Nikolova Evgenia N, Al-Hashimi Hashim M
Department of Chemistry, Biophysics and Chemical Biology Program, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA.
J Biomol NMR. 2009 Sep;45(1-2):9-16. doi: 10.1007/s10858-009-9350-y. Epub 2009 Jul 28.
DNA is a highly flexible molecule that undergoes functionally important structural transitions in response to external cellular stimuli. Atomic level spin relaxation NMR studies of DNA dynamics have been limited to short duplexes in which sensitivity to biologically relevant fluctuations occurring at nanosecond timescales is often inadequate. Here, we introduce a method for preparing residue-specific (13)C/(15)N-labeled elongated DNA along with a strategy for establishing resonance assignments and apply the approach to probe fast inter-helical bending motions induced by an adenine tract. Preliminary results suggest the presence of elevated A-tract independent end-fraying internal motions occurring at nanosecond timescales, which evade detection in short DNA constructs and that penetrate deep (7 bp) within the DNA helix and gradually fade away towards the helix interior.
DNA是一种高度灵活的分子，会响应外部细胞刺激而发生功能上重要的结构转变。对DNA动力学进行的原子水平自旋弛豫核磁共振研究一直局限于短双链体，其中对纳秒时间尺度上发生的生物学相关波动的敏感度往往不足。在此，我们介绍一种制备残基特异性（13）C/（15）N标记的延长DNA的方法以及一种建立共振归属的策略，并将该方法应用于探测由腺嘌呤序列诱导的快速螺旋间弯曲运动。初步结果表明，存在以纳秒时间尺度发生的、与腺嘌呤序列无关的、升高的末端磨损内部运动，这种运动在短DNA构建体中无法检测到，且会深入（7个碱基对）DNA螺旋内部，并逐渐向螺旋内部减弱。
