Mismatch destabilisation

A simple manner to obtain discrimination between mismatched and complementary strands is to use more stringent conditions varying the saline concentration (ionic strength) of the hybridisation buffer or adding chemical agents that destabilise the DNA duplex as formamide or urea. The presence of ions in DNA solutions stabilises the DNA... 

The base analogues 2-amino-6-(2-thienyl)purine and 2-amino-6-(2-furyl)purine (90) have been incorporated into ODN duplexes as potential nonhydrogen bonding base pairs with pyridin-2-one nucleoside. The thienyl derivative opposite pyridin-2-one was more stable than the N -dimethylaminopurine. The 5 -triphosphate derivative of the pyridin-2-one nucleoside was inserted opposite the thienylpurine derivative more efficiently than the natural dNTPs. RNA oligomers have been prepared using the phos-phoramidite monomer derived from 6-trifluoromethylpurine ribonucleoside as potential inhibitors of adenosine deaminase. The presence of the modification was destabilising in an RNA duplex, equivalent to an A-A mismatch. 

Deaza- and aza-analogues of guanosine have been examined primarily in hybridisation and primer extension studies. 1-Deaza-dG incorporated into ODN duplexes exhibited no preference for pairing with the natural nucleotides, and was more destabilising than a mismatch. In primer extension reactions it preferentially formed pairs with The importance of hydrogen bond... 

---