DNA Base Mismatches

The DNA-charge-transfer system consisting of Et and Zg as a distinct donor-acceptor couple was applied in order to detect DNA base mismatches and the aba-sic site as typical DNA lesion [46]. By using charge-transfer processes additionally to the emission properties of Et, the detection of base mismatches does not rely solely on the small differences in the hybridization energies between matched... 

Jackson BA, Barton JK. Recognition of DNA base mismatches by a rhodium intercala-tor.J Am Chem Soc 1997 119 12986-7. 

Ruba E, Hart JR, Barton JK. [Ru(bpy)2(L)]Q2 Luminescent metal complexes that bind DNA base mismatches. Inorg. Chem. 2004 43 4570-4578. 

DNA mismatch repair genes Genes that identify and correct errors in DNA base pairs during DNA replication. Mutations in the mismatch repair genes can lead to cancer by allowing abnormal cells to continue to grow. 

To test this sensitivity of photoinduced quenching to perturbations in the intervening base pair stack, an assembly was prepared containing an intervening CA base mismatch which disrupts locally the /r-stack between the donor and acceptor. We observed that the yield of CT was reduced in the DNA... 

The innate sensitivity of DNA-mediated CT to perturbations in the TT-stack has prompted us to employ this chemistry as a probe of stacking structure and dynamics. We have developed a new class of DNA-based diagnostic tools that diagnose DNA mutations such as single base-pair mismatches and lesions, analyze DNA-protein interactions, and probe the sequence-depen-dent dynamics and flexibility of DNA. These applications rely on electrochemical probing of CT in DNA films self-assembled on gold electrodes. 

Considerable amounts of quenching of the acridone emissions by guanine in the DNA occurred when guanine was close to acridone, which can be applied as a quencher-free probe (no additional quencher is required) for the detection of a special sequence of DNA. The DNA bearing acridone at the C5 position of inner thymidine could distinguish the opposite T-T base mismatch, while enhancement of discrimination ability is needed for the practical use of single nucleotide polymorphism (SNP) typing. 

The acridinium ester (AE) in an AE-labeled cDNA probe hybridized to target DNA is less likely to be hydrolyzed than in the unhybridized conformation (Fig. 10) [9-11]. Single-base mismatches in the duplex adjacent to the site of AE attachment disrupt this protection, resulting in rapid AE hydrolysis [11]. Hydrolysis by a weak base renders AE permanently nonchemiluminescent. After hydrolysis, it is possible to use the remaining chemiluminescence as a direct measure of the amount of hybrid present. This selective degradation process is a highly specific chemical hydrolysis reaction, which is sensitive to the local environment of the acridinium ester. The matched duplex can be detected and quantified readily, whereas the mismatched duplex produces a minimal signal. 

All DNA hybridization assays are subject to cross-hybridization, in which an oligonucleotide that is not a perfect sequence match hybridizes with the capture probe. The cross-hybridization in the OFRR was investigated using samples of oligonucleotides with either 0-, 1-, 2-, 5-, or 25-base mismatches when compared with the 25 base-pair biorecognition capture probe. The resulting resonant mode spectral shifts for the respective mismatch are plotted in Fig. 14.7b. The measurements show a difference of 1.3 pm and 2.8 pm for one and two base-pair... 

Fig. 10 (a) Photos of colorimetric changes in solutions of (7.9 x 10 5 M, on a monomer unit basis) (b) a) polymer b) polymer/DNA probe c) polymer/DNA probe/complementary DNA sequence d) polymer/DNA probe/1 base mismatched DNA sequence e) polymer/DNA probe/ 2 base mismatched DNA sequence after 5 min mixing at 55 C in 0.1 M NaCl/H20. B) UV-vis spectra of the above corresponding samples [19]... 

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-... 

In CSGE, mildly denaturing solvents in an appropriate buffer can accentuate conformational changes produced by single-base mismatches in heteroduplexed DNA. This increases the differences in electrophoretic mobility between heteroduplex and homoduplex. 

Nucleotide Chemistry The cells of many eukaryotic organisms have highly specialized systems that specifically repair G-T mismatches in DNA The mismatch is repaired to form a G=C (not A=T) base pair. This G-T mismatch repair mechanism occurs in addition to a more general system that repairs virtually all mismatches. Can you suggest why cells might require a specialized system to repair G-T mismatches ... 

FIGURE 25-7 An example of error correction by the 3 —>5 exonuclease activity of DNA polymerase I. Structural analysis has located the exonuclease activity ahead of the polymerase activity as the enzyme is oriented in its movement along the DNA. A mismatched base (here, a C-A mismatch) impedes translocation of DNA polymerase I to the next site. Sliding backward, the enzyme corrects the mistake with its 3 —>5 exonuclease activity, then resumes its polymerase activity in the 5 —>3 direction. 

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