Solution Structure of the Dodecamer d-(CATGGGCC-CATG)₂ is B-DNA. Experimental and Molecular Dynamics Study

Abstract

The DNA duplex d-(CATGGGCCCATG)₂ has been studied in solution by FTIR, NMR and CD. The experimental approaches have been complemented by series of large-scale unrestrained molecular dynamics simulation with explicit inclusion of solvent and counterions. Typical proton-proton distances extracted from the NMR spectra and the CD spectra are completely in agreement with slightly modified B-DNA. By molecular dynamics simulation, starting from A-type sugar pucker, a spontaneous repuckering to B-type sugar pucker was observed. Both experimental and theoretical approaches suggest for the dodecamer d- (CATGGGCCCATG)₂ under solution conditions puckering of all 2′-deoxyribose residues in the south conformation (mostly C2′-endo) and can exclude significant population of sugars in the north conformation (C3′-endo). NMR, FTIR and CD data are in agreement with a B-form of the dodecamer in solution. Furthermore, the duplex shows a cooperative B-A transition in solution induced by addition of trifluorethanol. This contrasts a recently published crystal structure of the same oligonucleotide found as an intermediate between B- and A- DNA where 23 out of 24 sugar residues were reported to adopt the north (N-type) conformation (C3′-endo) like in A-DNA(Ng, H. L., Kopka, M. L. and Dickerson, R. E., Proc. Natl. Acad. Sci. U S A 97, 2035–2039 (2000)). The simulated structures resemble standard B- DNA. They nevertheless show a moderate shift towards A-type stacking similar to that seen in the crystal, despite the striking difference in sugar puckers between the MD and X-ray structures. This is in agreement with preceding MD reports noticing special stacking features of G-tracts exhibiting a tendency towards the A-type stacking supported by the CD spectra also reflecting the G-tract stacking. MD simulations reveal several noticeable local conformational variations, such as redistribution of helical twist and base pair roll between the central GpC steps and the adjacent G-tract segments, as well as a substantial helical twist variability in the CpA(TpG) steps combined with a large positive base pair roll. These local variations are rather different from those seen in the crystal.

The results are discussed in terms of recent findings of DNA structures with mixed features of A-DNA and B-DNA.