Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures

R Owczarzy, Y You, BG Moreira, JA Manthey… - Biochemistry, 2004 - ACS Publications
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 …

Predicting stability of DNA duplexes in solutions containing magnesium and monovalent cations

R Owczarzy, BG Moreira, Y You, MA Behlke… - Biochemistry, 2008 - ACS Publications
Accurate predictions of DNA stability in physiological and enzyme buffers are important for
the design of many biological and biochemical assays. We therefore investigated the effects …

Predicting sequence‐dependent melting stability of short duplex DNA oligomers

R Owczarzy, PM Vallone, FJ Gallo… - Biopolymers …, 1997 - Wiley Online Library
Many important applications of DNA sequence‐dependent hybridization reactions have
recently emerged. This has sparked a renewed interest in analytical calculations of …

Melting temperatures of nucleic acids: discrepancies in analysis

R Owczarzy - Biophysical Chemistry, 2005 - Elsevier
Melting temperature, Tm, is an important property of nucleic acid duplexes. It is typically
determined from spectroscopic or calorimetric melting experiments. More than one analytical …

Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation

P Wu, S Nakano, N Sugimoto - European journal of …, 2002 - Wiley Online Library
A clear difference in the enthalpy changes derived from spectroscopic and calorimetric
measurements has recently been shown. The exact interpretation of this deviation varied …

Improved nearest-neighbor parameters for predicting DNA duplex stability

J SantaLucia, HT Allawi, PA Seneviratne - Biochemistry, 1996 - ACS Publications
Thermodynamic data were determined from UV absorbance vs temperature profiles of 23
oligonucleotides. These data were combined with data from the literature for 21 sequences …

Thermal stability of PNA/DNA and DNA/DNA duplexes by differential scanning calorimetry

MC Chakrabarti, FP Schwarz - Nucleic acids research, 1999 - academic.oup.com
Thermodynamics of the thermal dissociation transitions of 10 bp PNA/DNA duplexes and
their corresponding DNA/DNA duplexes in 10 mM sodium phosphate buffer (pH 7.0) were …

Sequence-dependent thermodynamic parameters for locked nucleic acid (LNA)− DNA duplex formation

PM McTigue, RJ Peterson, JD Kahn - Biochemistry, 2004 - ACS Publications
The design of modified nucleic acid probes, primers, and therapeutics is improved by
considering their thermodynamics. Locked nucleic acid (LNA) is one of the most useful …

Optical melting of 128 octamer DNA duplexes: effects of base pair location and nearest neighbors on thermal stability

MJ Doktycz, MD Morris, SJ Dormady, KL Beattie… - Journal of Biological …, 1995 - ASBMB
The use of short oligonucleotide probes is finding increased application in DNA sequencing
and genome characterization techniques, but a lack of knowledge of the hybridization …

Effects of hydration, ion release, and excluded volume on the melting of triplex and duplex DNA

CH Spink, JB Chaires - Biochemistry, 1999 - ACS Publications
The stability of DNA duplex and triplex structures not only depends on molecular forces such
as base pairing or tripling or electrostatic interactions but also is sensitive to its aqueous …