The performance of Betaine Enhancer Solution is superior compared to standard enhancers such as formamide, DMSO, TMAC, BSA and non-ionic detergents because of the following effects: Betaine binds preferentially to AT rich sequences in the major groove, thereby stabilizing AT rich regions of the DNA. Because AT forms 2 hydrogen bonds and GC forms 3, the bonding of AT is less stable than the one of GC. As a consequence of the stabilizing effect of Betaine on AT bonding, the stability of AT bonding and GC bonding is brought close to an equal level.

At the same time, Betaine has a sequence independent destabilizing effect on all DNA. The Tm of AT rich and GC rich sequences are equalized and the overall Tm is lowered.

Furthermore, Betaine aids the process of thermostable polymerases and reduces pauses in polymerization caused by secondary structure that can induce the polymerase to disassociate from the DNA strand.