메뉴 건너뛰기




Volumn 7, Issue 8, 2012, Pages

An in silico study of the differential effect of oxidation on two biologically relevant G-quadruplexes: Possible implications in oncogene expression

Author keywords

[No Author keywords available]

Indexed keywords

8 HYDROXYDEOXYGUANOSINE; DOUBLE STRANDED DNA; GUANINE QUADRUPLEX;

EID: 84865172051     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0043735     Document Type: Article
Times cited : (12)

References (37)
  • 1
    • 77950353700 scopus 로고    scopus 로고
    • Altered Gene Expression in the Werner and Bloom Syndromes is Associated with Sequences Having G-Quadruplex Forming Potential
    • Johnson JE, Cao K, Ryvkin P, Wang L-S, Johnson FB, ((2010)) Altered Gene Expression in the Werner and Bloom Syndromes is Associated with Sequences Having G-Quadruplex Forming Potential. Nucleic Acids Research 38:: 1114--1112.
    • (2010) Nucleic Acids Research , vol.38 , pp. 1112-1114
    • Johnson, J.E.1    Cao, K.2    Ryvkin, P.3    Wang, L.-S.4    Johnson, F.B.5
  • 2
    • 38349095525 scopus 로고    scopus 로고
    • Genomic Distribution and Functional Analyses of Potential G-Quadruplex-Forming Sequences in Saccharomyces cerevisiae
    • Hershman SG, Chen Q, Lee JY, Kozak ML, Yue P, et al. ((2008)) Genomic Distribution and Functional Analyses of Potential G-Quadruplex-Forming Sequences in Saccharomyces cerevisiae. Nucleic Acids Research 36:: 144--156.
    • (2008) Nucleic Acids Research , vol.36 , pp. 144-156
    • Hershman, S.G.1    Chen, Q.2    Lee, J.Y.3    Kozak, M.L.4    Yue, P.5
  • 3
    • 77955809107 scopus 로고    scopus 로고
    • Making Sense of G-Quadruplex and i-Motif Functions in Oncogene Promoters
    • Brooks TA, Kendrick S, Hurley L, ((2010)) Making Sense of G-Quadruplex and i-Motif Functions in Oncogene Promoters. FEBS Journal 277:: 3459--3469.
    • (2010) FEBS Journal , vol.277 , pp. 3459-3469
    • Brooks, T.A.1    Kendrick, S.2    Hurley, L.3
  • 4
    • 20144364292 scopus 로고    scopus 로고
    • Prevalence of Quadruplexes in the Human Genome
    • Huppert JL, Balasubramanian S, ((2005)) Prevalence of Quadruplexes in the Human Genome. Nucleic Acids Research 33:: 2908--2916.
    • (2005) Nucleic Acids Research , vol.33 , pp. 2908-2916
    • Huppert, J.L.1    Balasubramanian, S.2
  • 5
    • 33846928449 scopus 로고    scopus 로고
    • G-Quadruplexes in Promoters Throughout the Human Genome
    • Huppert JL, Balasubramanian S, ((2007)) G-Quadruplexes in Promoters Throughout the Human Genome. Nucleic Acids Research 35:: 406--413.
    • (2007) Nucleic Acids Research , vol.35 , pp. 406-413
    • Huppert, J.L.1    Balasubramanian, S.2
  • 6
    • 68549136741 scopus 로고    scopus 로고
    • G-Quadruplex Structures: in vivo Evidence and Function
    • Lipps HJ, Rhodes D, ((2007)) G-Quadruplex Structures: in vivo Evidence and Function. Trends in Cell Biology 19:: 414--422.
    • (2007) Trends in Cell Biology , vol.19 , pp. 414-422
    • Lipps, H.J.1    Rhodes, D.2
  • 7
    • 44949114282 scopus 로고    scopus 로고
    • FANCJ Helicase Defective in Fanconia Anemia and Breast Cancer Unwinds G-Quadruplex DNA to Defend Genomic Stability
    • Wu Y, Shin-ya K, Brosh RM, ((2008)) FANCJ Helicase Defective in Fanconia Anemia and Breast Cancer Unwinds G-Quadruplex DNA to Defend Genomic Stability. Molecular and Cellular Biology 28:: 4116--4128.
    • (2008) Molecular and Cellular Biology , vol.28 , pp. 4116-4128
    • Wu, Y.1    Shin-ya, K.2    Brosh, R.M.3
  • 8
    • 63449109208 scopus 로고    scopus 로고
    • Welcome the Family of FANCJ-like Helicases to the Block of Genome Stability Maintenace Proteins
    • Wu Y, Suhasini AN, Brosh RM, ((2009)) Welcome the Family of FANCJ-like Helicases to the Block of Genome Stability Maintenace Proteins. Cellular and Molecular Life Sciences 66:: 1209--1222.
    • (2009) Cellular and Molecular Life Sciences , vol.66 , pp. 1209-1222
    • Wu, Y.1    Suhasini, A.N.2    Brosh, R.M.3
  • 12
    • 13644267721 scopus 로고    scopus 로고
    • Solution Structure of the Biologically Relevant G-Quadruplex Element in the Human c-MYC Promoter. Implications for G-Quadruplex Stabilization
    • Ambrus A, Chen D, Dai J, Jones RA, Yang D, ((2005)) Solution Structure of the Biologically Relevant G-Quadruplex Element in the Human c-MYC Promoter. Implications for G-Quadruplex Stabilization. Biochemistry 44:: 2048--2058.
    • (2005) Biochemistry , vol.44 , pp. 2048-2058
    • Ambrus, A.1    Chen, D.2    Dai, J.3    Jones, R.A.4    Yang, D.5
  • 13
    • 37549000254 scopus 로고    scopus 로고
    • DNA Quadruplexes and Gene Regulation
    • Neidle S, Balasubramanian, S, editors. Cambridge: Royal Society of Chemistry
    • Dexheimer TS, Fry M, Hurley LH (2006) DNA Quadruplexes and Gene Regulation. In: Neidle S, Balasubramanian, S, editors. Quadruplex Nucleic Acids. Cambridge: Royal Society of Chemistry. 180-207.
    • (2006) Quadruplex Nucleic Acids , pp. 180-207
    • Dexheimer, T.S.1    Fry, M.2    Hurley, L.H.3
  • 14
    • 0029998428 scopus 로고    scopus 로고
    • Multiple Single-Stranded cis Elements are Associated with Activated Chromatin of the Human c-myc Gene In Vivo
    • Michelotti GA, Michelotti EF, Pullner A, Duncan RC, Erick D, et al. ((1996)) Multiple Single-Stranded cis Elements are Associated with Activated Chromatin of the Human c-myc Gene In Vivo. Molecular and Cellular Biology 16:: 2656--2669.
    • (1996) Molecular and Cellular Biology , vol.16 , pp. 2656-2669
    • Michelotti, G.A.1    Michelotti, E.F.2    Pullner, A.3    Duncan, R.C.4    Erick, D.5
  • 15
    • 0036597090 scopus 로고    scopus 로고
    • The Cationic Porphyrin TMPyP4 Down-Regulates c-MYC and Human Telomerase Reverse Transcriptase Expression and Inhibits Tumor Growth in Vivo
    • Grand CL, Han H, Munoz RM, Weitman S, Von Hoff DD, et al. ((2002)) The Cationic Porphyrin TMPyP4 Down-Regulates c-MYC and Human Telomerase Reverse Transcriptase Expression and Inhibits Tumor Growth in Vivo. Molecular Cancer Therapeutics 1:: 565--573.
    • (2002) Molecular Cancer Therapeutics , vol.1 , pp. 565-573
    • Grand, C.L.1    Han, H.2    Munoz, R.M.3    Weitman, S.4    von Hoff, D.D.5
  • 17
    • 78049395874 scopus 로고    scopus 로고
    • Solution Structures of all Parallel-Stranded Monomeric and Dimeric G-Quadruplex Scaffolds of the Human c-kit2 Promoter
    • Kuryavyi V, Phan AT, Patel DJ, ((2010)) Solution Structures of all Parallel-Stranded Monomeric and Dimeric G-Quadruplex Scaffolds of the Human c-kit2 Promoter. Nucleic Acids Research 38:: 6757--6773.
    • (2010) Nucleic Acids Research , vol.38 , pp. 6757-6773
    • Kuryavyi, V.1    Phan, A.T.2    Patel, D.J.3
  • 18
    • 0030049032 scopus 로고    scopus 로고
    • Damage to DNA by Reactive oxygen and Nytrogen Species: Role in Inflammatory Disease and Progression to Cancer
    • Wiseman H, Halliwell B, ((1996)) Damage to DNA by Reactive oxygen and Nytrogen Species: Role in Inflammatory Disease and Progression to Cancer. Biochemistry Journal 313:: 17--29.
    • (1996) Biochemistry Journal , vol.313 , pp. 17-29
    • Wiseman, H.1    Halliwell, B.2
  • 19
    • 0035878869 scopus 로고    scopus 로고
    • Repair of 8-oxodeoxyguanosine Lesions in Mitochondrial DNA Depends on the Oxoguanine DNA Glycosylase (OGG1) and 8-Oxoguanine Accumulates in the Mitochondrial DNA of OGG1-defective Mice
    • de Souza-Pinto NC, Eide L, Hogue BA, Thybo T, Stevnsner T, et al. ((2001)) Repair of 8-oxodeoxyguanosine Lesions in Mitochondrial DNA Depends on the Oxoguanine DNA Glycosylase (OGG1) and 8-Oxoguanine Accumulates in the Mitochondrial DNA of OGG1-defective Mice. Cancer Research 61:: 5378--5381.
    • (2001) Cancer Research , vol.61 , pp. 5378-5381
    • de Souza-Pinto, N.C.1    Eide, L.2    Hogue, B.A.3    Thybo, T.4    Stevnsner, T.5
  • 20
    • 1242284258 scopus 로고    scopus 로고
    • Accumulation of 8-oxo-2′-deoxyguanosine (as a Biomarker of Oxidative DNA Damage) in the Tissues of Aged Hamsters and Change in Antioxidant Enzyme Activities after Single Administration of N-nitrosobis(2-oxopropyl) amine
    • Takabayashi F, Tahara S, Kaneko T, Miyoshi Y, Harada N, ((2004)) Accumulation of 8-oxo-2′-deoxyguanosine (as a Biomarker of Oxidative DNA Damage) in the Tissues of Aged Hamsters and Change in Antioxidant Enzyme Activities after Single Administration of N-nitrosobis(2-oxopropyl) amine. Gerontology 50:: 57--63.
    • (2004) Gerontology , vol.50 , pp. 57-63
    • Takabayashi, F.1    Tahara, S.2    Kaneko, T.3    Miyoshi, Y.4    Harada, N.5
  • 21
    • 34250682662 scopus 로고    scopus 로고
    • Guanines are a Quartet's Best Friend: Impact of Base Substitutions on the Kinetics and Stability of Tetramolecular Quadruplexes
    • Gros J, Rosu F, Amrane S, De Cian A, Gabelica V, et al. ((2007)) Guanines are a Quartet's Best Friend: Impact of Base Substitutions on the Kinetics and Stability of Tetramolecular Quadruplexes. Nucleic Acids Research 35:: 3064--3075.
    • (2007) Nucleic Acids Research , vol.35 , pp. 3064-3075
    • Gros, J.1    Rosu, F.2    Amrane, S.3    de Cian, A.4    Gabelica, V.5
  • 22
    • 80052843514 scopus 로고    scopus 로고
    • G Quadruplexes Stabilised by 8-Oxo-2′-deoxyguanosine
    • Singh V, Benz A, Hartig JS, ((2011)) G Quadruplexes Stabilised by 8-Oxo-2′-deoxyguanosine. Chemistry A European Journal 17:: 10838--10843.
    • (2011) Chemistry A European Journal , vol.17 , pp. 10838-10843
    • Singh, V.1    Benz, A.2    Hartig, J.S.3
  • 25
    • 70449729915 scopus 로고    scopus 로고
    • Stability of Intramolecular Quadruplexes: Sequence Effects in the Central Loop
    • Guedin A, Alberti P, Mergny JL, ((2009)) Stability of Intramolecular Quadruplexes: Sequence Effects in the Central Loop. Nucleic Acids Research 37:: 5559--5567.
    • (2009) Nucleic Acids Research , vol.37 , pp. 5559-5567
    • Guedin, A.1    Alberti, P.2    Mergny, J.L.3
  • 26
    • 14344275144 scopus 로고    scopus 로고
    • Biological Aspects of DNA/RNA Quadruplexes
    • Shafer RH, Smirnov I, ((2001)) Biological Aspects of DNA/RNA Quadruplexes. Nucleic Acid Sci 56:: 209--227.
    • (2001) Nucleic Acid Sci , vol.56 , pp. 209-227
    • Shafer, R.H.1    Smirnov, I.2
  • 28
    • 48349103695 scopus 로고    scopus 로고
    • Effect of Loop Length Variation on Quadruplex-Watson Crick Duplex Competition
    • Kumar N, Sahoo B, Varun KAS, Maiti S, ((2008)) Effect of Loop Length Variation on Quadruplex-Watson Crick Duplex Competition. Nucleic Acids Research 36:: 4433--4442.
    • (2008) Nucleic Acids Research , vol.36 , pp. 4433-4442
    • Kumar, N.1    Sahoo, B.2    Varun, K.A.S.3    Maiti, S.4
  • 29
    • 71449125359 scopus 로고    scopus 로고
    • Telomeric D-Loops Containing 8-Oxo-2′-Deoxyguanosine are Preferred Substrates for Werner and Bloom Syndrome Helicases and are Bound by POT1
    • Ghosh A, Rossi ML, Aulds J, Croteau D, Bohr VA, ((2009)) Telomeric D-Loops Containing 8-Oxo-2′-Deoxyguanosine are Preferred Substrates for Werner and Bloom Syndrome Helicases and are Bound by POT1. Journal of Biological Chemistry 284:: 31074--31084.
    • (2009) Journal of Biological Chemistry , vol.284 , pp. 31074-31084
    • Ghosh, A.1    Rossi, M.L.2    Aulds, J.3    Croteau, D.4    Bohr, V.A.5
  • 30
    • 35848942604 scopus 로고    scopus 로고
    • Trisubstituted Isoalloxazines as a New Class of G-Quadruplex Binding Ligands: Small Molecule Regulation of c-Kit Oncogene Expression
    • Bejugam M, Sewitz S, Shirude PS, Rodriguez R, Shahid R, et al. ((2007)) Trisubstituted Isoalloxazines as a New Class of G-Quadruplex Binding Ligands: Small Molecule Regulation of c-Kit Oncogene Expression. Journal of the American Chemical Society 129:: 12926--12927.
    • (2007) Journal of the American Chemical Society , vol.129 , pp. 12926-12927
    • Bejugam, M.1    Sewitz, S.2    Shirude, P.S.3    Rodriguez, R.4    Shahid, R.5
  • 31
    • 77951529058 scopus 로고    scopus 로고
    • Global Gene Expression Analysis Reveals Differences in Cellular Responses to Hydroxyl- and Superoxide Anion Radical-Induced Oxidative Stress in Caco-2 Cells
    • Briede JJ, van Delft JMH, de Kok T, van Herwijnen MHM, Maas LM, ((2010)) Global Gene Expression Analysis Reveals Differences in Cellular Responses to Hydroxyl- and Superoxide Anion Radical-Induced Oxidative Stress in Caco-2 Cells. Toxicological Sciences 114:: 193--203.
    • (2010) Toxicological Sciences , vol.114 , pp. 193-203
    • Briede, J.J.1    van Delft, J.M.H.2    de Kok, T.3    van Herwijnen, M.H.M.4    Maas, L.M.5
  • 32
    • 0033593046 scopus 로고    scopus 로고
    • Site Specific Oxidation at GG and GGG Sequences in Double-Stranded DNA by Benzoyl Peroxide as a Tumor Promoter
    • Kawanishi S, Oikawa S, Murata M, Tsukitome H, Saito I, ((1999)) Site Specific Oxidation at GG and GGG Sequences in Double-Stranded DNA by Benzoyl Peroxide as a Tumor Promoter. Biochemistry 38:: 16733--16739.
    • (1999) Biochemistry , vol.38 , pp. 16733-16739
    • Kawanishi, S.1    Oikawa, S.2    Murata, M.3    Tsukitome, H.4    Saito, I.5
  • 34
    • 34250318638 scopus 로고    scopus 로고
    • Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of alpha/gamma Conformers
    • Perez A, Marchan I, Svozil D, Sponer J, Cheatham III TE, et al. ((2007)) Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of alpha/gamma Conformers. Biophysical Journal 92:: 3817--3829.
    • (2007) Biophysical Journal , vol.92 , pp. 3817-3829
    • Perez, A.1    Marchan, I.2    Svozil, D.3    Sponer, J.4    Cheatham III, T.E.5
  • 35
    • 77449091091 scopus 로고    scopus 로고
    • Molecular Modeling and Simulation of G-Quadruplexes and Quadruplex-Ligand Complexes
    • Baumann P, editor. Human Press
    • Haider S, Neidle S (2010) Molecular Modeling and Simulation of G-Quadruplexes and Quadruplex-Ligand Complexes. In: Baumann P, editor. G-Quadruplex DNA: Methods and Protocols. Human Press. 17-37.
    • (2010) G-Quadruplex DNA: Methods and Protocols , pp. 17-37
    • Haider, S.1    Neidle, S.2
  • 36
    • 0029831680 scopus 로고    scopus 로고
    • An Automated Approach for Clustering an Ensemble of NMR-Derived Protein Structures into Conformationally Related Subfamilies
    • Kelley LA, Gardner SP, Sutcliffe MJ, ((1996)) An Automated Approach for Clustering an Ensemble of NMR-Derived Protein Structures into Conformationally Related Subfamilies. Protein Engineering 9:: 1063--1065.
    • (1996) Protein Engineering , vol.9 , pp. 1063-1065
    • Kelley, L.A.1    Gardner, S.P.2    Sutcliffe, M.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.