Lacy Eilyn R, Nguyen Binh, Le Minh, Cox Kari K, OHare Caroline, Hartley John A, Lee Moses, Wilson W David
Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.
Nucleic Acids Res. 2004 Apr 2;32(6):2000-7. doi: 10.1093/nar/gkh515. Print 2004.
To complement available structure and binding results and to develop a detailed understanding of the basis for selective molecular recognition of T.G mismatches in DNA by imidazole containing polyamides, a full thermodynamic profile for formation of the T.G-polyamide complex has been determined. The amide-linked heterocycles f-ImImIm and f-PyImIm (where f is formamido group, Im is imidazole and Py is pyrrole) were studied by using biosensor-surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) with a T.G mismatch containing DNA hairpin duplex and a similar DNA with only Watson-Crick base pairs. Large negative binding enthalpies for all of the polyamide-DNA complexes indicate that the interactions are enthalpically driven. SPR results show slower complex formation and stronger binding of f-ImImIm to the T.G than to the match site. The thermodynamic analysis indicates that the enhanced binding to the T.G site is the result of better entropic contributions. Negative heat capacity changes for the complex are correlated with calculated solvent accessible surface area changes and indicate hydrophobic contributions to complex formation. DNase I footprinting analysis in a long DNA sequence provided supporting evidence that f-ImImIm binds selectively to T.G mismatch sites.
为补充现有的结构和结合结果，并深入了解含咪唑聚酰胺对DNA中T·G错配进行选择性分子识别的基础，已确定了T·G-聚酰胺复合物形成的完整热力学概况。通过生物传感器表面等离子体共振（SPR）和等温滴定量热法（ITC），使用含T·G错配的DNA发夹双链体和仅含沃森-克里克碱基对的类似DNA，研究了酰胺连接的杂环f-ImImIm和f-PyImIm（其中f是甲酰胺基，Im是咪唑，Py是吡咯）。所有聚酰胺-DNA复合物的大的负结合焓表明相互作用是由焓驱动的。SPR结果显示，f-ImImIm与T·G形成复合物的速度较慢，且与T·G的结合比对匹配位点的结合更强。热力学分析表明，与T·G位点结合增强是更好的熵贡献的结果。复合物的负热容变化与计算出的溶剂可及表面积变化相关，表明疏水作用对复合物形成有贡献。在长DNA序列中进行的DNase I足迹分析提供了支持性证据，证明f-ImImIm选择性结合到T·G错配位点。
