Amosova O, George J, Fresco J R
Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
Nucleic Acids Res. 1997 May 15;25(10):1930-4. doi: 10.1093/nar/25.10.1930.
3-Nitropyrrole (M) was introduced as a non-discriminating 'universal' base in nucleic acid duplexes by virtue of small size and a presumed tendency to stack but not hydrogen bond with canonical bases. However, the absence of thermally-induced hyperchromic changes by single-stranded deoxyoligomers in which M alternates with A or C residues shows that M does not stack strongly with A or C nearest neighbors. Yet, the insertion of a centrally located M opposite any canonical base in a duplex is sometimes even less destabilizing than that of some mismatches, and the variation in duplex stability is small. In triplexes, on the other hand, an M residue centrally located in the third strand reduces triplex stability drastically even when the X.Y target base pair is A.T or G. C in a homopurine. homopyrimidine segment. But, when the target duplex opposition is M-T and the third strand residue is T, the presence of M in the test triplet has little effect on triplex stability. Therefore, a lack of hydrogen bonding in an otherwise helix-compatible test triplet cannot be responsible for triplex destabilization when M is the third strand residue. Thus, M is non-discriminating and none-too-destabilizing in a duplex, but in a triplex it is extremely destabilizing when in the third strand.
3-硝基吡咯（M）因其体积小以及推测具有堆积倾向但不与标准碱基形成氢键的特性，被引入作为核酸双链体中一种无选择性的“通用”碱基。然而，在由M与A或C残基交替组成的单链脱氧寡聚物中，未观察到热诱导的增色变化，这表明M与A或C最近邻碱基的堆积作用不强。然而，在双链体中，位于中心位置的M与任何标准碱基配对时，其稳定性破坏程度有时甚至比某些错配还要小，并且双链体稳定性的变化很小。另一方面，在三链体中，即使X.Y靶碱基对在同型嘌呤-同型嘧啶片段中是A.T或G.C，位于第三链中心位置的M残基也会大幅降低三链体的稳定性。但是，当靶双链体配对为M-T且第三链残基为T时，测试三联体中M的存在对三链体稳定性影响很小。因此，当M为第三链残基时，在其他方面与螺旋兼容的测试三联体中缺乏氢键并不是三链体不稳定的原因。所以，M在双链体中无选择性且稳定性破坏作用不大，但在三链体中，当它位于第三链时，会极大地破坏稳定性。
