We report the thermodynamic contributions of loop length and loop sequence to the overall stability of DNA intramolecular pyrimidine triplexes. Two sets of triplexes were designed: in the first set, the C₅ loop closing the triplex stem was replaced with ^5′-CT_nC loops (n = 1–5), whereas in the second set, both the duplex and triplex loops were replaced with a ^5′-GCAA or ^5′-AACG tetraloop. For the triplexes with a ^5′-CT_nC loop, the triplex with five bases in the loop has the highest stability relative to the control. A loop length lower than five compromises the strength of the base-pair stacks without decreasing the thermal stability, leading to a decreased enthalpy, whereas an increase in the loop length leads to a decreased enthalpy and a higher entropic penalty. The incorporation of the GCAA loop yielded more stable triplexes, whereas the incorporation of AACG in the triplex loop yielded a less stable triplex due to an unfavorable enthalpy term. Thus, addition of the GCAA tetraloop can cause an increase in the thermodynamics of the triplex without affecting the sequence or melting behavior and may result in an additional layer of genetic regulation.

中文翻译：

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环长度和序列对带有TAT碱基三联体的DNA嘧啶三联体稳定性的影响

我们报告了环长度和环序列对DNA分子内嘧啶三联体的整体稳定性的热力学贡献。设计了两组三元组：在第一组中，将封闭三元组茎的C ₅环替换为^5'- CT _n C环（n = 1-5），而在第二组中，双工和三元环都用^5'- GCAA或^5'- AACG四环取代。对于具有^5'- CT _n的三元组在C回路中，回路中具有5个碱基的三元组相对于控件具有最高的稳定性。小于5的环长度在不降低热稳定性的情况下损害了碱基对叠层的强度，从而导致焓降低，而环长度的增加导致焓降低和熵损失更高。由于不利的焓项，GCAA环的引入产生了更稳定的三链体，而AACG在三链环中的引入产生了较不稳定的三链体。因此，添加GCAA四环可以增加三链体的热力学，而不会影响序列或解链行为，并可能导致额外的遗传调控层。