Nucleic acid base mismatch

The fluorescence of 2AP is strongly quenched by nucleic acid bases [17, 18, 24-29]. Time-correlated single-photon counting studies have shown that the interactions of 2AP with different nucleic acid bases significantly decrease the 2AP fluorescence hfetime [17, 24-29]. While the fluorescence lifetime of free 2AP in aqueous solution is about 10 ns, in double-stranded DNA the 2AP hfetimes are reduced to 30-50 ps. This effect has been used extensively to study the dynamics of mismatched base pairs [19, 21, 25, 30], local changes in dynamics of DNA molecules produced by their binding to the active sites of polymerases [26, 31-33], stacking interactions at abasic... 

C. G., Janowski B.A., Corey D. R. Inhibition of gene expression inside cells by peptide nucleic acids effect of mRNA target sequence, mismatched bases, and PNA length. Biochemistry 2001 40 53-64. 

To elaborate upon this scheme, the authors replaced the DNA-based capture strand with one that is based on peptide nucleic acid (PNA) in order to distinguish single nucleotide mismatches [34]. Since PNA does not have a phospho-diester backbone, a PNA-DNA duplex is more thermodynamically stable than DNA-DNA or RNA-RNA helices due to a lack of electrostatic repulsion between the two chains. PNAs have also been shown to be more selective. However, PNAs are more difficult to synthesize and PNA-DNA interactions are not as well understood as DNA-DNA binding. In this study, quaternary ammo-... 

Barawkar DA, Rajeef KG, Kumar VA, Ganesh KN (1996) Triplex formation at physiological pH by 5-Me-dC-N-4-(spermine) [X] oligodeoxynucleotides non protonation of N3 in X of X G C triad and effect of base mismatch ionic strength on triplex stabilities. Nucleic Acids Res 24 1229-1237... 

Molecular beacons (MBs) are hairpin-shaped oligonucleotides that report the presence of specific nucleic acids. The MBs have been immobihzed by Tan and co-workers [27] onto ultrasmall optical fibre probes through avidin-biotin binding. The MB-DNA biosensor detected its target DNA molecules, in real time, with selectivity for a single base-pair mismatch. This MB-DNA-biosensor was used by Perlette and Tan [28] for real-time monitoring of mRNA-DNA hybridization inside a living cell. 

Fig. 4.1. Amplified detection paths of a single-base mismatch in nucleic acids (a) using avidin and hiotin-labelled liposomes (h) using an avidin-Au-nanoparticle conjugate and the catalysed deposition of gold (c) using an avidin-alkaline phosphatase bioconjugate and the biocatalysed precipitation of the insoluble product 4. (Reproduced from Ref. [63] with permission from Elsevier.)...

Heaton, R.J., Peterson, A.W. and Georgiadis, R.M. Electrostatic surface plasmon resonance Direct electric field- induced hybridization and denaturation in monolayer nucleic acid films and label-free discrimination of base mismatches. Proceedings of the National Academy of Sciences of the United States of America, 2001, 98 (7), p. 3701-3704. 

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