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Volumn 42, Issue 11, 2014, Pages 7236-7246

Nascent RNA transcripts facilitate the formation of G-quadruplexes

Author keywords

[No Author keywords available]

Indexed keywords

DNA HYBRID; GUANINE QUADRUPLEX;

EID: 84903135003     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku416     Document Type: Article
Times cited : (17)

References (41)
  • 1
    • 0033609387 scopus 로고    scopus 로고
    • Complex dynamics and phase synchronization in spatially extended ecological systems
    • Blasius B. Huppert A. and Stone L. (1999) Complex dynamics and phase synchronization in spatially extended ecological systems. Nature 399 354-359.
    • (1999) Nature , vol.399 , pp. 354-359
    • Blasius, B.1    Huppert, A.2    Stone, L.3
  • 2
    • 84900331303 scopus 로고    scopus 로고
    • Molecular population dynamics of DNA structures in a Bcl-2 promoter sequence is regulated by small-molecules and the transcription factor hnRNP LL
    • in press doi:10.1093/nar/gku185
    • Cui Y. Koirala D. Kang H. Dhakal S. Yangyuoru P. Hurley L.H. and Mao H. (2014) Molecular population dynamics of DNA structures in a Bcl-2 promoter sequence is regulated by small-molecules and the transcription factor hnRNP LL. Nucleic Acids Res. in press doi:10.1093/nar/gku185.
    • (2014) Nucleic Acids Res.
    • Cui, Y.1    Koirala, D.2    Kang, H.3    Dhakal, S.4    Yangyuoru, P.5    Hurley, L.H.6    Mao, H.7
  • 3
    • 84875464903 scopus 로고    scopus 로고
    • Quantitative visualization of DNA G-quadruplex structures in human cells
    • Biffi G. Tannahill D. McCafferty J. and Balasubramanian S. (2013) Quantitative visualization of DNA G-quadruplex structures in human cells. Nat. Chem. 5 182-186.
    • (2013) Nat. Chem. , vol.5 , pp. 182-186
    • Biffi, G.1    Tannahill, D.2    McCafferty, J.3    Balasubramanian, S.4
  • 4
    • 79957556530 scopus 로고    scopus 로고
    • DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase
    • Paeschke K. Capra J.A. and Zakian V.A. (2011) DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase. Cell 145 678-691.
    • (2011) Cell , vol.145 , pp. 678-691
    • Paeschke, K.1    Capra, J.A.2    Zakian, V.A.3
  • 5
    • 0037015078 scopus 로고    scopus 로고
    • Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription
    • Siddiqui-Jain A. Grand C.L. Bearss D.J. and Hurley L.H. (2002) Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc. Natl. Acad. Sci. U.S.A. 99 11593-11598.
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 11593-11598
    • Siddiqui-Jain, A.1    Grand, C.L.2    Bearss, D.J.3    Hurley, L.H.4
  • 6
    • 30044448463 scopus 로고    scopus 로고
    • Extreme conformational diversity in human telomeric DNA
    • Lee J.Y. Okumus B. Kim D.S. and Ha T. (2005) Extreme conformational diversity in human telomeric DNA. Proc. Natl. Acad. Sci. U.S.A. 102 18938-18943.
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 18938-18943
    • Lee, J.Y.1    Okumus, B.2    Kim, D.S.3    Ha, T.4
  • 7
    • 84890418685 scopus 로고    scopus 로고
    • Structure of the human telomere in Na+ solution: An antiparallel (2+2) G-quadruplex scaffold reveals additional diversity
    • Lim K.W. Ng V.C.M. Mart́n-Pintado N. Heddi B. and Phan A.T. (2013) Structure of the human telomere in Na+ solution: an antiparallel (2+2) G-quadruplex scaffold reveals additional diversity. Nucleic Acids Res. 41 10556-10562.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 10556-10562
    • Lim, K.W.1    Ng, V.C.M.2    Mart́n-Pintado, N.3    Heddi, B.4    Phan, A.T.5
  • 8
    • 84873651708 scopus 로고    scopus 로고
    • Long-loop G-quadruplexes are misfolded population minorities with fast transition kinetics in human telomeric sequences
    • Koirala D. Ghimire C. Bohrer C. Sannohe Y. Sugiyama H. and Mao H. (2013) Long-loop G-quadruplexes are misfolded population minorities with fast transition kinetics in human telomeric sequences. J. Am. Chem. Soc. 135 2235-2241.
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 2235-2241
    • Koirala, D.1    Ghimire, C.2    Bohrer, C.3    Sannohe, Y.4    Sugiyama, H.5    Mao, H.6
  • 10
    • 77957032993 scopus 로고    scopus 로고
    • Telomeric repeat-containing RNA structure in living cells
    • Xu Y. Suzuki Y. Ito K. and Komiyama M. (2010) Telomeric repeat-containing RNA structure in living cells. Proc. Natl. Acad. Sci. U.S.A. 107 14579-14584.
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 14579-14584
    • Xu, Y.1    Suzuki, Y.2    Ito, K.3    Komiyama, M.4
  • 11
    • 0017396845 scopus 로고
    • Rates of formation and thermal stabilities of RNA:DNA and DNA:DNA duplexes at high concentrations of formamide
    • Casey J. and Davidson N. (1977) Rates of formation and thermal stabilities of RNA:DNA and DNA:DNA duplexes at high concentrations of formamide. Nucleic Acids Res. 4 1539-1552.
    • (1977) Nucleic Acids Res. , vol.4 , pp. 1539-1552
    • Casey, J.1    Davidson, N.2
  • 12
    • 84869006723 scopus 로고    scopus 로고
    • A hybrid G-quadruplex structure formed between RNA and DNA explains the extraordinary stability of the mitochondrial R-loop
    • Wanrooij P.H. Uhler J.P. Shi Y. Westerlund F. Falkenberg M. and Gustafsson C.M. (2012) A hybrid G-quadruplex structure formed between RNA and DNA explains the extraordinary stability of the mitochondrial R-loop. Nucleic Acids Res. 40 10334-10344.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 10334-10344
    • Wanrooij, P.H.1    Uhler, J.P.2    Shi, Y.3    Westerlund, F.4    Falkenberg, M.5    Gustafsson, C.M.6
  • 13
    • 84878526299 scopus 로고    scopus 로고
    • Co-transcriptional formation of DNA:RNA hybrid G-quadruplex and potential function as constitutional cis element for transcription control
    • Zheng K. Xiao S. Liu J. Zhang J. Hao Y. and Tan Z. (2013) Co-transcriptional formation of DNA:RNA hybrid G-quadruplex and potential function as constitutional cis element for transcription control. Nucleic Acids Res. 41 5533-5541.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 5533-5541
    • Zheng, K.1    Xiao, S.2    Liu, J.3    Zhang, J.4    Hao, Y.5    Tan, Z.6
  • 14
    • 84890411617 scopus 로고    scopus 로고
    • Bioinformatic analysis reveals an evolutional selection for DNA:RNA hybrid G-quadruplex structures as putative transcription regulatory elements in warm-blooded animals
    • Xiao S. Zhang J. Zheng K. Hao Y. and Tan Z. (2013) Bioinformatic analysis reveals an evolutional selection for DNA:RNA hybrid G-quadruplex structures as putative transcription regulatory elements in warm-blooded animals. Nucleic Acids Res. 41 10379-10390.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 10379-10390
    • Xiao, S.1    Zhang, J.2    Zheng, K.3    Hao, Y.4    Tan, Z.5
  • 15
    • 77956252000 scopus 로고    scopus 로고
    • Coexistence of two distinct G-quadruplex conformations in the hTERT promoter
    • Lim K.W. Lacroix L. Yue D.J. Lim J.K. Lim J.M. and Phan A.T. (2010) Coexistence of two distinct G-quadruplex conformations in the hTERT promoter. J. Am. Chem. Soc. 132 12331-12342.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 12331-12342
    • Lim, K.W.1    Lacroix, L.2    Yue, D.J.3    Lim, J.K.4    Lim, J.M.5    Phan, A.T.6
  • 19
    • 84893465164 scopus 로고    scopus 로고
    • Mechanism and manipulation of DNA:RNA hybrid G-quadruplex formation in transcription of G-rich DNA
    • Zhang J. Zheng K. Xiao S. Hao Y. and Tan Z. (2014) Mechanism and manipulation of DNA:RNA hybrid G-quadruplex formation in transcription of G-rich DNA. J. Am. Chem. Soc. 136 1381-1390.
    • (2014) J. Am. Chem. Soc. , vol.136 , pp. 1381-1390
    • Zhang, J.1    Zheng, K.2    Xiao, S.3    Hao, Y.4    Tan, Z.5
  • 20
    • 75649089282 scopus 로고    scopus 로고
    • Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA
    • Zheng K. Chen Z. Hao Y. and Tan Z. (2010) Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA. Nucleic Acids Res. 38 327-338.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 327-338
    • Zheng, K.1    Chen, Z.2    Hao, Y.3    Tan, Z.4
  • 21
    • 38949215796 scopus 로고    scopus 로고
    • An integrated laser-tweezers instrument for microanalysis of individual protein aggregates
    • Mao H. and Luchette P. (2008) An integrated laser-tweezers instrument for microanalysis of individual protein aggregates. Sensors and Actuators B: Chemical 129 764-771.
    • (2008) Sensors and Actuators B: Chemical , vol.129 , pp. 764-771
    • Mao, H.1    Luchette, P.2
  • 25
    • 84876044953 scopus 로고    scopus 로고
    • Structural and mechanical properties of individual human telomeric G-quadruplexes in molecularly crowded solutions
    • Dhakal S. Cui Y. Koirala D. Ghimire C. Kushwaha S. Yu Z. Yangyuoru P.M. and Mao H. (2013) Structural and mechanical properties of individual human telomeric G-quadruplexes in molecularly crowded solutions. Nucleic Acids Res. 41 3915-3923.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 3915-3923
    • Dhakal, S.1    Cui, Y.2    Koirala, D.3    Ghimire, C.4    Kushwaha, S.5    Yu, Z.6    Yangyuoru, P.M.7    Mao, H.8
  • 26
    • 84863341390 scopus 로고    scopus 로고
    • The tertiary DNA structure in the single-stranded hTERT promoter fragment unfolds and refolds by parallel pathways via cooperative or sequential events
    • Yu Z. Gaerig V. Cui Y. Kang H. Gokhale V. Zhao Y. Hurley L.H. andMao H. (2012) The tertiary DNA structure in the single-stranded hTERT promoter fragment unfolds and refolds by parallel pathways via cooperative or sequential events. J. Am. Chem. Soc. 134 5157-5164.
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 5157-5164
    • Yu, Z.1    Gaerig, V.2    Cui, Y.3    Kang, H.4    Gokhale, V.5    Zhao, Y.6
  • 27
    • 77954270742 scopus 로고    scopus 로고
    • Coexistence of an ILPR i-motif and a partially folded structure with comparable mechanical stability revealed at the single-molecule level
    • Dhakal S. Schonhoft J.D. Koirala D. Yu Z. Basu S. and Mao H. (2010) Coexistence of an ILPR i-motif and a partially folded structure with comparable mechanical stability revealed at the single-molecule level. J. Am. Chem. Soc. 132 8991-8997.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 8991-8997
    • Dhakal, S.1    Schonhoft, J.D.2    Koirala, D.3    Yu, Z.4    Basu, S.5    Mao, H.6
  • 28
    • 33746093492 scopus 로고    scopus 로고
    • Cotranscriptional processes and their influence on genome stability
    • Li X. and Manley J.L. (2006) Cotranscriptional processes and their influence on genome stability. Genes Dev. 20 1838-1847.
    • (2006) Genes Dev. , vol.20 , pp. 1838-1847
    • Li, X.1    Manley, J.L.2
  • 29
    • 0037474202 scopus 로고    scopus 로고
    • Binding of the priming nucleotide in the initiation of transcription by T7 RNA polymerase
    • Kuzmine I. Gottlieb P.A. and Martin C.T. (2003) Binding of the priming nucleotide in the initiation of transcription by T7 RNA polymerase. J. Biol. Chem. 278 2819-2823.
    • (2003) J. Biol. Chem. , vol.278 , pp. 2819-2823
    • Kuzmine, I.1    Gottlieb, P.A.2    Martin, C.T.3
  • 30
    • 77449111348 scopus 로고    scopus 로고
    • Biochemical techniques for the characterization of G-quadruplex structures: EMSA DMS footprinting and DNA polymerase stop assay
    • Sun D. and Hurley L.H. (2010) Biochemical techniques for the characterization of G-quadruplex structures: EMSA DMS footprinting and DNA polymerase stop assay. Methods Mol. Biol. 608 65-79.
    • (2010) Methods Mol. Biol. , vol.608 , pp. 65-79
    • Sun, D.1    Hurley, L.H.2
  • 31
    • 0037169496 scopus 로고    scopus 로고
    • Promoter clearance by T7 RNA polymerase
    • Liu C. and Martin C.T. (2002) Promoter clearance by T7 RNA polymerase. J. Biol. Chem. 277 2725-2731.
    • (2002) J. Biol. Chem. , vol.277 , pp. 2725-2731
    • Liu, C.1    Martin, C.T.2
  • 32
    • 84874270241 scopus 로고    scopus 로고
    • Non-B DNA structures show diverse conformations and complex transition kinetics comparable to RNA or proteins-A perspective from mechanical unfolding and refolding experiments
    • Yu Z. and Mao H. (2013) Non-B DNA structures show diverse conformations and complex transition kinetics comparable to RNA or proteins-a perspective from mechanical unfolding and refolding experiments. Chem. Rec. 13 102-116.
    • (2013) Chem. Rec. , vol.13 , pp. 102-116
    • Yu, Z.1    Mao, H.2
  • 33
    • 0001505226 scopus 로고    scopus 로고
    • Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids
    • Hardin C.C. Perry A.G. and White K. (2000) Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids. Biopolymers 56 147-194.
    • (2000) Biopolymers , vol.56 , pp. 147-194
    • Hardin, C.C.1    Perry, A.G.2    White, K.3
  • 34
    • 84856446581 scopus 로고    scopus 로고
    • Intramolecular folding in three tandem guanine repeats of human telomeric DNA
    • Koirala D. Mashimo T. Sannohe Y. Yu Z. Mao H. and Sugiyama H. (2012) Intramolecular folding in three tandem guanine repeats of human telomeric DNA. Chem. Commun. 48 2006-2008.
    • (2012) Chem. Commun. , vol.48 , pp. 2006-2008
    • Koirala, D.1    Mashimo, T.2    Sannohe, Y.3    Yu, Z.4    Mao, H.5    Sugiyama, H.6
  • 36
    • 50149118845 scopus 로고    scopus 로고
    • Thermal probing of E coli RNA polymerase off-pathway mechanisms
    • Mejia Y.X. Mao H. Forde N.R. and Bustamante C. (2008) Thermal probing of E. coli RNA polymerase off-pathway mechanisms. J. Mol. Biol. 382 628-637.
    • (2008) J. Mol. Biol. , vol.382 , pp. 628-637
    • Mejia, Y.X.1    Mao, H.2    Forde, N.R.3    Bustamante, C.4
  • 37
    • 84885427690 scopus 로고    scopus 로고
    • Mechanical affinity as a new metrics to evaluate binding events
    • Koirala D. Yangyuoru P.M. and Mao H. (2013) Mechanical affinity as a new metrics to evaluate binding events. Rev. Anal. Chem. 32 197-208.
    • (2013) Rev. Anal. Chem. , vol.32 , pp. 197-208
    • Koirala, D.1    Yangyuoru, P.M.2    Mao, H.3
  • 39
    • 79961120537 scopus 로고    scopus 로고
    • Improving free-energy estimates from unidirectional work measurements: Theory and experiment
    • 060601-1-5
    • Palassini M. and Ritort F. (2011) Improving free-energy estimates from unidirectional work measurements: theory and experiment. Phys. Rev. Lett. 107 060601-1-5.
    • (2011) Phys. Rev. Lett. , pp. 107
    • Palassini, M.1    Ritort, F.2
  • 40
    • 33845967859 scopus 로고    scopus 로고
    • Transient state kinetics of transcription elongation by T7 RNA polymerase
    • Anand V.S. and Patel S.S. (2006) Transient state kinetics of transcription elongation by T7 RNA polymerase. J. Biol. Chem. 281 35677-35685.
    • (2006) J. Biol. Chem. , vol.281 , pp. 35677-35685
    • Anand, V.S.1    Patel, S.S.2
  • 41
    • 79959861867 scopus 로고    scopus 로고
    • Detection of single nucleotide polymorphism using tension-dependent stochastic behavior of a single-molecule template
    • Koirala D. Yu Z. Dhakal S. and Mao H. (2011) Detection of single nucleotide polymorphism using tension-dependent stochastic behavior of a single-molecule template. J. Am. Chem. Soc. 133 9988-9991.
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 9988-9991
    • Koirala, D.1    Yu, Z.2    Dhakal, S.3    Mao, H.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.