Effects of cytosine hydroxymethylation on DNA strand separation

Biophysical Journal

Volumn 104, Issue 1, 2013, Pages 208-215

  Severin, Philip M D ^a   Zou, Xueqing ^b   Schulten, Klaus ^b,c   Gaub, Hermann E ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c University of Illinois at Urbana Champaign   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DNA;

ARTICLE; BIOMECHANICS; DNA METHYLATION; FLUORESCENCE; HYDROXYLATION; METABOLISM; MOLECULAR DYNAMICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; BIOMECHANICS; CYTOSINE; DNA; DNA METHYLATION; FLUORESCENCE; HYDROXYLATION; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA;

EID: 84872166103     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2012.11.013     Document Type: Article

References (55)

1. P.A. Jones, and D. Takai The role of DNA methylation in mammalian epigenetics Science 293 2001 1068 1070 (Pubitemid 32758075)
2. R. Jaenisch, and A. Bird Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals Nat. Genet. 33 Suppl 2003 245 254 (Pubitemid 36278835)
3. P.A. Jones DNA methylation and cancer Oncogene 21 2002 5358 5360 (Pubitemid 34983472)
4. R. Straussman, and D. Nejman H. Cedar Developmental programming of CpG island methylation profiles in the human genome Nat. Struct. Mol. Biol. 16 2009 564 571
5. A. Rottach, H. Leonhardt, and F. Spada DNA methylation-mediated epigenetic control J. Cell. Biochem. 108 2009 43 51
6. R.E. Thurman, and E. Rynes J.A. Stamatoyannopoulos The accessible chromatin landscape of the human genome Nature 489 2012 75 82
7. M. Tahiliani, and K.P. Koh A. Rao Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1 Science 324 2009 930 935
8. S. Kriaucionis, and N. Heintz The nuclear DNA base 5- hydroxymethylcytosine is present in Purkinje neurons and the brain Science 324 2009 929 930
9. M. Münzel, and D. Globisch T. Carell Quantification of the sixth DNA base hydroxymethylcytosine in the brain Angew. Chem. Int. Ed. Engl. 49 2010 5375 5377
10. M. Münzel, D. Globisch, and T. Carell 5-Hydroxymethylcytosine, the sixth base of the genome Angew. Chem. Int. Ed. Engl. 50 2011 6460 6468
11. M. Ko, and Y. Huang A. Rao Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2 Nature 468 2010 839 843
12. S. Ito, and A.C. D'Alessio Y. Zhang Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification Nature 466 2010 1129 1133
13. K. Iqbal, and S.-G. Jin P.E. Szabó Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine Proc. Natl. Acad. Sci. USA 108 2011 3642 3647
14. H. Wu, and Y. Zhang Tet1 and 5-hydroxymethylation: a genome-wide view in mouse embryonic stem cells Cell Cycle 10 2011 2428 2436
15. D. Schübeler Molecular biology. Epigenetic islands in a genetic ocean Science 338 2012 756 757
16. V. Valinluck, and H.-H. Tsai L.C. Sowers Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2) Nucleic Acids Res. 32 2004 4100 4108 (Pubitemid 39232282)
17. S.G. Jin, S. Kadam, and G.P. Pfeifer Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine Nucleic Acids Res. 38 2010 e125
18. N.W. Penn, and R. Suwalski R. Yura The presence of 5- hydroxymethylcytosine in animal deoxyribonucleic acid Biochem. J. 126 1972 781 790
19. A. Szwagierczak, and S. Bultmann H. Leonhardt Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA Nucleic Acids Res. 38 2010 e181
20. J. Feng, and Y. Zhou G. Fan Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons Nat. Neurosci. 13 2010 423 430
21. A.B. Robertson, and J.A. Dahl A. Klungland A novel method for the efficient and selective identification of 5-hydroxymethylcytosine in genomic DNA Nucleic Acids Res. 39 2011 e55
22. M. Wanunu, and D. Cohen-Karni M. Drndic Discrimination of methylcytosine from hydroxymethylcytosine in DNA molecules J. Am. Chem. Soc. 133 2011 486 492
23. 31P-NMR study Eur. J. Biochem. 229 1995 445 454
24. T.K. Wojdacz, A. Dobrovic, and L.L. Hansen Methylation-sensitive high-resolution melting Nat. Protoc. 3 2008 1903 1908
25. C. Bustamante, and Y.R. Chemla D. Izhaky Mechanical processes in biochemistry Annu. Rev. Biochem. 73 2004 705 748 (Pubitemid 39050384)
26. C. Prévost, M. Takahashi, and R. Lavery Deforming DNA: from physics to biology ChemPhysChem 10 2009 1399 1404
27. G.M.T. Cheetham, and T.A. Steitz Insights into transcription: structure and function of single-subunit DNA-dependent RNA polymerases Curr. Opin. Struct. Biol. 10 2000 117 123 (Pubitemid 30099336)
28. M.E. Hogan, and R.H. Austin Importance of DNA stiffness in protein-DNA binding specificity Nature 329 1987 263 266 (Pubitemid 17128973)
29. M.A. Young, and G. Ravishanker H.M. Berman Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes Biophys. J. 68 1995 2454 2468
30. M. de la Mata, and C.R. Alonso A.R. Kornblihtt A slow RNA polymerase II affects alternative splicing in vivo Mol. Cell 12 2003 525 532 (Pubitemid 37238937)
31. S. Shukla, and E. Kavak S. Oberdoerffer CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing Nature 479 2011 74 79
32. P.M. Severin, and X. Zou K. Schulten Cytosine methylation alters DNA mechanical properties Nucleic Acids Res. 39 2011 8740 8751
33. P.M. Severin, D. Ho, and H.E. Gaub A high throughput molecular force assay for protein-DNA interactions Lab Chip 11 2011 856 862
34. T. Strunz, and K. Oroszlan H.J. Güntherodt Dynamic force spectroscopy of single DNA molecules Proc. Natl. Acad. Sci. USA 96 1999 11277 11282 (Pubitemid 29487371)
35. C.H. Albrecht, H. Clausen-Schaumann, and H.E. Gaub Differential analysis of biomolecular rupture forces J. Phys. Condens. Matter 18 2006 81 99
36. D. Ho, and C. Dose H.E. Gaub Quantitative detection of small molecule/DNA complexes employing a force-based and label-free DNA-microarray Biophys. J. 96 2009 4661 4671
37. X.J. Lu, and W.K. Olson 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures Nucleic Acids Res. 31 2003 5108 5121 (Pubitemid 37441878)
38. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 33 38 27-28 (Pubitemid 26152973)
39. N. Foloppe, and A.D. MacKerell Jr. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data J. Comput. Chem. 21 2000 86 104
40. J.C. Phillips, and R. Braun K. Schulten Scalable molecular dynamics with NAMD J. Comput. Chem. 26 2005 1781 1802 (Pubitemid 43078511)
41. W.L. Jorgensen, and J. Chandrasekhar M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
42. G.J. Martyna, D.J. Tobias, and M.L. Klein Constant pressure molecular dynamics algorithms J. Chem. Phys. 101 1994 4177 4189
43. S.E. Feller, and Y. Zhang B.R. Brooks Constant pressure molecular dynamics simulation: the Langevin piston method J. Chem. Phys. 103 1995 4613 4621
44. M.B. Viani, and T.E. Schäffer P.K. Hansma Small cantilevers for force spectroscopy of single molecules J. Appl. Physiol. 86 1999 2258 2262 (Pubitemid 129562220)
45. S.-H. Chou, and K.-H. Chin Zipper-like Watson-Crick base-pairs J. Mol. Biol. 312 2001 753 768 (Pubitemid 33116739)
46. M. Sotomayor, and K. Schulten Single-molecule experiments in vitro and in silico Science 316 2007 1144 1148 (Pubitemid 46877468)
47. E.H. Lee, and J. Hsin K. Schulten Discovery through the computational microscope Structure 17 2009 1295 1306
48. R. Lohikoski, J. Timonen, and A. Laaksonen Molecular dynamics simulation of single DNA stretching reveals a novel structure Chem. Phys. Lett. 407 2005 23 29 (Pubitemid 40584079)
49. M. Santosh, and P.K. Maiti Force-induced DNA melting J. Phys. Condens. Matter 21 2009 034113
50. A. Balaeff, S.L. Craig, and D.N. Beratan B-DNA to zip-DNA: simulating a DNA transition to a novel structure with enhanced charge-transport characteristics J. Phys. Chem. A 115 2011 9377 9391
51. S.B. Smith, Y. Cui, and C. Bustamante Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules Science 271 1996 795 799
52. C. Bustamante, and S.B. Smith D. Smith Single-molecule studies of DNA mechanics Curr. Opin. Struct. Biol. 10 2000 279 285 (Pubitemid 30333096)
53. W. Cheng, and S. Dumont C. Bustamante NS3 helicase actively separates RNA strands and senses sequence barriers ahead of the opening fork Proc. Natl. Acad. Sci. USA 104 2007 13954 13959 (Pubitemid 350003319)
54. S. Dumont, and W. Cheng C. Bustamante RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP Nature 439 2006 105 108 (Pubitemid 43053637)
55. D.S. Johnson, and L. Bai M.D. Wang Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase Cell 129 2007 1299 1309 (Pubitemid 46962089)