Tm and Biophysics


This bibliography contains a list of research papers published by IDT scientists (bold). Click on the reference to read the PubMed abstract, or entire paper, if published in an open access journal. Otherwise, you will be able to obtain a PDF download of the paper through the PubMed site.

  1. Owczarzy R, You Y, Groth CL, Tataurov AV. (2011) Stability and mismatch discrimination of locked nucleic acid-DNA duplexes. Biochem, 50(43):9352–9367..
    New nearest-neighbor parameters correctly forecast the positive and negative effects of LNAs on mismatch discrimination. Specificity is enhanced in a majority of sequences and is dependent on mismatch type and adjacent base pairs.
  2. You Y, Tataurov AV, Owczarzy R. (2011) Measuring thermodynamic details of DNA hybridization using fluorescence. Biopolymers, 95(7):472–486.
  3. Owczarzy R, Moreira BG, You Y, Behlke MA, Walder JA. (2008) Predicting stability of DNA duplexes in solutions containing magnesium and monovalent cations. Biochem, 47:5336–5353.
  4. Tataurov AV, You Y, Owczarzy R. (2008) Predicting ultraviolet spectrum of single stranded and double stranded deoxyribonucleic acids. Biophys Chem, 133(1):66–70.
  5. Owczarzy R, Tataurov AV, Wu Y, Manthey JA, McQuisten KA, Almabrazi HG, Pedersen KF, Lin Y, Garretson J, McEntaggart NO, Sailor CA, Dawson RB, Peek AS. (2006) IDT SciTools: a suite for analysis and design of nucleic acid oligomers. Nucleic Acids Res, 36:W163–169.
  6. You Y, Moreira BG, Behlke MA, Owczarzy R. (2006) Design of LNA probes that improve mismatch discrimination.. Nucleic Acids Res, 34(8):e60.
    New guidelines are suggested for design of LNA probes [also relevant to design of BNA probes], which significantly improve mismatch discrimination in comparison with unmodified DNA probes.
  7. Owczarzy R. (2005) Melting temperatures of nucleic acids: discrepancies in analysis. Biophys Chem, 117(3):105–113.
  8. Moreira BG, You Y, Behlke MA, Owczarzy R. (2005) Effects of fluroescent dyes, quenchers, and dangling ends on DNA duplex stability. Biochem Biophys Res Comm, 327:473–484.
  9. Owczarzy R, You Y, Moreira BG, Manthey JA, Huang L, Behlke MA, Walder JA. (2004) Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. Biochem, 43(12):3537–3554.
  10. Owczarzy R, Dunietz I, Behlke MA, Klotz IM, Walder JA. (2003) Thermodynamic treatment of oligonucleotide duplex-simplex equilibria. Proc Natl Acad Sci USA, 100(25):14840–14845.
  11. Owczarzy R. (2001) Comments on "Calculation of the Energy of Transition Associated with Inversion in Double-Stranded DNA" [P.Aggarwal, D. Dollimore, Thermochim. Acta 284 (1996) 109]: a test. Thermochimica Acta, 373(2):153–160.