Cheng A J, Van Dyke M W
Department of Tumor Biology, University of Texas M.D. Anderson Cancer Center, Houston 77030.
Nucleic Acids Res. 1994 Nov 11;22(22):4742-7. doi: 10.1093/nar/22.22.4742.
The binding of guanosine/thymidine-rich oligodeoxyribonucleotides containing various deletions, extensions, and point mutations to polypurine DNA targets was investigated by DNase I footprinting. Intermolecular purine-purine-pyrimidine triple-helical DNA formation was best achieved using oligonucleotides 12 nucleotides in length. Longer oligonucleotides were slightly weaker in binding affinity, whereas shorter oligonucleotides were considerably weaker. Oligonucleotide extensions had a slight effect on triplex formation, while single point mutations located near the oligonucleotide ends had a greater effect. In the cases of extensions and point mutations, changes to the 3' end of the oligonucleotide had a consistently greater effect on triplex formation than changes to the 5' end. Such differences in triplex-forming ability were not caused by an intrinsic property of these oligonucleotides, since the same point mutated oligonucleotides could bind with high affinity to duplex DNAs containing complementary sites. Taken together, our data suggest that there may be an asymmetry involved in the process of purine-motif triplex formation, with interactions between the 3' end of the oligonucleotide and complementary sequences on the target duplex DNA being dominant.
通过DNA酶I足迹法研究了含有各种缺失、延伸和点突变的富含鸟苷/胸苷的寡脱氧核糖核苷酸与多嘌呤DNA靶标的结合。使用长度为12个核苷酸的寡核苷酸能最好地实现分子间嘌呤-嘌呤-嘧啶三链螺旋DNA的形成。较长的寡核苷酸结合亲和力稍弱，而较短的寡核苷酸则明显较弱。寡核苷酸延伸对三链体形成有轻微影响，而位于寡核苷酸末端附近的单点突变影响更大。在延伸和点突变的情况下，寡核苷酸3'端的变化对三链体形成的影响始终比对5'端的变化更大。三链体形成能力的这种差异并非由这些寡核苷酸的内在特性引起，因为相同的点突变寡核苷酸可以与含有互补位点的双链DNA高亲和力结合。综上所述，我们的数据表明，嘌呤基序三链体形成过程中可能存在不对称性，寡核苷酸3'端与靶标双链DNA上的互补序列之间的相互作用占主导地位。
