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Volumn 1860, Issue 1, 2016, Pages 1-7

Effects of cytosine methylation on DNA morphology: An atomic force microscopy study

Author keywords

Atomic force microscopy (AFM); DNA methylation; Persistence length

Indexed keywords

CYTOSINE;

EID: 84973409278     PISSN: 03044165     EISSN: 18728006     Source Type: Journal    
DOI: 10.1016/j.bbagen.2015.10.006     Document Type: Article
Times cited : (23)

References (43)
  • 1
    • 0037372003 scopus 로고    scopus 로고
    • Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals
    • Jaenisch, R., Bird, A., Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet. 33:Suppl (2003), 245–254.
    • (2003) Nat. Genet. , vol.33 , pp. 245-254
    • Jaenisch, R.1    Bird, A.2
  • 2
    • 0027378582 scopus 로고
    • Role for DNA methylation in genomic imprinting
    • Li, E., Beard, C., Jaenisch, R., Role for DNA methylation in genomic imprinting. Nature 366 (1993), 362–365.
    • (1993) Nature , vol.366 , pp. 362-365
    • Li, E.1    Beard, C.2    Jaenisch, R.3
  • 3
    • 84874194072 scopus 로고    scopus 로고
    • DNA methylation: roles in mammalian development
    • Smith, Z., Meissner, A., DNA methylation: roles in mammalian development. Nat. Rev. Genet. 14 (2013), 204–220.
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 204-220
    • Smith, Z.1    Meissner, A.2
  • 5
    • 84886099830 scopus 로고    scopus 로고
    • Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer
    • Plass, C., Pfister, S., Lindroth, A., Bogatyrova, O., Claus, R., Lichter, P., Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer. Nat. Rev. Genet. 14 (2013), 765–780.
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 765-780
    • Plass, C.1    Pfister, S.2    Lindroth, A.3    Bogatyrova, O.4    Claus, R.5    Lichter, P.6
  • 7
    • 0031792779 scopus 로고    scopus 로고
    • Identification and characterization of a family of mammalian methyl-CpG binding proteins
    • Hendrich, B., Bird, A., Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol. Cell. Biol. 18 (1998), 6538–6547.
    • (1998) Mol. Cell. Biol. , vol.18 , pp. 6538-6547
    • Hendrich, B.1    Bird, A.2
  • 9
    • 84876278080 scopus 로고    scopus 로고
    • Methylation-dependent and -independent genomic targeting principles of the MBD protein family
    • Baubec, T., Ivanek, R., Lienert, F., Schubeler, D., Methylation-dependent and -independent genomic targeting principles of the MBD protein family. Cell 153 (2013), 480–492.
    • (2013) Cell , vol.153 , pp. 480-492
    • Baubec, T.1    Ivanek, R.2    Lienert, F.3    Schubeler, D.4
  • 10
    • 68149157845 scopus 로고    scopus 로고
    • Rapid analysis of heterogeneously methylated DNA using digital methylation-sensitive high resolution melting: application to the CDKN2B (p15) gene
    • Candiloro, I., Mikeska, T., Hokland, P., Dobrovic, A., Rapid analysis of heterogeneously methylated DNA using digital methylation-sensitive high resolution melting: application to the CDKN2B (p15) gene. Epigenetics Chromatin, 1, 2008, 7.
    • (2008) Epigenetics Chromatin , vol.1 , pp. 7
    • Candiloro, I.1    Mikeska, T.2    Hokland, P.3    Dobrovic, A.4
  • 11
    • 42449142344 scopus 로고    scopus 로고
    • Sensitive melting analysis after real time- methylation specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection
    • Kristensen, L., Mikeska, T., Krypuy, M., Dobrovic, A., Sensitive melting analysis after real time- methylation specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection. Nucleic Acids Res., 36, 2008, e42.
    • (2008) Nucleic Acids Res. , vol.36
    • Kristensen, L.1    Mikeska, T.2    Krypuy, M.3    Dobrovic, A.4
  • 12
    • 65549117575 scopus 로고    scopus 로고
    • Quantitation of DNA methylation by melt curve analysis
    • Smith, E., Jones, M., Drew, P., Quantitation of DNA methylation by melt curve analysis. BMC Cancer, 9, 2009, 123.
    • (2009) BMC Cancer , vol.9 , pp. 123
    • Smith, E.1    Jones, M.2    Drew, P.3
  • 13
    • 84898538836 scopus 로고    scopus 로고
    • Single molecule mechanical manipulation for studying biological properties of proteins, DNA, and sugars
    • Scholl, Z., Li, Q., Marszalek, P., Single molecule mechanical manipulation for studying biological properties of proteins, DNA, and sugars. Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol. 6 (2014), 211–229.
    • (2014) Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol. , vol.6 , pp. 211-229
    • Scholl, Z.1    Li, Q.2    Marszalek, P.3
  • 16
    • 80052423145 scopus 로고    scopus 로고
    • Direct quantification of the attempt frequency determining the mechanical unfolding of Ubiquitin protein
    • Popa, I., Fernandez, J., Garcia-Manyes, S., Direct quantification of the attempt frequency determining the mechanical unfolding of Ubiquitin protein. J. Biol. Chem. 286 (2011), 31072–31079.
    • (2011) J. Biol. Chem. , vol.286 , pp. 31072-31079
    • Popa, I.1    Fernandez, J.2    Garcia-Manyes, S.3
  • 17
    • 84879401486 scopus 로고    scopus 로고
    • Force dependency of biochemical reactions measured by single-molecule force-clamp spectroscopy
    • Popa, I., Kosuri, P., Alegre-Cebollada, J., Garcia-Manyes, S., Fernandez, J., Force dependency of biochemical reactions measured by single-molecule force-clamp spectroscopy. Nat. Protoc. 8 (2013), 1261–1276.
    • (2013) Nat. Protoc. , vol.8 , pp. 1261-1276
    • Popa, I.1    Kosuri, P.2    Alegre-Cebollada, J.3    Garcia-Manyes, S.4    Fernandez, J.5
  • 19
    • 0035204816 scopus 로고    scopus 로고
    • DNA methylation-dependent chromatin fiber compaction in vivo and in vitro: requirement for linker histone
    • Karymov, M., Tomschik, M., Leuba, S., Caiafa, P., Zlatanova, J., DNA methylation-dependent chromatin fiber compaction in vivo and in vitro: requirement for linker histone. FASEB J. 15 (2001), 2631–2641.
    • (2001) FASEB J. , vol.15 , pp. 2631-2641
    • Karymov, M.1    Tomschik, M.2    Leuba, S.3    Caiafa, P.4    Zlatanova, J.5
  • 20
    • 84908679499 scopus 로고    scopus 로고
    • Hydroxymethylation of DNA influences nucleosomal conformation and stability in vitro
    • Mendonca, A., Chang, E., Liu, W., Yuan, C., Hydroxymethylation of DNA influences nucleosomal conformation and stability in vitro. BBA 1839 (2014), 1323–1329.
    • (2014) BBA , vol.1839 , pp. 1323-1329
    • Mendonca, A.1    Chang, E.2    Liu, W.3    Yuan, C.4
  • 21
    • 84871255668 scopus 로고    scopus 로고
    • Hydrophobicity of methylated DNA as a possible mechanism for gene silencing
    • Kaur, P., Plochberger, B., Costa, P., Cope, S., Vaiana, S., Lindsay, S., Hydrophobicity of methylated DNA as a possible mechanism for gene silencing. Phys. Biol., 9, 2012, 065001.
    • (2012) Phys. Biol. , vol.9 , pp. 065001
    • Kaur, P.1    Plochberger, B.2    Costa, P.3    Cope, S.4    Vaiana, S.5    Lindsay, S.6
  • 23
    • 80455168293 scopus 로고    scopus 로고
    • Cytosine methylation alters DNA mechanical properties
    • Severin, P., Zou, X., Gaub, H., Schulten, K., Cytosine methylation alters DNA mechanical properties. Nucleic Acids Res. 39 (2011), 8740–8751.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 8740-8751
    • Severin, P.1    Zou, X.2    Gaub, H.3    Schulten, K.4
  • 24
    • 76149143416 scopus 로고    scopus 로고
    • Regulation of DNA methylation using different tensions of double strands constructed in a defined DNA nanostructure
    • Endo, M., Katsuda, Y., Hidaka, K., Sugiyama, H., Regulation of DNA methylation using different tensions of double strands constructed in a defined DNA nanostructure. J. Am. Chem. Soc. 132 (2010), 1592–1597.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 1592-1597
    • Endo, M.1    Katsuda, Y.2    Hidaka, K.3    Sugiyama, H.4
  • 26
    • 0033949035 scopus 로고    scopus 로고
    • Atomic force microscopy studies of intercalation-induced changes in plasmid DNA tertiary structure
    • Pope, L.H., Davies, M.C., Laughton, C.A., Roberts, C.J., Tendler, S.J.B., Williams, P.M., Atomic force microscopy studies of intercalation-induced changes in plasmid DNA tertiary structure. J. Microsc. 199 (2000), 68–78.
    • (2000) J. Microsc. , vol.199 , pp. 68-78
    • Pope, L.H.1    Davies, M.C.2    Laughton, C.A.3    Roberts, C.J.4    Tendler, S.J.B.5    Williams, P.M.6
  • 27
    • 0029861327 scopus 로고    scopus 로고
    • A novel assay for drug-DNA binding mode, affinity, and exclusion number: scanning force microscopy
    • Coury, J.E., McFaillsom, L., Williams, L.D., Bottomley, L.A., A novel assay for drug-DNA binding mode, affinity, and exclusion number: scanning force microscopy. Proc. Natl. Acad. Sci. U. S. A. 93 (1996), 12283–12286.
    • (1996) Proc. Natl. Acad. Sci. U. S. A. , vol.93 , pp. 12283-12286
    • Coury, J.E.1    McFaillsom, L.2    Williams, L.D.3    Bottomley, L.A.4
  • 29
    • 0026495432 scopus 로고
    • Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads
    • Smith, S.B., Finzi, L., Bustamante, C., Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258 (1992), 1122–1126.
    • (1992) Science , vol.258 , pp. 1122-1126
    • Smith, S.B.1    Finzi, L.2    Bustamante, C.3
  • 30
    • 84982060514 scopus 로고
    • Rontgenuntersuchung geloster fadenmolekule
    • Kratky, O., Porod, G., Rontgenuntersuchung geloster fadenmolekule. Recl. Trav. Chim. Pays Bas 68 (1949), 1106–1122.
    • (1949) Recl. Trav. Chim. Pays Bas , vol.68 , pp. 1106-1122
    • Kratky, O.1    Porod, G.2
  • 32
    • 0030596081 scopus 로고    scopus 로고
    • Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by satistical polymer chain analysis
    • Rivetti, C., Guthold, M., Bustamante, C., Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by satistical polymer chain analysis. J. Mol. Biol. 264 (1996), 919–932.
    • (1996) J. Mol. Biol. , vol.264 , pp. 919-932
    • Rivetti, C.1    Guthold, M.2    Bustamante, C.3
  • 33
    • 84896689509 scopus 로고    scopus 로고
    • Unmethylated and methylated cpg dinucleotides distinctively regulate the physical properties of DNA
    • Jimenez-Useche, I., Shim, D., Yu, J., Yuan, C., Unmethylated and methylated cpg dinucleotides distinctively regulate the physical properties of DNA. Biopolymers 101 (2014), 517–524.
    • (2014) Biopolymers , vol.101 , pp. 517-524
    • Jimenez-Useche, I.1    Shim, D.2    Yu, J.3    Yuan, C.4
  • 34
    • 21144439049 scopus 로고    scopus 로고
    • Variational theory for a single polyelectrolyte chain revisited
    • Manghi, M., Netz, R., Variational theory for a single polyelectrolyte chain revisited. Eur. Phys. J. E Soft Matter 14 (2004), 67–77.
    • (2004) Eur. Phys. J. E Soft Matter , vol.14 , pp. 67-77
    • Manghi, M.1    Netz, R.2
  • 35
    • 68549135359 scopus 로고    scopus 로고
    • Scale-dependent electrostatic stiffening in biopolymers
    • Gubarev, A., Carrillo, J., Dobrynin, A., Scale-dependent electrostatic stiffening in biopolymers. Macromolecules 42 (2009), 5851–5860.
    • (2009) Macromolecules , vol.42 , pp. 5851-5860
    • Gubarev, A.1    Carrillo, J.2    Dobrynin, A.3
  • 37
    • 84931291822 scopus 로고    scopus 로고
    • Dependence of DNA persistence length on ionic strength of solutions with monovalent and divalent salts: A joint theory-experiment study
    • Brunet, A., Tardin, C., Salome, L., Rousseau, P., Destainville, N., Manghi, M., Dependence of DNA persistence length on ionic strength of solutions with monovalent and divalent salts: A joint theory-experiment study. Macromolecules 48 (2015), 3641–3652.
    • (2015) Macromolecules , vol.48 , pp. 3641-3652
    • Brunet, A.1    Tardin, C.2    Salome, L.3    Rousseau, P.4    Destainville, N.5    Manghi, M.6
  • 38
    • 0036922909 scopus 로고    scopus 로고
    • Structural effects of cytosine methylation on DNA sugar pucker studied by FTIR
    • Banyay, M., Graslund, A., Structural effects of cytosine methylation on DNA sugar pucker studied by FTIR. J. Mol. Biol. 324 (2002), 667–676.
    • (2002) J. Mol. Biol. , vol.324 , pp. 667-676
    • Banyay, M.1    Graslund, A.2
  • 41
    • 0035838814 scopus 로고    scopus 로고
    • Dissociation of surface functional groups and preferential adsorption of ions on self-assembled monolayers assessed by streaming potential and streaming current measurements
    • Schweiss, R., Welzel, P., Werner, C., Knoll, W., Dissociation of surface functional groups and preferential adsorption of ions on self-assembled monolayers assessed by streaming potential and streaming current measurements. Langmuir 17 (2001), 4304–4311.
    • (2001) Langmuir , vol.17 , pp. 4304-4311
    • Schweiss, R.1    Welzel, P.2    Werner, C.3    Knoll, W.4
  • 42
    • 33645296884 scopus 로고    scopus 로고
    • Inferring the effective thickness of polyelectrolytes from stretching measurements at various ionic strengths: applications to DNA and RNA
    • Toan, N., Micheletti, C., Inferring the effective thickness of polyelectrolytes from stretching measurements at various ionic strengths: applications to DNA and RNA. J. Phys. Condens. Matter, 18, 2006, S269.
    • (2006) J. Phys. Condens. Matter , vol.18 , pp. S269
    • Toan, N.1    Micheletti, C.2
  • 43
    • 77952413161 scopus 로고    scopus 로고
    • Reversed anionic Hofmeister series: The interplay of surface charge and surface polarity
    • Schwierz, N., Horinek, D., Netz, R.R., Reversed anionic Hofmeister series: The interplay of surface charge and surface polarity. Langmuir 26 (2010), 7370–7379.
    • (2010) Langmuir , vol.26 , pp. 7370-7379
    • Schwierz, N.1    Horinek, D.2    Netz, R.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.