The solution structure of a d[C(TTCG)G] DNA hairpin and comparison to the unusually stable RNA analogue

Abstract

The solution structure of the DNA analogue of the unusually stable r RNA hairpin, 5′-d[GGA-C(TTCG)GTCC]-3′, has been determined by NMR spectroscopy, and Its structure has been compared to that of the RNA molecule. The RNA molecule Is compact and rigid with a highly structured loop. However, the DNA molecule Is much less structured. The DNA hairpin contains a B-form stem of four base pairs. The terminal base pair frays, and the 3′-terminai nucleotides, Cli and C12, are in equilibrium between 2′-endo and 3′-endo conformations. Unlike the RNA loop, the DNA loop contains no syn nucleotides, and there is no evidence for base-base or base-phosphate hydrogen bonding in the loop. The loop is flexlble, and reveals no specific intemucleotide Interactions. © 1993 Oxford University Press.