Experimental Biomolecular Physics, Applied Physics, Royal Institute of Technology, Stockholm, SE-10691, Sweden.
Nucleic Acids Res. 2011 Feb;39(3):e17. doi: 10.1093/nar/gkq808. Epub 2010 Nov 10.
Ribonucleic acids are highly conserved essential parts of cellular life. RNA function is determined to a large extent by its hydrodynamic behaviour. The presented study proposes a strategy to predict the hydrodynamic behaviour of RNA single strands on the basis of the polymer size. By atom-level shell-modelling of high-resolution structures, hydrodynamic radius and diffusion coefficient of evolutionary conserved RNA single strands (ssRNA) were calculated. The diffusion coefficients D of 17-174 nucleotides (nt) containing ssRNA depended on the number of nucleotides N with D = 4.56 × 10(-10) N(-0.39) m(2) s(-1). The hydrodynamic radius R(H) depended on N with R(H) = 5.00 × 10(-10) N(0.38) m. An average ratio of the radius of gyration and the hydrodynamic radius of 0.98 ± 0.08 was calculated in solution. The empirical law was tested by in solution measured hydrodynamic radii and radii of gyration and was found to be highly consistent with experimental data of evolutionary conserved ssRNA. Furthermore, the hydrodynamic behaviour of several evolutionary unevolved ribonucleic acids could be predicted. Based on atom-level shell-modelling of high-resolution structures and experimental hydrodynamic data, empirical models are proposed, which enable to predict the translational diffusion coefficient and molecular size of short RNA single strands solely on the basis of the polymer size.
核糖核酸是细胞生命中高度保守的必需部分。RNA 的功能在很大程度上取决于其流体动力学行为。本研究提出了一种基于聚合物大小预测 RNA 单链流体动力学行为的策略。通过高分辨率结构的原子级壳模型，计算了进化保守的 RNA 单链（ssRNA）的流体力学半径和扩散系数。17-174 个核苷酸（nt）的 ssRNA 的扩散系数 D 取决于核苷酸数 N，D=4.56×10(-10) N(-0.39) m(2) s(-1)。流体力学半径 R(H) 取决于 N，R(H)=5.00×10(-10) N(0.38) m。在溶液中计算出的旋转半径与流体力学半径的平均比值为 0.98±0.08。通过在溶液中测量的流体力学半径和旋转半径对经验定律进行了检验，发现它与进化保守的 ssRNA 的实验数据高度一致。此外，还可以预测几种进化上未进化的核糖核酸的流体动力学行为。基于高分辨率结构的原子级壳模型和实验流体力学数据，提出了经验模型，这些模型能够仅根据聚合物大小预测短 RNA 单链的平移扩散系数和分子大小。
