X-ray structure of d(CGAA), parallel-stranded DNA duplex with homo base pairs.

To clarify whether the parallel right-handed duplex found in the d(GCGAAAGCT) crystal is possible to occur without the anti-parallel part, the crystal structures of d(CGAA) at pH6.0 and pH7.0 have been determined by X-ray analysis. There are two independent duplexes in the crystallographic asymmetric unit. In each duplex, two chains are aligned in parallel fashion to form a right-handed double helix through the homo base pair formations, the sugar puckers being essentially C2'-endo. The C1:C1 pair is achieved by hemi-protonation. The G2:G2, A3:A3 and A4:A4 pairs occur between the minor groove sites, between the major groove sites and between the Watson-Crick sites, respectively. In every pairing, the two bases are located at the trans positions to each other. These structural features are the same as those at pH7.0, suggesting that the C1:C1 pair is hemi-protonated even at the neutral condition.