Reaction Kinetics Study of Short DNA Strands Using a Maximum Entropy Method and Nonlinear Curve Fitting

Abstract

It is important to understand the formation of double-strand DNA (dsDNA) in a salt solution because it is one of the key reactions in life. A short cDNA strand pair was designed, and each single-strand DNA (ssDNA) was attached to a fluorescent dye that was either a donor or an acceptor of fluorescence resonance energy transfer. The fluorescence intensity was expected to change as time passed as the complementary pairs of ssDNAs formed dsDNAs. The concentration of dsDNA was theoretically calculated, and the measured data were consistent with theoretical results. The analysis of the nonlinear fitting method and the maximum entropy method detected that the reaction curve contains two major types of kinetics that likely represent the formation of dsDNA and mismatching.