Quantitative experimental determination of primer-dimer formation risk by free-solution conjugate electrophoresis.

ABSTRACT: DNA barcodes are short, unique ssDNA primers that "mark" individual biomolecules. To gain better understanding of biophysical parameters constraining primer-dimer formation between primers that incorporate barcode sequences, we have developed a capillary electrophoresis method that utilizes drag-tag-DNA conjugates to quantify dimerization risk between primer-barcode pairs. Results obtained with this unique free-solution conjugate electrophoresis approach are useful as quantitatively precise input data to parameterize computation models of dimerization risk. A set of fluorescently labeled, model primer-barcode conjugates were designed with complementary regions of differing lengths to quantify heterodimerization as a function of temperature. Primer-dimer cases comprised two 30-mer primers,

SUBMITTER: Desmarais SM 

PROVIDER: S-EPMC3416024 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature