title: The enhancement of PCR amplification by low molecular weight amides.
abstract: Amplification of a DNA target by the polymerase chain reaction (PCR) often requires laborious optimization efforts. In this regard, the use of certain organic chemicals such as dimethyl sulfoxide, polyethylene glycol, betaine and formamide as cosolvents has been found to be very helpful. Unfortunately, very little is known about the precise structural features that make these additives effective and, accordingly, the number of such chemicals currently known to enhance PCR is limited. In order to address these issues, we decided to focus on formamide and undertook an extensive study of low molecular weight amides as a class to see how changing the substituents in the amide structure influences its effect on PCR. We describe here the results of this study, which involved 11 different amides, and present observations that provide a cohesive picture of structure-activity relations in this group of additives. We found several of these amides to be exceptionally effective and introduce them as novel PCR enhancers.
authors.affiliation: Department of Chemistry, Princeton University, Princeton, NJ 08544, USA. rajchak@princeton.edu
authors.forename: R
authors.initials: R
authors.lastname: Chakrabarti
authors.forename: C E
authors.initials: CE
authors.lastname: Schutt
mesh_terms: D000081:Acetamides / Q000737:chemistry / Q000494:pharmacology; D000577:Amides / Q000737:chemistry* / Q000494:pharmacology; D000818:Animals; D002417:Cattle; D004247:DNA / Q000737:chemistry / Q000187:drug effects / Q000235:genetics*; D018076:DNA, Complementary / Q000737:chemistry / Q000187:drug effects / Q000235:genetics; D004121:Dimethyl Sulfoxide / Q000737:chemistry / Q000494:pharmacology; D005559:Formamides / Q000737:chemistry / Q000494:pharmacology; D006801:Humans; D008970:Molecular Weight; D009419:Nerve Tissue Proteins / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods*; D016755:Proto-Oncogene Proteins c-jun / Q000235:genetics; D011760:Pyrrolidinones / Q000737:chemistry / Q000494:pharmacology; D013329:Structure-Activity Relationship; D051317:Wiskott-Aldrich Syndrome Protein, Neuronal
chemical_list: D000081:Acetamides; D000577:Amides; D018076:DNA, Complementary; D005559:Formamides; D009419:Nerve Tissue Proteins; D016755:Proto-Oncogene Proteins c-jun; D011760:Pyrrolidinones; C495771:WASL protein, human; D051317:Wiskott-Aldrich Syndrome Protein, Neuronal; C031066:formamide; C030686:acetamide; D004247:DNA; C028537:2-pyrrolidone; D004121:Dimethyl Sulfoxide