The enhancement of PCR amplification by low molecular-weight sulfones

DNA amplification by polymerase chain reaction (PCR) is frequently complica ted by the problems of low yield and specificity, especially when the GC co ntent of the target sequence is high. A common approach to the optimization of such reactions is the addition of small quantities of certain organic c hemicals, such as dimethylsulfoxide (DMSO), betaine, polyethylene glycol an d formamide, to the reaction mixture. Even in the presence of such additive s, however, the amplification of GC-rich templates is often ineffective. In this paper, we introduce a novel class of PCR-enhancing compounds, the low molecular-weight sulfones, that are effective in the optimization of high GC template amplification. We describe here the results of an extensive str ucture-activity investigation in which we studied the effects of a series o f six different sulfones on PCR amplification. We identify two sulfones, su lfolane and methyl sulfone, that are especially potent enhancers of high GC template amplification, and show that these compounds often outperform DMS O and betaine, two of the most effective PCR enhancers currently used. We c onclude with a brief discussion of the role that the sulfone functional gro up may play in such enhancement. (C) 2001 Elsevier Science B.V. All rights reserved.