title: Calorimetric and Spectroscopic Analysis of the Thermal Stability of Short Duplex DNA-Containing Sugar and Base-Modified Nucleotides.
abstract: Base- and sugar-modified analogs of DNA and RNA are finding ever expanding use in medicine and biotechnology as tools to better tailor structured oligonucleotides by altering their thermal stability, nuclease resistance, base-pairing specificity, antisense activity, or cellular uptake. Proper deployment of these chemical modifications generally requires knowledge of how each affects base-pairing properties and thermal stabilities. Here, we describe in detail how differential scanning calorimetry and UV spectroscopy may be used to quantify the melting thermodynamics of short dsDNA containing chemically modified nucleosides in one or both strands. Insights are provided into why and how the presence of highly stable base pairs containing modified nucleosides can alter the nature of calorimetry or melting spectroscopy data, and how each experiment must therefore be conducted to ensure high-quality melting thermodynamics data are obtained. Strengths and weaknesses of the two methods when applied to chemically modified duplexes are also addressed.
authors.affiliation: Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Kareem
authors.initials: K
authors.lastname: Fakhfakh
authors.affiliation: Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Curtis B
authors.initials: CB
authors.lastname: Hughesman
authors.affiliation: Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: A
authors.initials: A
authors.lastname: Louise Creagh
authors.affiliation: Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Vincent
authors.initials: V
authors.lastname: Kao
authors.affiliation: Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada; RES'EAU Water Research Network, Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada. Electronic address: israels@chbe.ubc.ca.
authors.forename: Charles
authors.initials: C
authors.lastname: Haynes
mesh_terms: D002152:Calorimetry, Differential Scanning; D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D009711:Nucleotides; D009841:Oligonucleotides; D004247:DNA
keywords: DNA; DNA melting thermodynamics; Differential scanning calorimetry; Locked nucleic acid; UV spectroscopy