Gao Qiang, Satake Hiroyuki, Dai Qing, Ono Katsuya, Nishizawa Seiichi, Teramae Norio
Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.
Nucleic Acids Symp Ser (Oxf). 2005(49):219-20. doi: 10.1093/nass/49.1.219.
By using UV thermal denaturation and isothermal titration calorimetry (ITC), we examine the binding behaviors of a hydrogen bond-forming ligand, 2-acetylamino-7-methyl-1,8-naphthyridine (AcMND), with a guanine base opposite an abasic site (AP site) in a DNA duplex (5'-TCC AGX GCA AC-3'/3'-AGG TCG CGT TG-5', X = AP site, G = target). In the presence of AcMND, the melting temperature (Tm) of the AP site-containing DNA duplex increases by 8.6 degrees C while hardly any change in Tm is observed for a corresponding normal duplex that has no AP sites. The examination by ITC reveals that, in solutions buffered to pH 7.0 (at 10 degrees C, I = 0.11 M), AcMND is able to recognize guanine base with a 1:1 binding constant of 3.4x10(5) M(-1). The ligand-nucleotide interaction is clearly enthalpy driven, with deltaH(o) of -12.5 kcal/mol. We discuss these binding functions of AcMND at the AP site with a view towards development of ligand-based assay for SNPs (single-nucleotide polymorphisms) typing.
通过使用紫外热变性和等温滴定量热法（ITC），我们研究了一种形成氢键的配体2-乙酰氨基-7-甲基-1,8-萘啶（AcMND）与DNA双链体（5'-TCC AGX GCA AC-3'/3'-AGG TCG CGT TG-5'，X = 无碱基位点，G = 靶标）中与无碱基位点（AP位点）相对的鸟嘌呤碱基的结合行为。在存在AcMND的情况下，含AP位点的DNA双链体的解链温度（Tm）升高了8.6℃，而对于相应的无AP位点的正常双链体，Tm几乎没有变化。ITC检测表明，在缓冲至pH 7.0的溶液中（在10℃，I = 0.11 M），AcMND能够识别鸟嘌呤碱基，结合常数为1:1，为3.4x10(5) M(-1)。配体与核苷酸的相互作用明显由焓驱动，ΔH(o)为-12.5 kcal/mol。我们讨论了AcMND在AP位点的这些结合功能，以期开发基于配体的单核苷酸多态性（SNP）分型检测方法。
