메뉴 건너뛰기




Volumn 42, Issue 9, 2014, Pages 5755-5764

Molecular population dynamics of DNA structures in a bcl-2 promoter sequence is regulated by small molecules and the transcription factor hnRNP LL

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL COMPOUND; CYTOSINE; PROTEIN BCL 2; SMALL MOLECULE IMC 48; SMALL MOLECULE IMC 76; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR HNRNP LL; UNCLASSIFIED DRUG;

EID: 84900331303     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku185     Document Type: Article
Times cited : (33)

References (46)
  • 4
    • 84857080591 scopus 로고    scopus 로고
    • Functional complexity and regulation through RNA dynamics
    • Dethoff, E.A., Chugh, J., Mustoe, A.M. and Al-Hashimi, H.M. (2012) Functional complexity and regulation through RNA dynamics. Nature, 482, 322-330
    • (2012) Nature , vol.482 , pp. 322-330
    • Dethoff, E.A.1    Chugh, J.2    Mustoe, A.M.3    Al-Hashimi, H.M.4
  • 5
    • 77953231020 scopus 로고    scopus 로고
    • The folding cooperativity of a protein is controlled by its chain topology
    • Shank, E.A., Cecconi, C., Dill, J.W., Marqusee, S. and Bustamante, C. (2010) The folding cooperativity of a protein is controlled by its chain topology. Nature, 465, 637-640
    • (2010) Nature , vol.465 , pp. 637-640
    • Shank, E.A.1    Cecconi, C.2    Dill, J.W.3    Marqusee, S.4    Bustamante, C.5
  • 6
    • 84901324417 scopus 로고    scopus 로고
    • RNA tertiary and secondary unfolding monitored by mechanical stretching of single molecules
    • Onoa, G.B., Liphardt, J.T., Smith, S.B., Tinoco, I. and Bustamante, C.J. (2001) RNA tertiary and secondary unfolding monitored by mechanical stretching of single molecules. Biophys. J., 80, 155a
    • (2001) Biophys. J. , vol.80
    • Onoa, G.B.1    Liphardt, J.T.2    Smith, S.B.3    Tinoco, I.4    Bustamante, C.J.5
  • 7
    • 38849204944 scopus 로고    scopus 로고
    • Direct observation of hierarchical folding in single riboswitch aptamers
    • DOI 10.1126/science.1151298
    • Greenleaf, W.J., Frieda, K.L., Foster, D.A., Woodside, M.T. and Block, S.M. (2008) Direct observation of hierarchical folding in single riboswitch aptamers. Science, 319, 630-633. (Pubitemid 351197067
    • (2008) Science , vol.319 , Issue.5863 , pp. 630-633
    • Greenleaf, W.J.1    Frieda, K.L.2    Foster, D.A.N.3    Woodside, M.T.4    Block, S.M.5
  • 9
    • 0038497542 scopus 로고
    • Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid
    • Watson, J.D. and Crick, F.H. (1953) Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature, 171, 737-738
    • (1953) Nature , vol.171 , pp. 737-738
    • Watson, J.D.1    Crick, F.H.2
  • 11
    • 0024787884 scopus 로고
    • Monovalent cation-induced structure of telomeric DNA: The G-quartet model
    • DOI 10.1016/0092-8674(89)90610-7
    • Williamson, J.R., Raghuraman, M.K. and Cech, T.R. (1989) Monovalent cation-induced structure of telomeric DNA: The G-quartet model. Cell, 59, 871-880. (Pubitemid 20022377
    • (1989) Cell , vol.59 , Issue.5 , pp. 871-880
    • Williamson, J.R.1    Raghuraman, M.K.2    Cech, T.R.3
  • 12
    • 1042268168 scopus 로고    scopus 로고
    • G-quartets 40 years later: From 5-GMP to molecular biology and supramolecular chemistry
    • Davis, J.T. (2004) G-quartets 40 years later: From 5-GMP to molecular biology and supramolecular chemistry. Angew. Chem. Int. Ed., 43, 668-698
    • (2004) Angew. Chem. Int. Ed. , vol.43 , pp. 668-698
    • Davis, J.T.1
  • 13
    • 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. and Mao, 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    Hurley, L.H.7    Mao, H.8
  • 14
    • 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
  • 15
    • 16544387620 scopus 로고    scopus 로고
    • DNA structural changes as the basis for a nanomolecular device
    • Alberti, P. and Mergny, J.L. (2004) DNA structural changes as the basis for a nanomolecular device. Cell. Mol. Biol., 50, 241-253
    • (2004) Cell. Mol. Biol , vol.50 , pp. 241-253
    • Alberti, P.1    Mergny, J.L.2
  • 16
    • 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. USA., 102, 18938-18943
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 18938-18943
    • Lee, J.Y.1    Okumus, B.2    Kim, D.S.3    Ha, T.4
  • 17
    • 80053518905 scopus 로고    scopus 로고
    • PH-induced intramolecular folding dynamics of i-motif DNA
    • Choi, J., Kim, S., Tachikawa, T., Fujitsuka, M. and Majima, T. (2011) pH-induced intramolecular folding dynamics of i-motif DNA. J. Am. Chem. Soc., 133, 16146-16153
    • (2011) J. Am. Chem. Soc , vol.133 , pp. 16146-16153
    • Choi, J.1    Kim, S.2    Tachikawa, T.3    Fujitsuka, M.4    Majima, T.5
  • 18
    • 0023788886 scopus 로고
    • Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis
    • Sen, D. and Gilbert, W. (1988) Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature, 334, 364-366
    • (1988) Nature , vol.334 , pp. 364-366
    • Sen, D.1    Gilbert, W.2
  • 19
    • 0027278767 scopus 로고
    • A tetrameric DNA structure with protonated cytosine.cytosine base pairs
    • Gehring, K., Leroy, J.L. and Gúeron, M. (1993) A tetrameric DNA structure with protonated cytosine.cytosine base pairs. Nature, 363, 561-564
    • (1993) Nature , vol.363 , pp. 561-564
    • Gehring, K.1    Leroy, J.L.2    Gúeron, M.3
  • 21
    • 0029956118 scopus 로고    scopus 로고
    • Inability of rna to form the i-motif: Implications for triplex formation
    • Lacroix, L., Mergny, J-L., Leroy, J-L. and H́elène, C. (1996) Inability of RNA to form the i-motif: Implications for triplex formation. Biochemistry, 35, 8715-8722
    • (1996) Biochemistry , vol.35 , pp. 8715-8722
    • Lacroix, L.1    Mergny, J.-L.2    Leroy, J.-L.3    H́elène, C.4
  • 23
    • 84861895605 scopus 로고    scopus 로고
    • G-quadruplex and i-motif are mutually exclusive in ILPR double-stranded DNA
    • Dhakal, S., Yu, Z., Konik, R., Cui, Y., Koirala, D. and Mao, H. (2012) G-quadruplex and i-motif are mutually exclusive in ILPR double-stranded DNA. Biophys. J., 102, 2575-2584
    • (2012) Biophys. J. , vol.102 , pp. 2575-2584
    • Dhakal, S.1    Yu, Z.2    Konik, R.3    Cui, Y.4    Koirala, D.5    Mao, H.6
  • 24
    • 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
  • 25
    • 33744472232 scopus 로고    scopus 로고
    • G-quadruplex formation within the promoter of the KRAS proto-oncogene and its effect on transcription
    • DOI 10.1093/nar/gkl286
    • Cogoi, S. and Xodo, L.E. (2006) G-quadruplex formation within the promoter of the KRAS proto-oncogene and its effect on transcription. Nucleic Acids Res., 34, 2536-2549. (Pubitemid 43985618
    • (2006) Nucleic Acids Research , vol.34 , Issue.9 , pp. 2536-2549
    • Cogoi, S.1    Xodo, L.E.2
  • 26
    • 71549131009 scopus 로고    scopus 로고
    • PH-modulatedWatson-Crick duplex-qaudruplex equilibria of guanine-rich and cytosine-rich DNA sequences 140 base pairs upstream of the c-kit transcription intiation site
    • Bucek, P., Jaumot, J., Avino, A., Eritja, R. and Gargallo, R. (2009) pH-modulatedWatson-Crick duplex-qaudruplex equilibria of guanine-rich and cytosine-rich DNA sequences 140 base pairs upstream of the c-kit transcription intiation site. Chem. Eur. J., 15, 12663-12671
    • (2009) Chem. Eur. J. , vol.15 , pp. 12663-12671
    • Bucek, P.1    Jaumot, J.2    Avino, A.3    Eritja, R.4    Gargallo, R.5
  • 27
    • 0034716937 scopus 로고    scopus 로고
    • The solution structure and internal motions of a fragment of the cytidine-rich strand of the human telomere
    • Phan, A.T., Gueron, M. and Leroy, J.L. (2000) The solution structure and internal motions of a fragment of the cytidine-rich strand of the human telomere. J. Mol. Biol., 299, 123-144
    • (2000) J. Mol. Biol , vol.299 , pp. 123-144
    • Phan, A.T.1    Gueron, M.2    Leroy, J.L.3
  • 28
    • 0032531972 scopus 로고    scopus 로고
    • Intercalated cytosine motif and novel adenine clusters in the crystal structure of the tetrahymena telomere
    • DOI 10.1093/nar/26.20.4696
    • Cai, L., Chen, L., Raghavan, S., Ratliff, R., Myozis, R. and Rich, A. (1998) Intercalated cytosine motif and novel adenine clusters in the crystal structure of the Tetrahymena telomere. Nucleic Acids Res., 26, 4696-4705. (Pubitemid 28466618
    • (1998) Nucleic Acids Research , vol.26 , Issue.20 , pp. 4696-4705
    • Cai, L.1    Chen, L.2    Raghavan, S.3    Ratliff, R.4    Moyzis, R.5    Rich, A.6
  • 31
    • 84901314629 scopus 로고    scopus 로고
    • Population and genotype dynamics in three externally driven environments
    • William, A. and Nelson, E.M.F.J.W. (2005) Population and genotype dynamics in three externally driven environments. Nature, 433, 413-417
    • (2005) Nature , vol.433 , pp. 413-417
    • William, A.1    Nelson, E.M.F.J.W.2
  • 32
    • 84896496345 scopus 로고    scopus 로고
    • The dynamic character of the bcl2 promoter i-motif provides a mechanism for modulation of gene expression by compounds that bindselectively to the alternative dna hairpin structure
    • doi: 10.1021/ja410934b
    • Kendrick, S., Kang, H-J., Akiyama, Y., Agrawal, P., Gokhale, V., Yang, D., Hecht, S.M. and Hurley, L.H. (2014) The dynamic character of the BCL2 promoter i-Motif provides a mechanism for modulation of gene expression by compounds that bindselectively to the alternative DNA hairpin structure. J. Am. Chem. Soc., doi: 10.1021/ja410934b
    • (2014) J. Am. Chem. Soc
    • Kendrick, S.1    Kang, H.-J.2    Akiyama, Y.3    Agrawal, P.4    Gokhale, V.5    Yang, D.6    Hecht, S.M.7    Hurley, L.H.8
  • 33
    • 84896516232 scopus 로고    scopus 로고
    • The transcriptional complex between the bcl2 i-motif and hnrnp ll is a molecular switch to control gene expression
    • doi: 10.1021/ja4109352
    • Kang, H-J., Kendrick, S., Hecht, S.M. and Hurley, L.H. (2014) The transcriptional complex between the BCL2 i-motif and hnRNP LL Is a molecular switch to control gene expression. J. Am. Chem. Soc., doi: 10.1021/ja4109352
    • (2014) J. Am. Chem. Soc
    • Kang, H.-J.1    Kendrick, S.2    Hecht, S.M.3    Hurley, L.H.4
  • 34
    • 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
  • 35
    • 27144527479 scopus 로고    scopus 로고
    • Regulation of bacterial gene expression by riboswitches
    • Winkler, W.C. and Breaker, R.R. (2005) Regulation of bacterial gene expression by riboswitches. Annu. Rev. Microbiol., 59, 487-517
    • (2005) Annu. Rev. Microbiol , vol.59 , pp. 487-517
    • Winkler, W.C.1    Breaker, R.R.2
  • 36
    • 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
  • 37
    • 38949215796 scopus 로고    scopus 로고
    • An integrated laser-Tweezers instrument for microanalysis of individual protein aggregates
    • DOI 10.1016/j.snb.2007.09.052, PII S0925400507007733
    • Mao, H. and Luchette, P. (2008) An integrated laser tweezers instrument for microanalysis of individual protein aggregates. Sensors Actuators B, 129, 764-771. (Pubitemid 351221292
    • (2008) Sensors and Actuators, B: Chemical , vol.129 , Issue.2 , pp. 764-771
    • Mao, H.1    Luchette, P.2
  • 40
    • 84862643626 scopus 로고    scopus 로고
    • Intramolecular folding in human ILPR fragment with three C-rich repeats
    • Dhakal, S., Lafontaine, J.L., Yu, Z., Koirala, D. and Mao, H. (2012) Intramolecular folding in human ILPR fragment with three C-rich repeats. PLoS ONE, 7, e39271
    • (2012) PLoS ONE , vol.7
    • Dhakal, S.1    Lafontaine, J.L.2    Yu, Z.3    Koirala, D.4    Mao, H.5
  • 41
    • 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
  • 43
    • 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
  • 45
    • 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. USA., 99, 11593-11598
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 11593-11598
    • Siddiqui-Jain, A.1    Grand, C.L.2    Bearss, D.J.3    Hurley, L.H.4
  • 46
    • 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.