Ren J, Chaires J B
Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS 39216-4505, USA.
Biochemistry. 1999 Dec 7;38(49):16067-75. doi: 10.1021/bi992070s.
The sequence and structural selectivity of 15 different DNA binding agents was explored using a novel, thermodynamically rigorous, competition dialysis procedure. In the competition dialysis method, 13 different nucleic acid structures were dialyzed against a common ligand solution. More ligand accumulated in the dialysis tube containing the structural form with the highest ligand binding affinity. DNA structural forms included in the assay ranged from single-stranded forms, through a variety of duplex forms, to multistranded triplex and tetraplex forms. Left-handed Z-DNA, RNA, and a DNA-RNA hybrid were also represented. Standard intercalators (ethidium, daunorubicin, and actinomycin D) served as control compounds and were found to show structural binding preferences fully consistent with their previously published behavior. Standard groove binding agents (DAPI, distamycin, and netropsin) showed a strong preference for AT-rich duplex DNA forms, along with apparently strong binding to the poly(dA)-poly(dT) triplex. Thermal denaturation studies revealed the apparent triplex binding to be complex, and perhaps to result from displacement of the third strand. Putative triplex (BePI, coralyne, and berberine) and tetraplex [H(2)TmPyP, 5,10,15, 20-tetrakis[4-(trimethylammonio)phenyl]-21H,23H-porphine, and N-methyl mesoporphyrin IX] selective agents showed in many cases less dramatic binding selectivity than anticipated from published reports that compared their binding to only a few structural forms. Coralyne was found to bind strongly to single-stranded poly(dA), a novel and previously unreported interaction. Finally, three compounds (berenil, chromomycin A, and pyrenemethylamine) whose structural preferences are largely unknown were examined. Pyrenemethylamine exhibited an unexpected and unprecedented preference for duplex poly(dAdT).
使用一种新颖的、热力学严格的竞争透析程序，探究了15种不同DNA结合剂的序列和结构选择性。在竞争透析法中，将13种不同的核酸结构与一种常见的配体溶液进行透析。更多的配体积聚在含有与配体结合亲和力最高的结构形式的透析管中。测定中包括的DNA结构形式从单链形式，到各种双链形式，再到多链三链体和四链体形式。左手Z-DNA、RNA和DNA-RNA杂交体也有代表。标准嵌入剂（溴化乙锭、柔红霉素和放线菌素D）用作对照化合物，发现其显示出的结构结合偏好与先前发表的行为完全一致。标准沟结合剂（DAPI、偏端霉素和纺锤菌素）对富含AT的双链DNA形式表现出强烈偏好，同时对聚（dA）-聚（dT）三链体也表现出明显的强结合。热变性研究表明，与三链体的明显结合很复杂，可能是由于第三条链的置换所致。推定的三链体（BePI、珊瑚灵和黄连素）和四链体[H(2)TmPyP、5,10,15,20-四（4-三甲基铵苯基）-21H,23H-卟啉和N-甲基中卟啉IX]选择性剂在许多情况下显示出的结合选择性不如已发表报告预期的那么显著，那些报告仅将它们与少数结构形式的结合进行了比较。发现珊瑚灵与单链聚（dA）强烈结合，这是一种新颖且先前未报道的相互作用。最后，研究了三种结构偏好基本未知的化合物（贝尼尔、色霉素A和芘甲胺）。芘甲胺对双链聚（dAdT）表现出意想不到且前所未有的偏好。
