Minor groove binders (MGBs)

/Minor groove binders (MGBs)

Minor groove binders (MGBs)

2017-12-05T14:03:27+00:00December 5th, 2017|

These dsMinor groove binders (MGBs)DNA-binding agents are attached to the 3’ end of TaqMan® probes to increase the Tm value (by stabilization of hybridization) and to design shorter probes. Longer probes reduce design flexibility and are less sensitive to mismatch discrimination. Shorter probes make it easier to use short conserved or unique sequences for hybridization. MGBs also reduce background fluorescence and increase dynamic range due to increased efficiency of reporter quenching due to shorter distances between the reporter and quencher and the use of non-fluorescent (dark) quenchers (NFQ) at the 3’ end instead of fluorescence dyes like TAMRA. By allowing the use of shorter probes with higher Tm values, MGBs enhances mismatch discrimination in genotyping assays and also gene dosage discrimination. Thus, advantages of MGB probes are (i) increased duplex stability which reduces non-specific probe hybridization and results in low background fluorescence during the 5′ nuclease PCR assay, (ii) shorter probes for hybridization-based assays (a 12mer MGB probe has the same Tm as a no-MGB 27mer probe) (Kutyavin, 2000), (iii) increased sequence specificity for better mismatch recognition due to larger differences between Tm values of matched and mismatched probes (Yao, 2006) and (iv) better signal-to-noise ratio due to having a NFQ at the 3’ end. An alternative to MGB probes which also shortens probe length is LNA (Letertre, 2003; Johnson, 2004) and BHQplusTM. See ABI Allelic Discrimination with TaqMan® Probes and MGB Primer & Probe Design on Primer Express.

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