Mismatches oligomer hybridization

The luminescence of the hybridized [Ru(phen)2(dppz)]2+ derivative may be used to characterize the molecular assembly (77). Dilution experiments show that intercalation is intramolecular at concentrations <5 mM duplex addition of unmodified duplex to the covalently bound duplex results in <5% change in the luminescence. The results of experiments performed on duplexes containing mismatches in various positions along the duplex are also consistent with intramolecular intercalation. In this series, luminescence is higher for mismatches near the ruthenated end of the oligomer, where the ruthenium complex can intercalate intramolecularly and stabilize the mismatched site. 

Maskos and Southern (1992) designed a linker for the synthesis of oligomers on glass supports which is resistant to ammonia treatment. The system appears to be highly specific in hybridization and sensitive to single mismatches. Their predictable behavior should make this system very useful for hybridization and for the isolation of DNA-binding proteins. 

Fig. 2. Hybridization of Affymetrix HuSNP GenChips using biotinylated PCR probes synthesized from individual or pooled DNA samples. A SNP marker is represented by four oligomer quartets in which two perfect matches (PM) correspond to allele A and B, respectively, and two mismatches (MM) correspond to homomeric bases of the respective SNP. As shown in the individual SNP markers and pooled SNP markers, individual genotypes could be called according intensities of allele A, B, or AB. Pooled allele lie-quencies could be derived from intensity ratio of allele A and B using arctangent transformation.

Fig. 3. Hybridization of Affymetrix Mu6500 GenChip using biotinylated cRNA probes synthesized from brain cDNAs of dopamine (DAT) and serotonin (SET) transporter gene knockout mice or double (DAT/SET) knockout mice. A gene transcript is represented by 11-16 oligomers in perfect matches (PM, upper squares) and mismatches (MM, lower squares). The hybridization intensities of the perfect matches from one knockout mouse brain are compared.

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