The stability of DNA duplexes is dependent on a complex array of hydrogen bonding among amino and carbonyl groups of the heteroaromatic bases and surrounding water molecules, as well as base stacking interactions. Duplex stability can be significantly increased by adding a further hydrogen bond to a base pair, for example by modifying the regular A-T base pair containing two hydrogen bonds with the 2-amino-A-T base pair containing three hydrogen bonds. Another popular strategy is to use a hydrophobic natural or unnatural modification to displace water molecules from the duplex to generate a stabilizing effect. Examples of this strategy are the use of 5-Me-dC or 5-propynyl-dU. With three hydrogen bonds, the C-G base pair has a big effect on duplex stability. A strategy to normalize the effects of C-G and A-T base pairing is to destabilize the C-G base pair to the same strength as the A-T base pair by partially blocking one hydrogen bond using N4-Et-C.
Glen Research offers a wide range of products for research in selective duplex stabilization.
New cap structures allow for the preparation of hybridization probes with increased affinity for complementary sequences.
An elegant way of circumventing inaccuracies due to differences in GC content would be to use a modified base that normalized the stability of the GC and AT base pairs.
Oligonucleotides containing LNA exhibit unprecedented thermal stabilities towards complementary DNA and RNA, which allows excellent mismatch discrimination.
The design of primers is frequently complicated by the degeneracy of the genetic code. Three strategies are now available to confront this problem: Mixed base addition, 2'-deoxyInosine or 2'-deoxyNebularine and a universal nucleoside,