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Measuring the groove width    1. Limitations    2. Algorithms used    3. Minor groove width    4. Major groove width    Close window

Helix and bending analysis of nucleic acid double helix structures

1. Limitations

If the algorithm for calculating the groove width fails, it may happen that no graphs are plotted. Spikes in the plots also indicate numerical problems and are meaningless. Users should check the plausibility of the plots carefully.

2. Algorithms used

The width of the major and minor groove of a double helix is calculated with CURVES. CURVES uses splines to connect the reference atoms of each strand. Usually the P atoms are chosen as reference atoms, but for the minor groove also the C4' and the C1' atoms yield valuable information. The CURVES algorithm is superior to simple methods where just the closest distance between phosphates across the minor or major groove is measured. The nucleotides of the phosphates which are closest to each other do not form a base pair. They are rather separated by two or three other base pairs. Therefore, the P-P distances cannot be assigned unambiguously to particular base pairs. The algorithm used by CURVES solves this problem by projecting the groove width on the global helical axis. This also allows the calculation of the depth of the groove.

CURVES does not yield meaningful values of the groove parameters for all structures. Problems arise from numerical instabilities as well as from geometrical distortions of the double helix and from missing backbone atoms. For some structures the groove parameters are not calculated at all. In other cases unusual high and steep peaks occur in the plots. Spikes of the groove width are meaningless. The real width of the grooves changes only smoothly because the radius of the atoms involved is 1.5 Å to 2.0 Å. To prevent plotting of meaningless values we skip points where the depth of the groove is negative. Nevertheless, you have to check the plausibility of the plots carefully.

3. Minor groove width

Commonly the width of the minor groove is determined from the interstrand P-P distance. But also C4' and C1' can be used as reference atoms. Using C1' yields the width at the bottom of the minor groove. C4' is most appropriate for measuring the inside width which is relevant for the binding of drugs like netropsin and HOECHST 33254.

4. Major groove width

Only P is used as reference atom for the major groove width. For A-helices it often happens that the calculation of the major groove width fails. No graph is plotted in these cases.