Nucleic mismatched base pairs

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... 

Ikuta, S., Takagi, Wallace, R. B., and Itakura, K. (1987) Dissociation kinetics of 19 base paired oligonucleotide -DNA duplexes containing different single mismatched base pairs. Nucleic Acid Res. 15,797-811. 

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. 

In addition to probe concentration and availability, the length of the probe and the complexity of the nucleic acids affect hybridization rates. Rates are directly proportional to the square root of the probe length and inversely proportional to complexity, defined as the total number of base pairs present in nonrepeating sequences. Mismatches up to about 10% have little effect on hybridization rates. 

The transmission of genetic information requires accmate base pairing between nucleic acids. This includes translation of mRNA into protein by the ribosome on which accurate selection of aa-tRNA depends upon the correct pairing of three bases between the mRNA codon and the tRNA anticodon. For example, the codon-anticodon mismatches are efficiently rejected with error frequencies as low as 10. Plausible mechanisms for the involvement of the ribosome in the decoding of mRNA codon tRNA anticodon (Ogle et al, 2003 Rodnina and Wintermeyer, 2001) include ... 

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