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Volumn 39, Issue SUPPL. 1, 2011, Pages

Non-B DB: A database of predicted non-B DNA-forming motifs in mammalian genomes

Author keywords

[No Author keywords available]

Indexed keywords

DNA Z;

EID: 78651265529     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1170     Document Type: Article
Times cited : (68)

References (57)
  • 1
    • 73749085274 scopus 로고    scopus 로고
    • Non-B DNA structure-induced genetic instability and evolution
    • Zhao, J., Bacolla, A., Wang, G. and Vasquez, K.M. (2010) Non-B DNA structure-induced genetic instability and evolution. Cell. Mol. Life Sci., 67, 43-62.
    • (2010) Cell. Mol. Life Sci. , vol.67 , pp. 43-62
    • Zhao, J.1    Bacolla, A.2    Wang, G.3    Vasquez, K.M.4
  • 2
    • 47649109401 scopus 로고    scopus 로고
    • Quadruplex DNA crystal structures and drug design
    • Neidle, S. and Parkinson, G.N. (2008) Quadruplex DNA crystal structures and drug design. Biochimie, 90, 1184-1196.
    • (2008) Biochimie , vol.90 , pp. 1184-1196
    • Neidle, S.1    Parkinson, G.N.2
  • 4
    • 77954215844 scopus 로고    scopus 로고
    • Crystal structure of an intermolecular 2:1 complex between adenine and thymine. Evidence for both Hoogsteen and 'quasi-Watson- Crick' interactions
    • Chandrasekhar, S., Naik, T.R., Nayak, S.K. and Row, T.N. (2010) Crystal structure of an intermolecular 2:1 complex between adenine and thymine. Evidence for both Hoogsteen and 'quasi-Watson- Crick' interactions. Bioorg. Med. Chem. Lett., 20, 3530-3533.
    • (2010) Bioorg. Med. Chem. Lett. , vol.20 , pp. 3530-3533
    • Chandrasekhar, S.1    Naik, T.R.2    Nayak, S.K.3    Row, T.N.4
  • 5
    • 38049030699 scopus 로고    scopus 로고
    • Human telomere, oncogenic promoter and 50-UTR G-quadruplexes: Diverse higher order DNA and RNA targets for cancer therapeutics
    • Patel, D.J., Phan, A.T. and Kuryavyi, V. (2007) Human telomere, oncogenic promoter and 50-UTR G-quadruplexes: Diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Res., 35, 7429-7455.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 7429-7455
    • Patel, D.J.1    Phan, A.T.2    Kuryavyi, V.3
  • 6
    • 64549099313 scopus 로고    scopus 로고
    • Circular dichroism and conformational polymorphism of DNA
    • Kypr, J., Kejnovska, I., Renciuk, D. and Vorlickova, M. (2009) Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res., 37, 1713-1725.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1713-1725
    • Kypr, J.1    Kejnovska, I.2    Renciuk, D.3    Vorlickova, M.4
  • 7
    • 79961193493 scopus 로고
    • DNA Structures part B: Chemical and electrophoretic analysis of DNA
    • Elsevier/Academic Press, San Diego, CA
    • Lilley, D.M.J. and Dahlberg, J.E. (eds), (1992), DNA Structures part B: Chemical and electrophoretic analysis of DNA, Methods Enzymol, Vol. 212. Elsevier/Academic Press, San Diego, CA, pp. 139-155.
    • (1992) Methods Enzymol , vol.212 , pp. 139-155
    • Lilley, D.M.J.1    Dahlberg, J.E.2
  • 8
    • 38449106276 scopus 로고    scopus 로고
    • Discovery of alternative DNA structures: A heroic decade 1979-1989)
    • Mirkin, S.M. (2008) Discovery of alternative DNA structures: A heroic decade (1979-1989). Front. Biosci., 13, 1064-1071.
    • (2008) Front. Biosci. , vol.13 , pp. 1064-1071
    • Mirkin, S.M.1
  • 9
    • 0037803571 scopus 로고    scopus 로고
    • Timeline: Z-DNA: The long road to biological function
    • Rich, A. and Zhang, S. (2003) Timeline: Z-DNA: The long road to biological function. Nat. Rev. Genet., 4, 566-572.
    • (2003) Nat. Rev. Genet. , vol.4 , pp. 566-572
    • Rich, A.1    Zhang, S.2
  • 10
    • 8444231721 scopus 로고    scopus 로고
    • Non-B DNA conformations, genomic rearrangements, and human disease
    • Bacolla, A. and Wells, R.D. (2004) Non-B DNA conformations, genomic rearrangements, and human disease. J. Biol. Chem., 279, 47411-47414.
    • (2004) J. Biol. Chem. , vol.279 , pp. 47411-47414
    • Bacolla, A.1    Wells, R.D.2
  • 11
    • 58549108193 scopus 로고    scopus 로고
    • The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA reveals an unusual binding mode to Z-DNA
    • Ha, S.C., Kim, D., Hwang, H.Y., Rich, A., Kim, Y.G. and Kim, K.K. (2008) The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA reveals an unusual binding mode to Z-DNA. Proc. Natl Acad. Sci. USA, 105, 20671-20676.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 20671-20676
    • Ha, S.C.1    Kim, D.2    Hwang, H.Y.3    Rich, A.4    Kim, Y.G.5    Kim, K.K.6
  • 12
    • 64349102519 scopus 로고    scopus 로고
    • Pilin gene variation in Neisseria gonorrhoeae: Reassessing the old paradigms
    • Hill, S.A. and Davies, J.K. (2009) Pilin gene variation in Neisseria gonorrhoeae: Reassessing the old paradigms. FEMS Microbiol. Rev., 33, 521-530.
    • (2009) FEMS Microbiol. Rev. , vol.33 , pp. 521-530
    • Hill, S.A.1    Davies, J.K.2
  • 13
    • 0021324522 scopus 로고
    • Structural intermediates of deletion mutagenesis: A role for palindromic DNA
    • Glickman, B.W. and Ripley, L.S. (1984) Structural intermediates of deletion mutagenesis: A role for palindromic DNA. Proc. Natl Acad. Sci. USA, 81, 512-516.
    • (1984) Proc. Natl Acad. Sci. USA , vol.81 , pp. 512-516
    • Glickman, B.W.1    Ripley, L.S.2
  • 17
    • 77956406859 scopus 로고    scopus 로고
    • The constitutional t(11;22): Implications for a novel mechanism responsible for gross chromosomal rearrangements
    • Kurahashi, H., Inagaki, H., Ohye, T., Kogo, H., Tsutsumi, M., Kato, T., Tong, M. and Emanuel, B.S. (2010) The constitutional t(11;22): Implications for a novel mechanism responsible for gross chromosomal rearrangements. Clin. Genet., 78, 299-309.
    • (2010) Clin. Genet. , vol.78 , pp. 299-309
    • Kurahashi, H.1    Inagaki, H.2    Ohye, T.3    Kogo, H.4    Tsutsumi, M.5    Kato, T.6    Tong, M.7    Emanuel, B.S.8
  • 19
    • 67349159689 scopus 로고    scopus 로고
    • Further delineation of nonhomologous-based recombination and evidence for subtelomeric segmental duplications in 1p36 rearrangements
    • D'Angelo, C.S., Gajecka, M., Kim, C.A., Gentles, A.J., Glotzbach, C.D., Shaffer, L.G. and Koiffmann, C.P. (2009) Further delineation of nonhomologous-based recombination and evidence for subtelomeric segmental duplications in 1p36 rearrangements. Hum. Genet., 125, 551-563.
    • (2009) Hum. Genet. , vol.125 , pp. 551-563
    • D'Angelo, C.S.1    Gajecka, M.2    Kim, C.A.3    Gentles, A.J.4    Glotzbach, C.D.5    Shaffer, L.G.6    Koiffmann, C.P.7
  • 21
    • 38549092075 scopus 로고    scopus 로고
    • QuadBase: Genome-wide database of G4 DNA-occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes
    • Yadav, V.K., Abraham, J.K., Mani, P., Kulshrestha, R. and Chowdhury, S. (2008) QuadBase: Genome-wide database of G4 DNA-occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes. Nucleic Acids Res., 36, D381-D385.
    • (2008) Nucleic Acids Res. , vol.36
    • Yadav, V.K.1    Abraham, J.K.2    Mani, P.3    Kulshrestha, R.4    Chowdhury, S.5
  • 22
    • 71549153177 scopus 로고    scopus 로고
    • TTS mapping: Integrative WEB tool for analysis of triplex formation target DNA sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome
    • Jenjaroenpun, P. and Kuznetsov, V.A. (2009) TTS mapping: Integrative WEB tool for analysis of triplex formation target DNA sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome. BMC Genomics, 10 (Suppl. 3), S9.
    • (2009) BMC Genomics , vol.10 , Issue.SUPPL. 3
    • Jenjaroenpun, P.1    Kuznetsov, V.A.2
  • 23
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: A program to analyze DNA sequences
    • Benson, G. (1999) Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 573-580
    • Benson, G.1
  • 24
    • 40249084264 scopus 로고    scopus 로고
    • Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes
    • Eddy, J. and Maizels, N. (2008) Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes. Nucleic Acids Res., 36, 1321-1333.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 1321-1333
    • Eddy, J.1    Maizels, N.2
  • 25
    • 0022801415 scopus 로고
    • A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences
    • Ho, P.S., Ellison, M.J., Quigley, G.J. and Rich, A. (1986) A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. EMBO J., 5, 2737-2744.
    • (1986) EMBO J. , vol.5 , pp. 2737-2744
    • Ho, P.S.1    Ellison, M.J.2    Quigley, G.J.3    Rich, A.4
  • 26
    • 59649102989 scopus 로고    scopus 로고
    • Thermogenomics: Thermodynamic-based approaches to genomic analyses of DNA structure
    • Ho, P.S. (2009) Thermogenomics: Thermodynamic-based approaches to genomic analyses of DNA structure. Methods, 47, 159-167.
    • (2009) Methods , vol.47 , pp. 159-167
    • Ho, P.S.1
  • 27
    • 0026752148 scopus 로고
    • Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes
    • Schroth, G.P., Chou, P.J. and Ho, P.S. (1992) Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes. J. Biol. Chem., 267, 11846-11855.
    • (1992) J. Biol. Chem. , vol.267 , pp. 11846-11855
    • Schroth, G.P.1    Chou, P.J.2    Ho, P.S.3
  • 29
    • 0024512460 scopus 로고
    • The level of Z-DNA in metabolically active, permeabilized mammalian cell nuclei is regulated by torsional strain
    • Wittig, B., Dorbic, T. and Rich, A. (1989) The level of Z-DNA in metabolically active, permeabilized mammalian cell nuclei is regulated by torsional strain. J. Cell Biol., 108, 755-764.
    • (1989) J. Cell Biol. , vol.108 , pp. 755-764
    • Wittig, B.1    Dorbic, T.2    Rich, A.3
  • 31
    • 0019932819 scopus 로고
    • Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions
    • Singleton, C.K., Klysik, J., Stirdivant, S.M. and Wells, R.D. (1982) Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions. Nature, 299, 312-316.
    • (1982) Nature , vol.299 , pp. 312-316
    • Singleton, C.K.1    Klysik, J.2    Stirdivant, S.M.3    Wells, R.D.4
  • 32
    • 0023686302 scopus 로고
    • Influence of DNA sequence and supercoiling on the process of cruciform formation
    • Courey, A.J. and Wang, J.C. (1988) Influence of DNA sequence and supercoiling on the process of cruciform formation. J. Mol. Biol., 202, 35-43.
    • (1988) J. Mol. Biol. , vol.202 , pp. 35-43
    • Courey, A.J.1    Wang, J.C.2
  • 33
    • 0023904210 scopus 로고
    • Non-B right-handed DNA conformations of homopurine.homopyrimidine sequences in the murine immunoglobulin C alpha switch region
    • Collier, D.A., Griffin, J.A. and Wells, R.D. (1988) Non-B right-handed DNA conformations of homopurine.homopyrimidine sequences in the murine immunoglobulin C alpha switch region. J. Biol. Chem., 263, 7397-7405.
    • (1988) J. Biol. Chem. , vol.263 , pp. 7397-7405
    • Collier, D.A.1    Griffin, J.A.2    Wells, R.D.3
  • 34
    • 0022097138 scopus 로고
    • The physical chemistry of cruciform structures in supercoiled DNA molecules
    • Lilley, D.M., Gough, G.W., Hallam, L.R. and Sullivan, K.M. (1985) The physical chemistry of cruciform structures in supercoiled DNA molecules. Biochimie, 67, 697-706.
    • (1985) Biochimie , vol.67 , pp. 697-706
    • Lilley, D.M.1    Gough, G.W.2    Hallam, L.R.3    Sullivan, K.M.4
  • 35
    • 0026440765 scopus 로고
    • Transcriptionally driven cruciform formation in vivo
    • Dayn, A., Malkhosyan, S. and Mirkin, S.M. (1992) Transcriptionally driven cruciform formation in vivo. Nucleic Acids Res., 20, 5991-5997.
    • (1992) Nucleic Acids Res. , vol.20 , pp. 5991-5997
    • Dayn, A.1    Malkhosyan, S.2    Mirkin, S.M.3
  • 37
    • 0035947688 scopus 로고    scopus 로고
    • PKD1 unusual DNA conformations are recognized by nucleotide excision repair
    • Bacolla, A., Jaworski, A., Connors, T.D. and Wells, R.D. (2001) PKD1 unusual DNA conformations are recognized by nucleotide excision repair. J. Biol. Chem., 276, 18597-18604.
    • (2001) J. Biol. Chem. , vol.276 , pp. 18597-18604
    • Bacolla, A.1    Jaworski, A.2    Connors, T.D.3    Wells, R.D.4
  • 38
    • 38849132828 scopus 로고    scopus 로고
    • The functional response of upstream DNA to dynamic supercoiling in vivo
    • Kouzine, F., Sanford, S., Elisha-Feil, Z. and Levens, D. (2008) The functional response of upstream DNA to dynamic supercoiling in vivo. Nat. Struct. Mol. Biol., 15, 146-154.
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , pp. 146-154
    • Kouzine, F.1    Sanford, S.2    Elisha-Feil, Z.3    Levens, D.4
  • 39
    • 0030901608 scopus 로고    scopus 로고
    • Measurement of unrestrained negative supercoiling and topological domain size in living human cells
    • Kramer, P.R. and Sinden, R.R. (1997) Measurement of unrestrained negative supercoiling and topological domain size in living human cells. Biochemistry, 36, 3151-3158.
    • (1997) Biochemistry , vol.36 , pp. 3151-3158
    • Kramer, P.R.1    Sinden, R.R.2
  • 40
    • 0028894813 scopus 로고
    • In vivo binding of trimethylpsoralen detects DNA structural alterations associated with transcribing regions in the human beta-globin cluster
    • Jimenez-Ruiz, A., Zhang, Q. and Shen, C.K. (1995) In vivo binding of trimethylpsoralen detects DNA structural alterations associated with transcribing regions in the human beta-globin cluster. J. Biol. Chem., 270, 28978-28981.
    • (1995) J. Biol. Chem. , vol.270 , pp. 28978-28981
    • Jimenez-Ruiz, A.1    Zhang, Q.2    Shen, C.K.3
  • 41
    • 0025932034 scopus 로고
    • Evidence for torsional stress in transcriptionally activated chromatin
    • Leonard, M.W. and Patient, R.K. (1991) Evidence for torsional stress in transcriptionally activated chromatin. Mol. Cell. Biol., 11, 6128-6138.
    • (1991) Mol. Cell. Biol. , vol.11 , pp. 6128-6138
    • Leonard, M.W.1    Patient, R.K.2
  • 42
    • 0035902524 scopus 로고    scopus 로고
    • The architecture of the human Rad54-DNA complex provides evidence for protein translocation along DNA
    • Ristic, D., Wyman, C., Paulusma, C. and Kanaar, R. (2001) The architecture of the human Rad54-DNA complex provides evidence for protein translocation along DNA. Proc. Natl Acad. Sci. USA, 98, 8454-8460.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 8454-8460
    • Ristic, D.1    Wyman, C.2    Paulusma, C.3    Kanaar, R.4
  • 43
    • 65849303734 scopus 로고    scopus 로고
    • Human genomic Z-DNA segments probed by the Z alpha domain of ADAR2
    • Li, H., Xiao, J., Li, J., Lu, L., Feng, S. and Droge, P. (2009) Human genomic Z-DNA segments probed by the Z alpha domain of ADAR2. Nucleic Acids Res., 37, 2737-2746.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 2737-2746
    • Li, H.1    Xiao, J.2    Li, J.3    Lu, L.4    Feng, S.5    Droge, P.6
  • 47
    • 70350686719 scopus 로고    scopus 로고
    • The role of DNA shape in protein-DNA recognition
    • Rohs, R., West, S.M., Sosinsky, A., Liu, P., Mann, R.S. and Honig, B. (2009) The role of DNA shape in protein-DNA recognition. Nature, 461, 1248-1253.
    • (2009) Nature , vol.461 , pp. 1248-1253
    • Rohs, R.1    West, S.M.2    Sosinsky, A.3    Liu, P.4    Mann, R.S.5    Honig, B.6
  • 49
    • 70350125551 scopus 로고    scopus 로고
    • Triplet repeat length bias and variation in the human transcriptome
    • Molla, M., Delcher, A., Sunyaev, S., Cantor, C. and Kasif, S. (2009) Triplet repeat length bias and variation in the human transcriptome. Proc. Natl Acad. Sci. USA, 106, 17095-17100.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 17095-17100
    • Molla, M.1    Delcher, A.2    Sunyaev, S.3    Cantor, C.4    Kasif, S.5
  • 50
    • 40549105825 scopus 로고    scopus 로고
    • An introduction to BioPerl
    • Stajich, J.E. (2007) An introduction to BioPerl. Methods Mol. Biol., 406, 535-548.
    • (2007) Methods Mol. Biol. , vol.406 , pp. 535-548
    • Stajich, J.E.1
  • 51
    • 60149086624 scopus 로고    scopus 로고
    • BioDBnet: The biological database network
    • Mudunuri, U., Che, A., Yi, M. and Stephens, R.M. (2009) bioDBnet: The biological database network. Bioinformatics, 25, 555-556.
    • (2009) Bioinformatics , vol.25 , pp. 555-556
    • Mudunuri, U.1    Che, A.2    Yi, M.3    Stephens, R.M.4
  • 52
    • 0023796273 scopus 로고
    • The chemistry and biology of unusual DNA structures adopted by oligopurine.oligopyrimidine sequences
    • Wells, R.D., Collier, D.A., Hanvey, J.C., Shimizu, M. and Wohlrab, F. (1988) The chemistry and biology of unusual DNA structures adopted by oligopurine.oligopyrimidine sequences. FASEB J., 2, 2939-2949.
    • (1988) FASEB J. , vol.2 , pp. 2939-2949
    • Wells, R.D.1    Collier, D.A.2    Hanvey, J.C.3    Shimizu, M.4    Wohlrab, F.5
  • 54
    • 0028087782 scopus 로고
    • The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA
    • Ho, P.S. (1994) The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA. Proc. Natl Acad. Sci. USA, 91, 9549-9553.
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 9549-9553
    • Ho, P.S.1
  • 56
    • 0842299592 scopus 로고    scopus 로고
    • DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum
    • Stefl, R., Wu, H., Ravindranathan, S., Sklenar, V. and Feigon, J. (2004) DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum. Proc. Natl Acad. Sci. USA, 101, 1177-1182.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 1177-1182
    • Stefl, R.1    Wu, H.2    Ravindranathan, S.3    Sklenar, V.4    Feigon, J.5
  • 57
    • 77953697462 scopus 로고    scopus 로고
    • A measure of bending in nucleic acids structures applied to A-tract DNA
    • Lankas, F., Spackova, N., Moakher, M., Enkhbayar, P. and Sponer, J. (2010) A measure of bending in nucleic acids structures applied to A-tract DNA. Nucleic Acids Res., 38, 3414-3422.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 3414-3422
    • Lankas, F.1    Spackova, N.2    Moakher, M.3    Enkhbayar, P.4    Sponer, J.5


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