddocks, D Petkeviciute, K Zakrzewska
Affiliations

Conformational analysis of nucleic acids revisited: Curves+

R Lavery et al. Nucleic Acids Res. 2009 Sep.

Abstract

We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algorithmically simpler and computationally much faster than the earlier Curves approach, although it still provides both helical and backbone parameters, including a curvilinear axis and parameters relating the position of the bases to this axis. It additionally provides a full analysis of groove widths and depths. Curves+ can also be used to analyse molecular dynamics trajectories. With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamics.

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Figures

Figure 1.
Figure 1.
Two-dimensional surface representing the distance (vertical axis, in Å) between points along the backbones of a double-stranded B-DNA oligomer. The groove widths appear as the valleys (marked by red arrows) on either side of the diagonal (in the centre of the figure). Points which are the same distance along each backbone yield vectors roughly perpendicular to the helical axis of the oligomer. Moving further up the axis pointing left (5′→3′ backbone) rotates the vectors until they span the minor groove, while moving up the axis pointing right (3′→5′ backbone) leads to spanning the major groove. The surface colour shows variations in inter-backbone distance, from 9 Å (dark blue) to 38 Å (dark red). The largest distances naturally occur for vectors which link the two 3'-ends (left-hand corner) or the two 5′-ends (right-hand corner) of the backbones.
Figure 2.
Figure 2.
The helical axis of the d(CTGCTATAAAAGGCTG) 16-mer bound to TBP calculated with Curves+ (blue) and with Curves 6.0 (red). The side-on (left) and end-on (right) views illustrate the extent of the bending (and its out-of-plane nature) induced by the minor groove-bound protein. Despite the new algorithm, the two analyses give virtually identical results.
Figure 3.
Figure 3.
Comparison of the d(CTGCTATAAAAGGCTG) 16-mer in B-DNA (left) and TBP-bound (right) conformations. The backbone spline curves are shown in red, while the vectors defining the minor and major groove widths are shown in purple and orange respectively. The helical axis is shown in blue.
Figure 4.
Figure 4.
The variation of the minor (solid line) and major (dotted line) groove widths (Å) along the d(CTGCTATAAAAGGCTG) TBP-bound oligomer (with the protein in positions 5–11). The arrows show the corresponding minor and major groove widths in a canonical B-DNA oligomer and emphasize the localized inversion in groove dimensions induced by protein binding.
Figure 5.
Figure 5.
Time series of the C9pG10 twist from a 50 ns molecular dynamics simulation of d(GCCGCGCGCGCGCGCGGC) in explicit water (A) and a histogram of the twist fluctuations derived from the four most central CpG steps of the same oligomer during the trajectory (B).
Figure 6.
Figure 6.
Fluctuations of axis bend for all dinucleotide steps in an 89-bp minicircle during a 2 ns segment of a molecular dynamics trajectory. The base pair positions are given on the horizontal axis and time (ps) increases along the vertical axis. The colour bar shows the variations in bend from 0° (dark blue) to 11° (dark red).
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