RESUMO
DNA and RNA oligomers are used in a myriad of diverse biological and biochemical experiments. These oligonucleotides are designed to have unique biophysical, chemical and hybridization properties. We have created an integrated set of bioinformatics tools that predict the properties of native and chemically modified nucleic acids and assist in their design. Researchers can select PCR primers, probes and antisense oligonucleotides, find the most suitable sequences for RNA interference, calculate stable secondary structures, and evaluate the potential for two sequences to interact. The latest, most accurate thermodynamic algorithms and models are implemented. This free software is available at http://www.idtdna.com/SciTools/SciTools.aspx.
Assuntos
Oligonucleotídeos/química , Software , Primers do DNA/química , Internet , Conformação de Ácido Nucleico , Sondas de Oligonucleotídeos/química , Oligonucleotídeos Antissenso/química , RNA Interferente Pequeno/químicaRESUMO
Melting temperatures, T(m), were systematically studied for a set of 92 DNA duplex oligomers in a variety of sodium ion concentrations ranging from 69 mM to 1.02 M. The relationship between T(m) and ln [Na(+)] was nonlinear over this range of sodium ion concentrations, and the observed melting temperatures were poorly predicted by existing algorithms. A new empirical relationship was derived from UV melting data that employs a quadratic function, which better models the melting temperatures of DNA duplex oligomers as sodium ion concentration is varied. Statistical analysis shows that this improved salt correction is significantly more accurate than previously suggested algorithms and predicts salt-corrected melting temperatures with an average error of only 1.6 degrees C when tested against an independent validation set of T(m) measurements obtained from the literature. Differential scanning calorimetry studies demonstrate that this T(m) salt correction is insensitive to DNA concentration. The T(m) salt correction function was found to be sequence-dependent and varied with the fraction of G.C base pairs, in agreement with previous studies of genomic and polymeric DNAs. The salt correction function is independent of oligomer length, suggesting that end-fraying and other end effects have little influence on the amount of sodium counterions released during duplex melting. The results are discussed in the context of counterion condensation theory.
