Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins
Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins
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DOI：
10.1021/ja016310e
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发表时间：
2001-11-07
影响因子：
15
通讯作者：
Armitage, BA
中科院分区：
文献类型：
--
作者：
Kushon, SA;Jordan, JP;Armitage, BA
用吸光度减色谱(ABS)、圆二色谱(CD)和比色法检测PNA/DNA双链，观察到一系列PNA和DNA探针与一组异常稳定的四环基序DNA发夹的结合。这些结果表明，这些靶发夹可以形成稳定的PNA-DNA和DNA-DNA双链，即使所得到的双链的熔融温度比发夹靶的熔融温度低50℃。发夹/单链和发夹/发夹相互作用都在这些研究的范围内。研究表明，靶分子和探针分子中的二级结构都能降低探针-靶双链的熔化温度和自由能。杂交的动力学分析产生的反应速度比两条非结构链之间的杂交慢160倍。靶和探针二级结构对杂交造成的热力学和动力学障碍是反义药物特别是诊断探针持续发展的重要问题。
The binding of a series of PNA and DNA probes to a group of unusually stable DNA hairpins of the tetraloop motif has been observed using absorbance hypochromicity (ABS), circular dichroism (CD), and a colorimetric assay for PNA/DNA duplex detection. These results indicate that both stable PNA-DNA and DNA-DNA duplexes can be formed with these target hairpins, even when the melting temperatures for the resulting duplexes are up to 50 degreesC lower than that of the hairpin target. Both hairpin/single-stranded and hairpin/hairpin interactions are considered in the scope of these studies. Secondary structures in both target and probe molecules are shown to depress the melting temperatures and free energies of the, probe-target duplexes. Kinetic analysis of hybridization yields reaction rates that are up to 160-fold slower than hybridization between two unstructured strands. The thermodynamic and kinetic obstacles to hybridization imposed by both target and probe secondary structure are significant concerns for the continued development of antisense agents and especially diagnostic probes.