3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR.
TLDR
It is found that the introduction of more than one 3-nitropyrrole residue at dispersed positions into primers significantly reduced their efficiency in PCR and sequencing reactions.Abstract:
3-Nitropyrrole and 5-nitroindole have been assessed as universal bases in primers for dideoxy DNA sequencing and in the polymerase chain reaction (PCR). In contrast to a previous report, we have found that the introduction of more than one 3-nitropyrrole residue at dispersed positions into primers significantly reduced their efficiency in PCR and sequencing reactions. Primers containing 5-nitroindole at multiple dispersed positions were similarly affected; for both bases only a small number of substitutions were tolerated. In PCR experiments neither base, when incorporated into primers in codon third positions, was as effective as hypoxanthine, which was incorporated in six codon third positions in a 20mer oligomer. However, primers containing up to four consecutive 5-nitroindole substitutions performed well in both PCR and sequencing reactions. Consecutive 3-nitropyrrole substitutions were tolerated, but less well in comparable reactions.read more
Citations
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References
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Journal ArticleDOI
5-Nitroindole as an universal base analogue
David Loakes,Daniel M. Brown +1 more
TL;DR: 3-Nitropyrrole, whilst not discriminating between the natural bases, was found to lead to considerable destabilisation of the duplexes, particularly when multiple substitutions were made, in contrast to the 5-nitroindole nucleoside.
Journal ArticleDOI
A universal nucleoside for use at ambiguous sites in DNA primers
TL;DR: An alternative to previous universal nucleoside candidates1–9 is designed, l-(2'-deoxy-β-D-ribofuranosyl)-3-nitropyrrole (designated M), which max-imizes stacking while minimizing hydrogen-bonding interactions without sterically disrupting a DNA duplex.
Journal ArticleDOI
Synthesis and biophysical studies of short oligodeoxynucleotides with novel modifications: a possible approach to the problem of mixed base oligodeoxynucleotide synthesis.
T.A. Millican,G.A. Mock,M.A. Chauncey,T.P. Patel,M.A.W. Eaton,J. Gunning,S.D. Cutbush,Stephen Neidle,J. John Mann +8 more
TL;DR: Oligodeoxynucleotides containing these analogues having been synthesised and hybridized to their complementary strands and shown to be less stable than either the totally complementary duplex or those containing A.C.T mismatches.
Journal ArticleDOI
In vitro replication study of modified bases in ras sequences.
Hiroyuki Kamiya,Tomoki Sakaguchi,Naoko Murata,Masahiro Fujimuro,Hiroyuki Miura,Hiroyuki Ishikawa,Miho Shimizu,Hideo Inoue,Susumu Nishimura,Akio Matsukage,Chikahide Masutani,Fumio Hanaoka,Eiko Ohtsuka +12 more
TL;DR: In this paper, DNA templates containing a modified base (O6-methylguanine, 8-hydroxyguanines, xanthine or hypoxanthine) which was located in nucleotide sequences corresponding to the 12th or 61st codon of a ras gene were synthesized and deoxynucleotide incorporation opposite the lesions was investigated.