Slow Rotational Dynamics of Cytosine NH 2 Groups in Double-Stranded DNA.

Aromatic NH 2 groups are essential as hydrogen-bond donors in secondary structures of DNA and RNA. Although rapid rotations of NH 2 groups of adenine and guanine bases were previously characterized, there has been a lack of quantitative information about slow rotations of cytosine NH 2 groups in Watson-Crick base pairs. In this study, using an NMR method we had recently developed, we determined the kinetic rate constants and energy barriers for cytosine NH 2 rotations in a 15-base-pair DNA duplex. Our data show that the rotational dynamics of cytosine NH 2 groups depend on local environments. Qualitative correlation between the ranges of 15 N chemical shifts and rotational time scales for various NH 2 groups of nucleic acids and proteins illuminates a relationship between the partial double-bond character of the C-N bond and the time scale for NH 2 rotations.