Department of Chemistry, Allegheny College , 520 North Main Street, Meadville, Pennsylvania 16335, United States.
Biochemistry. 2013 Feb 5;52(5):765-72. doi: 10.1021/bi3013005. Epub 2013 Jan 28.
The rates of duplex formation for two octamers of DNA (5' d-CACGGCTC/5' d-GAGCCGTG and 5' d-CACAGCAC/5' d-GTGCTGTG), the homologous RNA, and both sets of hybrids in 1 M NaCl buffer have been measured using stopped-flow spectroscopy. In addition, the thermodynamic parameters, ΔH° and ΔS°, have been determined for the same sequences under the same buffer conditions using optical melting techniques. These data reveal a linear free energy relationship between the free energy of activation for denaturation and the change in free energy for formation of the duplexes. This relationship indicates that these duplex formation reactions occur through a common unstructured transition state that is more similar to the single strands in solution than to the ensuing duplex. In addition, these data confirm that the greater stability of RNA duplexes relative to that of homologous DNA and hybrid duplexes is controlled by the denaturation rate and not the duplex formation rate.
使用停流光谱法测量了两条八聚体 DNA（5' d-CACGGCTC/5' d-GAGCCGTG 和 5' d-CACAGCAC/5' d-GTGCTGTG）、同源 RNA 以及两套杂交双链在 1 M NaCl 缓冲液中的双链形成速率。此外，还使用光学融解技术在相同缓冲条件下测定了相同序列的热力学参数ΔH°和ΔS°。这些数据表明，在变性的活化自由能和双链形成的自由能变化之间存在线性自由能关系。该关系表明，这些双链形成反应通过一个共同的无结构过渡态进行，该过渡态与溶液中的单链更相似，而与随后的双链则不相似。此外，这些数据证实 RNA 双链相对于同源 DNA 和杂交双链的更高稳定性是由变性速率而不是双链形成速率控制的。
