Effects of trimethylamine N-oxide and urea on DNA duplex and G-quadruplex

References

• Minton AP. Molecular crowding: analysis of effects of high concentrations of inert cosolutes on biochemical equilibria and rates in terms of volume exclusion. Methods Enzymol. 1998;295:127–149.
   Google Scholar
• Zimmerman SB, Minton AP. Macromolecular crowding: biochemical, biophysical, and physiological consequences. Annu Rev Biophys Biomol Struct. 1993;22:27–65.10.1146/annurev.bb.22.060193.000331
   PubMedGoogle Scholar
• Minton AP. The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J Biol Chem. 2001;276:10577–10580.10.1074/jbc.R100005200
   PubMed Web of Science ®Google Scholar
• Yancey PH, Clark ME, Hand SC, et al. Living with water stress: evolution of osmolyte systems. Science. 1982;217:1214–1222.10.1126/science.7112124
   PubMed Web of Science ®Google Scholar
• Sakamoto A, Murata N. The role of glycine betaine in the protection of plants from stress: clues from transgenic plants. Plant Cell Environ. 2002;25:163–171.
   PubMed Web of Science ®Google Scholar
• Yancey PH. Organic osmolytes as compatible, metabolic and counteracting cytoprotectants in high osmolarity and other stresses. J Exp Biol. 2005;208:2819–2830.10.1242/jeb.01730
   PubMed Web of Science ®Google Scholar
• Yancey PH, Siebenaller JF. Co-evolution of proteins and solutions: protein adaptation versus cytoprotective micromolecules and their roles in marine organisms. J Exp Biol. 2015;218:1880–1896.10.1242/jeb.114355
   PubMed Web of Science ®Google Scholar
• Lin TY, Timasheff SN. Why do some organisms use a urea-methylamine mixture as osmolyte? Thermodynamic compensation of urea and trimethylamine N-oxide interactions with protein. Biochemistry. 1994;33:12695–12701.
   Google Scholar
• Canchi DR, García AE. Cosolvent effects on protein stability Annu. Rev Phys Chem. 2013;64:273–293.10.1146/annurev-physchem-040412-110156
   PubMed Web of Science ®Google Scholar
• Treberg JR, Driedzic WR. Maintenance and accumulation of trimethylamine oxide by winter skate (Leucoraja ocellata): reliance on low whole animal losses rather than synthesis. Am J Physiol. 2006;291:R1790–8.
   Web of Science ®Google Scholar
• Forster RP, Goldstein L. Intracellular osmoregulatory role of amino acids and urea in marine elasmobranchs. Am J Physiol. 1976;230:925–931.
   PubMed Web of Science ®Google Scholar
• Seibel BA, Walsh PJ. Trimethylamine oxide accumulation in marine animals: relationship to acylglycerol storage. J Exp Biol. 2002;205:297–306.
   PubMed Web of Science ®Google Scholar
• Cayley S, Record MT Jr. Roles of cytoplasmic osmolytes, water, and crowding in the response of Escherichia coli to osmotic stress: biophysical basis of osmoprotection by glycine betaine. Biochemistry. 2003;42:12596–12609.10.1021/bi0347297
   PubMed Web of Science ®Google Scholar
• Sarma R, Paul S. Exploring the molecular mechanism of trimethylamine- N -oxide’s ability to counteract the protein denaturing effects of urea. J Phys Chem B. 2013;117:5691–5704.10.1021/jp401750v
   PubMed Web of Science ®Google Scholar
• Barone G, Del Vecchio P, Esposito D, et al. Effect of osmoregulatory solutes on the thermal stability of calf-thymus DNA. J Chem Soc Faraday Trans. 1996;92:1361–1367.10.1039/ft9969201361
   Google Scholar
• Rees WA, Yager TD, Korte J, et al. Betaine can eliminate the base pair composition dependence of DNA melting. Biochemistry. 1993;32:137–144.10.1021/bi00052a019
   PubMed Web of Science ®Google Scholar
• Aslanyan VM, Babayan YS, Arutyunyan SG. Conformation and thermal stability of DNA in aqueous urea solutions. Biophysics. 1984;29:410–414.
   Google Scholar
• Gluick TC, Yadav S. Trimethylamine N -oxide stabilizes RNA tertiary structure and attenuates the denaturating effects of urea. J Am Chem Soc. 2003;125:4418–4419.10.1021/ja0292997
   PubMed Web of Science ®Google Scholar
• Gluick TC, Wills NM, Gesteland RF, et al. Folding of an mRNA pseudoknot required for stop codon readthrough: effects of mono- and divalent ions on stability. Biochemistry. 1997;36:16173–16186.10.1021/bi971362v
   PubMed Web of Science ®Google Scholar
• Schwinefus JJ, Kuprian MJ, Lamppa JW, et al. Human telomerase RNA pseudoknot and hairpin thermal stability with glycine betaine and urea: preferential interactions with RNA secondary and tertiary structures. Biochemistry. 2007;46:9068–9079.10.1021/bi602637v
   PubMed Web of Science ®Google Scholar
• Lambert D, Draper DE. Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg2+ interactions. J Mol Biol. 2007;370:993–1005.10.1016/j.jmb.2007.03.080
   PubMed Web of Science ®Google Scholar
• Schwinefus JJ, Menssen RJ, Kohler JM, et al. Quantifying the temperature dependence of glycine—betaine RNA duplex destabilization. Biochemistry. 2013;52:9339–9346.10.1021/bi400765d
   PubMed Web of Science ®Google Scholar
• Phan AT, Kuryavyi V, Luu KN, et al. Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution. Nucleic Acids Res. 2007;35:6517–6525.10.1093/nar/gkm706
   PubMed Web of Science ®Google Scholar
• Sugimoto N, Nakano M, Nakano S. Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes. Biochemistry. 2000;39:11270–11281.10.1021/bi000819p
   PubMed Web of Science ®Google Scholar
• Ohmichi T, Nakano S, Miyoshi D, et al. Long RNA dangling end has large energetic contribution to duplex stability. J Am Chem Soc. 2002;124:10367–10372.10.1021/ja0255406
   PubMed Web of Science ®Google Scholar
• Sugimoto N, Nakano S, Katoh M, et al. Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry. 1995;34:11211–11216.
   Google Scholar
• Nakano S, Fujimoto M, Hara H, et al. Nucleic acid duplex stability: influence of base composition on cation effects. Nucleic Acids Res. 1999;27:2957–2965.10.1093/nar/27.14.2957
   Google Scholar
• Goobes R, Kahana N, Cohen O, et al. Metabolic buffering exerted by macromolecular crowding on DNA-DNA interactions: origin and physiological significance. Biochemistry. 2003;42:2431–2440.10.1021/bi026775x
   PubMed Web of Science ®Google Scholar
• Gabelica V, Maeda R, Fujimoto T, et al. Multiple and cooperative binding of fluorescence light-up probe thioflavin T with human telomere DNA G-quadruplex. Biochemistry. 2013;52:5620–5628.10.1021/bi4006072
   PubMed Web of Science ®Google Scholar
• Nakano S, Miyoshi D, Sugimoto N. Effects of molecular crowding on the structures, interactions, and functions of nucleic acids. Chem Rev. 2014;114:2733–2758.
   PubMed Web of Science ®Google Scholar
• Bloomfield VA, Crothers DM and Tinoco Jr I. Nucleic acids: structures, properties, and functions (University Science Books) Chapter 6; p. 190–196.
   Google Scholar
• Dai J, Dexheimer TS, Chen D, et al. An Intramolecular G-quadruplex structure with mixed parallel/antiparallel G-strands formed in the human BCL-2 promoter region in solution. J Am Chem Soc. 2006;128:1096–1098.10.1021/ja055636a
   PubMed Web of Science ®Google Scholar
• Miyoshi D, Nakamura K, Tateishi-Karimata H, et al. Hydration of Watson−Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions. J Am Chem Soc. 2009;131:3522–3531.10.1021/ja805972a
   PubMed Web of Science ®Google Scholar
• Miyoshi D, Karimata H, Sugimoto N. Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions. J Am Chem Soc. 2006;128:7957–7963.10.1021/ja061267m
   PubMed Web of Science ®Google Scholar
• Hua L, Zhou R, Thirumalai D, et al. Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding. Proc Natl Sci USA. 2008;105:16928–16933.10.1073/pnas.0808427105
   PubMed Web of Science ®Google Scholar
• Nakano S, Karimata H, Ohmichi T, et al. The effect of molecular crowding with nucleotide length and cosolute structure on DNA duplex stability. J Am Chem Soc. 2004;126:14330–14331.10.1021/ja0463029
   PubMed Web of Science ®Google Scholar
• Dong Q, Stellwagen E, Stellwagen NC. Monovalent cation binding in the minor groove of DNA A-tracts. Biochemistry. 2009;48:1047–1055.10.1021/bi8020718
   PubMed Web of Science ®Google Scholar
• Holmstrom ED, Dupuis NF, Nesbitt DJ. Kinetic and thermodynamic origins of osmolyte-influenced nucleic acid folding. J Phys Chem B. 2015;119:3687–3696.10.1021/jp512491n
   PubMed Web of Science ®Google Scholar
• Tateishi-Karimata H, Sugimoto N. A-T base pairs are more stable than G-C base pairs in a hydrated ionic liquid. Angew Chem Int Engl. 2012;51:1416–1419.
   PubMed Web of Science ®Google Scholar
• Nakano M, Tateishi-Karimata H, Tanaka S, et al. Choline ion interactions with DNA atoms explain unique stabilization of A–T base pairs in DNA duplexes: a microscopic view. J Phys Chem B. 2014;118:379–389.10.1021/jp406647b
   PubMed Web of Science ®Google Scholar
• Hud NV, Sklenář V, Feigon J. Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending. J Mol Biol. 1999;286:651–660.10.1006/jmbi.1998.2513
   PubMed Web of Science ®Google Scholar
• Dong Q, Stellwagen E, Stellwagen NC. Monovalent cation binding in the minor groove of DNA A-tracts. Biochemistry. 2009;48:1047–1055.10.1021/bi8020718
   PubMed Web of Science ®Google Scholar