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Volumn , Issue SUPPL.73, 2012, Pages

Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool)

Author keywords

Alternative DNA structure; Cruciform; G quadruplex; Hairpin; nBMST; Non B DNA; Nucleotide sequence analysis; Polybrowse; Slipped DNA; Tandem repeats; Triplex; Z DNA

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; DNA CONFORMATION; DNA SEQUENCE; GENETIC POLYMORPHISM; PRIORITY JOURNAL; SEARCH ENGINE; SEQUENCE ANALYSIS; WEB BROWSER; ANIMAL; BIOLOGY; CHEMISTRY; CONFORMATION; HUMAN; INTERNET; METHODOLOGY; NUCLEIC ACID DATABASE; NUCLEOTIDE MOTIF;

EID: 84863846988     PISSN: 19348266     EISSN: 19348258     Source Type: Journal    
DOI: 10.1002/0471142905.hg1807s73     Document Type: Article
Times cited : (29)

References (62)
  • 1
    • 0025225261 scopus 로고
    • Potential ZDNAelements surround the breakpoints of chromosome translocation within the 5' flanking region of bcl-2 gene
    • Adachi, M. and Tsujimoto, Y. 1990. Potential ZDNAelements surround the breakpoints of chromosome translocation within the 5' flanking region of bcl-2 gene. Oncogene 5:1653-1657.
    • (1990) Oncogene , vol.5 , pp. 1653-1657
    • Adachi, M.1    Tsujimoto, Y.2
  • 2
    • 44849120649 scopus 로고    scopus 로고
    • Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition
    • Akagi, K., Li, J., Stephens, R.M., Volfovsky, N., and Symer, D.E. 2008. Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition. Genome Res. 18:869-880.
    • (2008) Genome Res , vol.18 , pp. 869-880
    • Akagi, K.1    Li, J.2    Stephens, R.M.3    Volfovsky, N.4    Symer, D.E.5
  • 4
    • 8444231721 scopus 로고    scopus 로고
    • Non-BDNAconformations, genomic rearrangements, and human disease
    • Bacolla,A. andWells, R.D. 2004. Non-BDNAconformations, 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
  • 5
    • 65249186097 scopus 로고    scopus 로고
    • Non-B DNA conformations as determinants of mutagenesis and human disease
    • Bacolla, A. and Wells, R.D. 2009. Non-B DNA conformations as determinants of mutagenesis and human disease. Mol. Carcinog. 48:273-285.
    • (2009) Mol. Carcinog. , vol.48 , pp. 273-285
    • Bacolla, A.1    Wells, R.D.2
  • 6
    • 0024437912 scopus 로고
    • Alternating purine-pyrimidine tracts may promote chromosomal translocations seen in a variety of human lymphoid tumours
    • Boehm, T., Mengle-Gaw, L., Kees, U.R., Spurr, N., Lavenir, I., Forster, A., and Rabbitts, T.H. 1989. Alternating purine-pyrimidine tracts may promote chromosomal translocations seen in a variety of human lymphoid tumours. EMBO J. 8:2621-2631.
    • (1989) EMBO J , vol.8 , pp. 2621-2631
    • Boehm, T.1    Mengle-Gaw, L.2    Kees, U.R.3    Spurr, N.4    Lavenir, I.5    Forster, A.6    Rabbitts, T.H.7
  • 7
    • 59849089676 scopus 로고    scopus 로고
    • Microsatellite repeat instability and neurological disease
    • Brouwer, J.R., Willemsen, R., and Oostra, B.A. 2009. Microsatellite repeat instability and neurological disease. Bioessays 31:71-83.
    • (2009) Bioessays , vol.31 , pp. 71-83
    • Brouwer, J.R.1    Willemsen, R.2    Oostra, B.A.3
  • 8
    • 68449102464 scopus 로고    scopus 로고
    • An alternative DNA structure is necessary for pilin antigenic variation in Neisseria gonorrhoeae
    • Cahoon, L.A. and Seifert, H.S. 2009. An alternative DNA structure is necessary for pilin antigenic variation in Neisseria gonorrhoeae. Science 325:764-767.
    • (2009) Science , vol.325 , pp. 764-767
    • Cahoon, L.A.1    Seifert, H.S.2
  • 11
    • 80052971350 scopus 로고    scopus 로고
    • On the sequence-directed nature of human gene mutation: The role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease
    • Cooper, D.N., Bacolla, A., Ferec, C., Vasquez, K.M., Kehrer-Sawatzki, H., and Chen, J.M. 2011. On the sequence-directed nature of human gene mutation: The role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease. Hum. Mutat. 32:1075-1099.
    • (2011) Hum. Mutat. , vol.32 , pp. 1075-1099
    • Cooper, D.N.1    Bacolla, A.2    Ferec, C.3    Vasquez, K.M.4    Kehrer-Sawatzki, H.5    Chen, J.M.6
  • 13
    • 44149093809 scopus 로고    scopus 로고
    • Molecular mechanisms and diagnosis of chromosome 22q11 2 rearrangements
    • Emanuel, B.S. 2008. Molecular mechanisms and diagnosis of chromosome 22q11.2 rearrangements. Dev. Disabil. Res. Rev. 14:11-18.
    • (2008) Dev. Disabil. Res. Rev. , vol.14 , pp. 11-18
    • Emanuel, B.S.1
  • 14
    • 39549086548 scopus 로고    scopus 로고
    • ATR protects the genome against CGG CCG-repeat expansion in Fragile X premutation mice
    • Entezam, A. and Usdin, K. 2008. ATR protects the genome against CGG.CCG-repeat expansion in Fragile X premutation mice. Nucleic Acids Res. 36:1050-1056.
    • (2008) Nucleic Acids Res , vol.36 , pp. 1050-1056
    • Entezam, A.1    Usdin, K.2
  • 15
    • 0344531043 scopus 로고    scopus 로고
    • Instability of the fragile X syndrome repeat in mice: The effect of age, diet and mutations in genes that affect DNA replication, recombination and repair proficiency
    • Fleming, K., Riser, D.K., Kumari, D., and Usdin, K. 2003. Instability of the fragile X syndrome repeat in mice: The effect of age, diet and mutations in genes that affect DNA replication, recombination and repair proficiency. Cytogenet. Genome Res. 100:140-146.
    • (2003) Cytogenet. Genome Res. , vol.100 , pp. 140-146
    • Fleming, K.1    Riser, D.K.2    Kumari, D.3    Usdin, K.4
  • 16
    • 33646168124 scopus 로고    scopus 로고
    • Msh3 is a limiting factor in the formation of intergenerational CTG expansions in DM1 transgenic mice
    • Foiry, L., Dong, L., Savouret, C., Hubert, L., te Riele, H., Junien, C., and Gourdon, G. 2006. Msh3 is a limiting factor in the formation of intergenerational CTG expansions in DM1 transgenic mice. Hum. Genet. 119:520-526.
    • (2006) Hum. Genet. , vol.119 , pp. 520-526
    • Foiry, L.1    Dong, L.2    Savouret, C.3    Hubert, L.4    Te Riele, H.5    Junien, C.6    Gourdon, G.7
  • 18
    • 0041620247 scopus 로고    scopus 로고
    • TRACTS: A program to map oligopurine. oligopyrimidine and other binary DNA tracts
    • Gal, M., Katz, T., Ovadia, A., and Yagil, G. 2003. TRACTS: A program to map oligopurine. oligopyrimidine and other binary DNA tracts. Nucleic Acids Res 31:3682-3685.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3682-3685
    • Gal, M.1    Katz, T.2    Ovadia, A.3    Yagil, G.4
  • 19
    • 4444323468 scopus 로고    scopus 로고
    • Pms2 is a genetic enhancer of trinucleotide CAG. CTG repeat somatic mosaicism: Implications for the mechanism of triplet repeat expansion
    • Gomes-Pereira, M., Fortune, M.T., Ingram, L., McAbney, J.P., and Monckton, D.G. 2004. Pms2 is a genetic enhancer of trinucleotide CAG. CTG repeat somatic mosaicism: Implications for the mechanism of triplet repeat expansion. Hum. Mol. Genet. 13:1815-1825.
    • (2004) Hum. Mol. Genet. , vol.13 , pp. 1815-1825
    • Gomes-Pereira, M.1    Fortune, M.T.2    Ingram, L.3    McAbney, J.P.4    Monckton, D.G.5
  • 20
    • 59949101230 scopus 로고    scopus 로고
    • Chromosomal instability mediated by non-B DNA: Cruciform conformation and not DNA sequence is responsible for recurrent translocation in humans
    • Inagaki, H., Ohye, T., Kogo, H., Kato, T., Bolor, H., Taniguchi, M., Shaikh, T.H., Emanuel, B.S., and Kurahashi, H. 2009. Chromosomal instability mediated by non-B DNA: Cruciform conformation and not DNA sequence is responsible for recurrent translocation in humans. Genome Res. 19:191-198.
    • (2009) Genome Res , vol.19 , pp. 191-198
    • Inagaki, H.1    Ohye, T.2    Kogo, H.3    Kato, T.4    Bolor, H.5    Taniguchi, M.6    Shaikh, T.H.7    Emanuel, B.S.8    Kurahashi, H.9
  • 22
    • 0031025934 scopus 로고    scopus 로고
    • The second case of a t(17;22) in a family with neurofibromatosis type 1: Sequence analysis of the breakpoint regions
    • Kehrer-Sawatzki, H., Haussler, J., Krone,W., Bode, H., Jenne, D.E., Mehnert, K.U., Tummers, U., and Assum, G. 1997. The second case of a t(17;22) in a family with neurofibromatosis type 1: Sequence analysis of the breakpoint regions. Hum. Genet. 99:237-247.
    • (1997) Hum. Genet. , vol.99 , pp. 237-247
    • Kehrer-Sawatzki, H.1    Haussler, J.2    Krone, W.3    Bode, H.4    Jenne, D.E.5    Mehnert, K.U.6    Tummers, U.7    Assum, G.8
  • 23
    • 33747860882 scopus 로고    scopus 로고
    • QGRS Mapper: A web-based server for predictingG-quadruplexes in nucleotide sequences
    • Kikin, O., D'Antonio, L., and Bagga, P.S. 2006. QGRS Mapper: A web-based server for predictingG-quadruplexes in nucleotide sequences. Nucleic Acids Res. 34:W676-W682.
    • (2006) Nucleic Acids Res , vol.34
    • Kikin, O.1    D'Antonio, L.2    Bagga, P.S.3
  • 24
    • 33644877945 scopus 로고    scopus 로고
    • GRSDB: A database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences
    • Kostadinov, R., Malhotra, N., Viotti, M., Shine, R., D'Antonio, L., and Bagga, P. 2006. GRSDB: A database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences. Nucleic Acids Res. 34:D119-D124.
    • (2006) Nucleic Acids Res , vol.34
    • Kostadinov, R.1    Malhotra, N.2    Viotti, M.3    Shine, R.4    D'Antonio, L.5    Bagga, P.6
  • 27
    • 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
  • 29
    • 65849303734 scopus 로고    scopus 로고
    • Human genomic Z-DNAsegments probed by the Z alpha domain ofADAR1
    • Li, H., Xiao, J., Li, J., Lu, L., Feng, S., and Droge, P. 2009. Human genomic Z-DNAsegments probed by the Z alpha domain ofADAR1. 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
  • 30
    • 79951904498 scopus 로고    scopus 로고
    • Transcriptioninduced DNA toxicity at trinucleotide repeats: Double bubble is trouble
    • Lin, Y. and Wilson, J.H. 2011. Transcriptioninduced DNA toxicity at trinucleotide repeats: Double bubble is trouble. Cell Cycle 10:611-618.
    • (2011) Cell Cycle , vol.10 , pp. 611-618
    • Lin, Y.1    Wilson, J.H.2
  • 31
    • 77649144557 scopus 로고    scopus 로고
    • Repeat instability as the basis for human diseases and as a potential target for therapy
    • Lopez Castel, A., Cleary, J.D., and Pearson, C.E. 2010. Repeat instability as the basis for human diseases and as a potential target for therapy. Nat. Rev. Mol. Cell. Biol. 11:165-170.
    • (2010) Nat. Rev. Mol. Cell. Biol. , vol.11 , pp. 165-170
    • Lopez Castel, A.1    Cleary, J.D.2    Pearson, C.E.3
  • 32
    • 0032708840 scopus 로고    scopus 로고
    • Msh2 deficiency prevents in vivo somatic instability of the CAG repeat in Huntington disease transgenicmice
    • Manley, K., Shirley, T.L., Flaherty, L., and Messer, A. 1999. Msh2 deficiency prevents in vivo somatic instability of the CAG repeat in Huntington disease transgenicmice. Nat. Genet. 23:471-473.
    • (1999) Nat. Genet. , vol.23 , pp. 471-473
    • Manley, K.1    Shirley, T.L.2    Flaherty, L.3    Messer, A.4
  • 33
    • 77958109197 scopus 로고    scopus 로고
    • Mechanisms of trinucleotide repeat instability during human development
    • McMurray, C.T. 2010. Mechanisms of trinucleotide repeat instability during human development. Nat. Rev. Genet. 11:786-799.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 786-799
    • McMurray, C.T.1
  • 34
    • 67349104211 scopus 로고    scopus 로고
    • Molecular mechanisms underlying polyalanine diseases
    • Messaed, C. and Rouleau, G.A. 2009. Molecular mechanisms underlying polyalanine diseases. Neurobiol. Dis. 34:397-405.
    • (2009) Neurobiol. Dis. , vol.34 , pp. 397-405
    • Messaed, C.1    Rouleau, G.A.2
  • 35
    • 34250878426 scopus 로고    scopus 로고
    • Expandable DNA repeats and human disease
    • Mirkin, S.M. 2007. Expandable DNA repeats and human disease. Nature 447:932-940.
    • (2007) Nature , vol.447 , pp. 932-940
    • Mirkin, S.M.1
  • 36
    • 34547692622 scopus 로고    scopus 로고
    • Trinucleotide repeat disorders
    • Orr, H.T. and Zoghbi, H.Y. 2007. Trinucleotide repeat disorders. Annu. Rev. Neurosci. 30:575-621.
    • (2007) Annu. Rev. Neurosci. , vol.30 , pp. 575-621
    • Orr, H.T.1    Zoghbi, H.Y.2
  • 39
    • 77953659252 scopus 로고    scopus 로고
    • Long intronic GAA repeats causing Friedreich ataxia impede transcription elongation
    • Punga, T. and Buhler,M. 2010. Long intronic GAA repeats causing Friedreich ataxia impede transcription elongation. EMBO Mol. Med. 2:120-129.
    • (2010) EMBO Mol. Med. , vol.2 , pp. 120-129
    • Punga, T.1    Buhler, M.2
  • 41
    • 33747819216 scopus 로고    scopus 로고
    • Quadfinder: Server for identification and analysis of quadruplex-forming motifs in nucleotide sequences
    • Scaria, V., Hariharan, M., Arora, A., and Maiti, S. 2006. Quadfinder: Server for identification and analysis of quadruplex-forming motifs in nucleotide sequences. Nucleic Acids Res. 34:W683-W685.
    • (2006) Nucleic Acids Res , vol.34
    • Scaria, V.1    Hariharan, M.2    Arora, A.3    Maiti, S.4
  • 42
    • 0026752148 scopus 로고
    • Mapping Z-DNA in the human genome. Computeraidedmapping 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. Computeraidedmapping 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
  • 47
    • 79958724230 scopus 로고    scopus 로고
    • Analysis of a breakpoint cluster reveals insight into themechanism of intrachromosomal amplification in a lymphoid malignancy
    • Sinclair, P.B., Parker, H., An, Q., Rand, V., Ensor, H., Harrison, C. J., and Strefford, J.C. 2011. Analysis of a breakpoint cluster reveals insight into themechanism of intrachromosomal amplification in a lymphoid malignancy. Hum. Mol. Genet. 20:2591-2602.
    • (2011) Hum. Mol. Genet. , vol.20 , pp. 2591-2602
    • Sinclair, P.B.1    Parker, H.2    An, Q.3    Rand, V.4    Ensor, H.5    Harrison, C.J.6    Strefford, J.C.7
  • 48
    • 77949831756 scopus 로고    scopus 로고
    • Structural variation in the human genome and its role in disease
    • Stankiewicz, P. and Lupski, J.R. 2010. Structural variation in the human genome and its role in disease. Annu. Rev. Med. 61:437-455.
    • (2010) Annu. Rev. Med. , vol.61 , pp. 437-455
    • Stankiewicz, P.1    Lupski, J.R.2
  • 52
    • 0037081784 scopus 로고    scopus 로고
    • Somatic expansion behaviour of the (CTG)n repeat in myotonic dystrophy knock-in mice is differentially affected by Msh3 and Msh6 mismatch-repair proteins
    • van den Broek, W.J., Nelen, M.R., Wansink, D.G., Coerwinkel, M.M., te Riele, H., Groenen, P.J., and Wieringa, B. 2002. Somatic expansion behaviour of the (CTG)n repeat in myotonic dystrophy knock-in mice is differentially affected by Msh3 and Msh6 mismatch-repair proteins. Hum. Mol. Genet. 11:191-198.
    • (2002) Hum. Mol. Genet. , vol.11 , pp. 191-198
    • van den Broek, W.J.1    Nelen, M.R.2    Wansink, D.G.3    Coerwinkel, M.M.4    Te Riele, H.5    Groenen, P.J.6    Wieringa, B.7
  • 53
    • 0020526912 scopus 로고
    • The frequency and mutation-rate of balanced autosomal rearrangements in man estimated from prenatal geneticstudies for advanced maternal age
    • Vandyke, D.L., Weiss, L., Roberson, J.R., and Babu, V.R. 1983. The frequency and mutation-rate of balanced autosomal rearrangements in man estimated from prenatal geneticstudies for advanced maternal age. Am. J. Hum. Genet. 35:301-308.
    • (1983) Am. J. Hum. Genet. , vol.35 , pp. 301-308
    • Vandyke, D.L.1    Weiss, L.2    Roberson, J.R.3    Babu, V.R.4
  • 54
    • 34249907843 scopus 로고    scopus 로고
    • Non-B DNA conformations, mutagenesis and disease
    • Wells, R.D. 2007. Non-B DNA conformations, mutagenesis and disease. Trends Biochem. Sci. 32:271-278.
    • (2007) Trends Biochem. Sci. , vol.32 , pp. 271-278
    • Wells, R.D.1
  • 55
    • 44949208513 scopus 로고    scopus 로고
    • DNA triplexes and Friedreich ataxia
    • Wells, R.D. 2008. DNA triplexes and Friedreich ataxia. FASEB J. 22:1625-1634.
    • (2008) FASEB J , vol.22 , pp. 1625-1634
    • Wells, R.D.1
  • 56
    • 22244446185 scopus 로고    scopus 로고
    • Advances in mechanisms of genetic instability related to hereditary neurological diseases
    • Wells, R.D., Dere, R., Hebert, M.L., Napierala, M., and Son, L.S. 2005. Advances in mechanisms of genetic instability related to hereditary neurological diseases. Nucleic Acids Res. 33:3785-3798.
    • (2005) Nucleic Acids Res , vol.33 , pp. 3785-3798
    • Wells, R.D.1    Dere, R.2    Hebert, M.L.3    Napierala, M.4    Son, L.S.5
  • 58
    • 0033566892 scopus 로고    scopus 로고
    • Structure and possible mechanisms of TEL-AML1 gene fusions in childhood acute lymphoblastic leukemia
    • Wiemels, J.L. and Greaves, M. 1999. Structure and possible mechanisms of TEL-AML1 gene fusions in childhood acute lymphoblastic leukemia. Cancer Res. 59:4075-4082.
    • (1999) Cancer Res , vol.59 , pp. 4075-4082
    • Wiemels, J.L.1    Greaves, M.2
  • 59
    • 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
  • 60
    • 38549157087 scopus 로고    scopus 로고
    • Greglist: A database listing potential G-quadruplex regulated genes
    • Zhang, R., Lin, Y., and Zhang, C.T. 2008. Greglist: A database listing potential G-quadruplex regulated genes. Nucleic Acids Res. 36:D372-D376.
    • (2008) Nucleic Acids Res , vol.36
    • Zhang, R.1    Lin, Y.2    Zhang, C.T.3
  • 61
    • 73749085274 scopus 로고    scopus 로고
    • Non-BDNAstructure-induced genetic instability and evolution
    • Zhao, J., Bacolla, A.,Wang, G., and Vasquez, K.M. 2010. Non-BDNAstructure-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


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