Zacharias M, Hagerman P J
Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Denver 80262, USA.
Biophys J. 1997 Jul;73(1):318-32. doi: 10.1016/S0006-3495(97)78072-X.
Bends in nucleic acid helices can be quantified in a transient electric birefringence (TEB) experiment from the ratio of the terminal decay times of the bent molecule and its fully duplex counterpart (tau-ratio method). The apparent bend angles can be extracted from the experimental tau-ratios through the application of static (equilibrium-ensemble) hydrodynamic models; however, such models do not properly address the faster component(s) of the birefringence decay profile, which can represent up to 80% of the total birefringence signal for large band angles. To address this latter issue, the relative amplitudes of the components in the birefringence decay profile have been analyzed through a series of Brownian dynamics (BD) simulations. Decay profiles have been simulated for three-, five-, and nine-bead models representing RNA molecules with central bends of 30 degrees, 60 degrees, and 90 degrees, and with various degrees of associated angle dispersion. The BD simulations are in close agreement with experimental results for the fractional amplitudes, suggesting that both amplitudes and terminal tau-ratios can be used as a measure of the magnitudes of bends in the helix axis. Although the current results indicate that it is generally not possible to distinguish between relatively fixed and highly flexible bends from single tau-ratio measurements, because they can lead to similar reductions in terminal decay time and amplitude, measurements of the dependence of the fractional amplitudes on helix length may afford such a distinction.
在瞬态电场双折射（TEB）实验中，可以通过弯曲分子与其完全双链对应物的末端衰减时间之比（τ 比方法）来量化核酸螺旋中的弯曲。表观弯曲角度可以通过应用静态（平衡系综）流体动力学模型从实验 τ 比中提取；然而，此类模型并未恰当地处理双折射衰减曲线的较快成分，对于大弯曲角度而言，该成分可占总双折射信号的 80%。为了解决后一个问题，已通过一系列布朗动力学（BD）模拟分析了双折射衰减曲线中各成分的相对振幅。已针对代表具有 30 度、60 度和 90 度中心弯曲且具有不同程度相关角度分散的 RNA 分子的三珠、五珠和九珠模型模拟了衰减曲线。BD 模拟在分数振幅方面与实验结果密切一致，这表明振幅和末端 τ 比均可用作螺旋轴弯曲程度的度量。尽管当前结果表明，通常无法通过单次 τ 比测量区分相对固定的弯曲和高度灵活的弯曲，因为它们可能导致末端衰减时间和振幅出现类似的降低，但分数振幅对螺旋长度的依赖性测量可能会实现这种区分。
