Effect of the 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole residue on the stability of DNA duplexes and triplexes.
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.
Amosova
O
O
Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
George
J
J
Fresco
J R
JR
D000225:Adenine; D001482:Base Composition; D001483:Base Sequence; D002151:Calorimetry; D003596:Cytosine; D004247:DNA / Q000737:chemistry*; D003853:Deoxyribonucleosides; D006147:Guanine; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011758:Pyrroles; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D013941:Thymine
D003853:Deoxyribonucleosides; D009838:Oligodeoxyribonucleotides; D011758:Pyrroles; C087515:3-nitropyrrole 2'-deoxyribonucleoside; C094911:3-nitropyrrole; D006147:Guanine; D003596:Cytosine; D004247:DNA; D000225:Adenine; D013941:Thymine