Loakes D, Hill F, Brown D M, Salisbury S A
Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
J Mol Biol. 1997 Jul 18;270(3):426-35. doi: 10.1006/jmbi.1997.1129.
The nature of DNA containing the deoxyribosyl derivative of 5-nitroindole has been investigated. 5-Nitroindole has been shown to give good stability when present in duplexes opposite natural bases, with only slightly reduced melting temperatures. However, enhanced stability occurs when it is incorporated as an additional bulged base in duplexes. It also markedly enhances the stability of duplexes when it is present as a pendant base at either the 5' or 3'-ends of the two strands. The stabilisation is presumed to be due to enhanced stacking interactions for the nitroindole base. Oligomers containing a number of consecutive 5-nitroindole residues form stable, stacked secondary structures. An oligomer containing 21 such substitutions is presumed to exist as a hairpin structure. This was further investigated by circular dichroism melting experiments, which demonstrated that the single-stranded oligomer contains significant secondary structure in the region of the 5-nitroindole tract, which appears to contain a double-stranded stem. X-ray analysis of 5-nitroindole deoxyriboside provides some indication of how the mode of stacking observed in crystals of the nucleoside may also be responsible for stabilising secondary structures of oligonucleotides.
对含有5-硝基吲哚脱氧核糖基衍生物的DNA的性质进行了研究。已表明，当5-硝基吲哚存在于双链体中与天然碱基相对时，具有良好的稳定性，只是解链温度略有降低。然而，当它作为额外的凸起碱基掺入双链体中时，稳定性会增强。当它作为侧链碱基存在于两条链的5'或3'-末端时，也会显著增强双链体的稳定性。这种稳定作用据推测是由于硝基吲哚碱基的堆积相互作用增强所致。含有多个连续5-硝基吲哚残基的寡聚物形成稳定的堆积二级结构。含有21个此类取代的寡聚物据推测以发夹结构存在。通过圆二色性熔解实验对此进行了进一步研究，实验表明单链寡聚物在5-硝基吲哚区域含有显著的二级结构，该区域似乎包含一个双链茎。对5-硝基吲哚脱氧核苷的X射线分析提供了一些线索，说明在核苷晶体中观察到的堆积模式可能也有助于稳定寡核苷酸的二级结构。
