Thermodynamic dissection of the substrate-ribozyme interaction in the hammerhead ribozyme.
Thermodynamic dissection of the substrate-ribozyme interaction in the hammerhead ribozyme.
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锤头核酶中底物-核酶相互作用的热力学剖析。
DOI：
10.1021/bi981740b
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发表时间：
1998
期刊：
影响因子：
--
通讯作者：
Uhlenbeck,OC
中科院分区：
文献类型：
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作者：
Hertel,KJ;Stage-Zimmermann,TK;Ammons,G;Uhlenbeck,OC
比较了10种不同锤头的底物识别螺旋长度和序列不同的锤头状核酶与底物结合的自由能。选择这些锤头是因为核酶和底物寡核苷酸都没有形成可检测的替代二级结构。观察到的结合自由能在−8到−24 kcal/mol之间变化，如果对催化核心使用ΔG°核心= +3.3 ± 1 kcal/mol的恒定能量惩罚，则与从最近邻自由能计算的结合能非常一致。一组含有竞争性发夹二级结构的底物与核酶的结合较弱，其结合量与发夹形成的预测自由能一致。这些热力学的结论允许预测底物结合亲和力的核酶底物对的任何螺旋长度和序列，因此，应该是非常有价值的合理设计的核酶基因失活。
The free energy of substrate binding to the hammerhead ribozyme was compared for 10 different hammerheads that differed in the length and sequence of their substrate recognition helices. These hammerheads were selected because neither ribozyme nor substrate oligonucleotide formed detectable alternate secondary structures. The observed free energies of binding varied from −8 to −24 kcal/mol and agreed very well with binding energies calculated from the nearest-neighbor free energies if a constant energetic penalty of ΔG°core= +3.3 ± 1 kcal/mol is used for the catalytic core. A set of substrates that contained a competing hairpin secondary structure showed weaker binding to the ribozyme by an amount consistent with the predicted free energy for hairpin formation. These thermodynamic conclusions permit the prediction of substrate binding affinities for ribozyme−substrate pairs of any helix length and sequence, and thus, should be very valuable for the rational design of ribozymes directed toward gene inactivation.