title: Can A Denaturant Stabilize DNA? Pyridine Reverses DNA Denaturation in Acidic pH.
abstract: The stability of DNA is highly dependent on the properties of the surrounding solvent, such as ionic strength, pH, and the presence of denaturants and osmolytes. Addition of pyridine is known to unfold DNA by replacing π-π stacking interactions between bases, stabilizing conformations in which the nucleotides are solvent exposed. We show here experimental and theoretical evidences that pyridine can change its role and in fact stabilize the DNA under acidic conditions. NMR spectroscopy and MD simulations demonstrate that the reversal in the denaturing role of pyridine is specific, and is related to its character as pseudo groove binder. The present study sheds light on the nature of DNA stability and on the relationship between DNA and solvent, with clear biotechnological implications.
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), Joint BSC-IRB Research Program in Computational Biology, Barcelona (Spain).|Department of Chemistry, University of Cambridge, Cambridge CB2 1EW (UK).
authors.forename: Guillem
authors.initials: G
authors.lastname: Portella
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), Joint BSC-IRB Research Program in Computational Biology, Barcelona (Spain).
authors.forename: Montserrat
authors.initials: M
authors.lastname: Terrazas
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), Joint BSC-IRB Research Program in Computational Biology, Barcelona (Spain).|Barcelona Supercomputing Center, Barcelona (Spain).
authors.forename: Núria
authors.initials: N
authors.lastname: Villegas
authors.affiliation: Instituto de Química Física Rocasolano, CSIC, Madrid (Spain).
authors.forename: Carlos
authors.initials: C
authors.lastname: González
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), Joint BSC-IRB Research Program in Computational Biology, Barcelona (Spain). modesto.orozco@irbbarcelona.org.|Department of Biochemistry and Molecular Biology, University of Barcelona (Spain). modesto.orozco@irbbarcelona.org.
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
mesh_terms: D000143:Acids / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D056004:Molecular Dynamics Simulation; D009691:Nucleic Acid Denaturation; D011725:Pyridines / Q000737:chemistry*
chemical_list: D000143:Acids; D011725:Pyridines; D004247:DNA; C023666:pyridine
keywords: NMR spectroscopy; denaturant; ion-DNA interactions; molecular dynamics; nucleic acid thermodynamics