Locked nucleic acids (LNA; symbols of bases, +A, +C, +G, and +T) are introduced into chemically synthesized oligonucleotides to increase duplex stability and specificity. To understand these effects, we have determined thermodynamic parameters of consecutive LNA nucleotides. We present guidelines for the design of LNA oligonucleotides and introduce free online software that predicts the stability of any LNA duplex oligomer.
View Article and Find Full Text PDFModern real-time PCR systems make it easy to monitor fluorescence while temperature is varied for hundreds of samples in parallel, permitting high-throughput studies. We employed such system to investigate melting transitions of ordered nucleic acid structures into disordered random coils. Fluorescent dye and quencher were attached to oligonucleotides in such a way that changes of fluorescence intensity with temperature indicated progression of denaturation.
View Article and Find Full Text PDFDNA 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.
View Article and Find Full Text PDFSynthetic oligodeoxynucleotides are widely used in many biological, biochemical and biophysical applications. The concentration, composition and structure of DNA are often determined from its ultraviolet spectrum. Although parameters for use with the nearest-neighbor model for prediction of extinction coefficients of single stranded DNAs at 260 nm were published some time ago, similar parameters for other wavelengths or for use with DNA duplexes have not been reported.
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