Oligonucleotide melting temperatures under PCR conditions: nearest-neighbor corrections for Mg(2+), deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas

Abstract

Background: Many techniques in molecular biology depend on the oligonucleotide melting temperature (T(m)), and several formulas have been developed to estimate T(m). Nearest-neighbor (N-N) models provide the highest accuracy for T(m) prediction, but it is not clear how to adjust these models for the effects of reagents commonly used in PCR, such as Mg(2+), deoxynucleotide triphosphates (dNTPs), and dimethyl sulfoxide (DMSO).

Methods: The experimental T(m)s of 475 matched or mismatched target/probe duplexes were obtained in our laboratories or were compiled from the literature based on studies using the same real-time PCR platform. This data set was used to evaluate the contributions of [Mg(2+)], [dNTPs], and [DMSO] in N-N calculations. In addition, best-fit coefficients for common empirical formulas based on GC content, length, and the equivalent sodium ion concentration of cations [Na(+)(eq)] were obtained by multiple regression.

Results: When we used [Na(+)(eq)] = [Monovalent cations] + 120(square root of ([Mg2+]-[dNTPs])) (the concentrations in this formula are mmol/L) to correct DeltaS(0) and a DMSO term of 0.75 degrees C (%DMSO), the SE of the N-N T(m) estimate was 1.76 degrees C for perfectly matched duplexes (n = 217). Alternatively, the empirical formula T(m) ( degrees C) = 77.1 degrees C + 11.7 x log[Na(+)(eq)] + 0.41(%GC) - 528/bp - 0.75 degrees C(%DMSO) gave a slightly higher SE of 1.87 degrees C. When all duplexes (matched and mismatched; n = 475) were included in N-N calculations, the SE was 2.06 degrees C.

Conclusions: This robust model, accounting for the effects of Mg(2+), DMSO, and dNTPs on oligonucleotide T(m) in PCR, gives reliable T(m) predictions using thermodynamic N-N calculations or empirical formulas.