Slow Rotational Dynamics of Cytosine NH₂Groups in Double-Stranded DNA

Aromatic NH₂groups are essential as hydrogen-bond donors in secondary structures of DNA and RNA. Although rapid rotations of NH₂groups of adenine and guanine bases were previously characterized, there has been a lack of quantitative information about slow rotations of cytosine NH₂groups 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 NH₂rotations in a 15-base-pair DNA duplex. Our data show that the rotational dynamics of cytosine NH₂groups depend on local environments. Qualitative correlation between the ranges of ¹⁵N chemical shifts and rotational time scales for various NH₂groups of nucleic acids and proteins illuminates a relationship between the partial double-bond character of the C-N bond and the time scale for NH₂rotations.