Porschke D, Jung M
Max Planck Institut für biophysikalische Chemie, Göttingen-Nikolausberg, West Germany.
J Biomol Struct Dyn. 1985 Jun;2(6):1173-84. doi: 10.1080/07391102.1985.10507631.
The conformation of single stranded oligonucleotides is analysed by measurements of their rotation time constants. The oligomers are aligned to some degree by short electric field pulses; after pulse termination the transition to a random orientation is followed by measurements of the linear dichroism. An efficient deconvolution procedure is developed for evaluation of the experimental data obtained in the ns-time range. The increase of rotation time constants observed for chain lengths in the range from 14 to 22 residues are interpreted according to a weakly bending rod model providing a persistence length and a Stokes' diameter. The Stokes' diameters obtained for ribo- and deoxyriboadenylates are about 13A, in approximate agreement with the expectation for a single stranded helix. The persistence length L = 53A corresponding to approximately 16 nucleotide residues found for riboadenylates at 2 degrees C appears to reflect relatively strong stacking interactions at this temperature. However, a comparison with the average length of stacked residues evaluated from available thermodynamic parameters of base stacking indicate that unstacked residues are not completely flexible. Apparently the ribose-phosphate chain provides an essential contribution to the stiffness of oligomers and polymers, even when the bases are unstacked. Addition of 100 microM Mg2+ leads to an increase of the persistence length to 88A. Corresponding measurements with deoxyriboadenylates show a slightly lower value of the persistence length than that found for riboadenylates. Addition of LysTrpLys and LysTyrLys to A(pA)19 leads to an increase of the rotation time constant, which corresponds approximately to a length increment by one residue per bound peptide. Since controls performed with LysLeuLys do not show any similar effect, the increase of the time constants induced by LysTrpLys and LysTyrLys is attributed to intercalation of the aromatic amino acids.
通过测量单链寡核苷酸的旋转时间常数来分析其构象。寡聚物通过短电场脉冲在一定程度上排列；脉冲终止后，测量线性二色性以跟踪向随机取向的转变。开发了一种有效的去卷积程序，用于评估在纳秒时间范围内获得的实验数据。对于14至22个残基范围内的链长所观察到的旋转时间常数的增加，根据弱弯曲杆模型进行解释，该模型提供了一个持久长度和一个斯托克斯直径。核糖腺苷酸和脱氧核糖腺苷酸的斯托克斯直径约为13埃，与单链螺旋的预期大致相符。在2℃时，核糖腺苷酸的持久长度L = 53埃，对应于大约16个核苷酸残基，这似乎反映了在此温度下相对较强的堆积相互作用。然而，与根据碱基堆积的可用热力学参数评估的堆积残基的平均长度进行比较表明，未堆积的残基并非完全灵活。显然，即使碱基未堆积，核糖磷酸链也对寡聚物和聚合物的刚度有重要贡献。添加100 microM Mg2+会导致持久长度增加到88埃。对脱氧核糖腺苷酸的相应测量显示，持久长度的值略低于核糖腺苷酸。向A(pA)19添加LysTrpLys和LysTyrLys会导致旋转时间常数增加，这大致相当于每个结合肽增加一个残基的长度增量。由于用LysLeuLys进行的对照未显示任何类似效果，因此LysTrpLys和LysTyrLys诱导的时间常数增加归因于芳香族氨基酸的嵌入。
