메뉴 건너뛰기




Volumn 41, Issue 6, 2013, Pages 3915-3923

Structural and mechanical properties of individual human telomeric G-quadruplexes in molecularly crowded solutions

Author keywords

[No Author keywords available]

Indexed keywords

ACETONITRILE; BOVINE SERUM ALBUMIN; DIMETHYL SULFOXIDE; DNA FRAGMENT; GUANINE QUADRUPLEX;

EID: 84876044953     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt038     Document Type: Article
Times cited : (78)

References (48)
  • 1
    • 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
  • 2
    • 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
  • 3
    • 79953313413 scopus 로고    scopus 로고
    • Targeting G-quadruplexes in gene promoters: A novel anticancer strategy? Nat
    • Balasubramanian, S., Hurley, L.H. and Neidle, S. (2011) Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? Nat. Rev. Drug Discov., 10, 261-275.
    • (2011) Rev. Drug Discov. , vol.10 , pp. 261-275
    • Balasubramanian, S.1    Hurley, L.H.2    Neidle, S.3
  • 4
    • 68549136741 scopus 로고    scopus 로고
    • G-quadruplex structures: In vivo evidence and function
    • Lipps, H.J. and Rhodes, D. (2009) G-quadruplex structures: in vivo evidence and function. Trends Cell Biol., 19, 414-422.
    • (2009) Trends Cell Biol. , vol.19 , pp. 414-422
    • Lipps, H.J.1    Rhodes, D.2
  • 5
    • 0037142071 scopus 로고    scopus 로고
    • Crystal structure of parallel quadruplexes from human telomeric DNA
    • Parkinson, G.N., Lee, M.P. and Neidle, S. (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature, 417, 876-880.
    • (2002) Nature , vol.417 , pp. 876-880
    • Parkinson, G.N.1    Lee, M.P.2    Neidle, S.3
  • 6
    • 79959509289 scopus 로고    scopus 로고
    • Structure of human telomeric DNA in crowded solution
    • Heddi,B. and Phan, A.T. (2011) Structure of human telomeric DNA in crowded solution. J. Am. Chem. Soc., 133, 9824-9833.
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 9824-9833
    • Heddi, B.1    Phan, A.T.2
  • 7
    • 34249846802 scopus 로고    scopus 로고
    • Structure of the intramolecular human telomeric G-quadruplex in potassium solution: A novel adenine triple formation
    • Dai, J., Punchihewa, C., Ambrus, A., Chen, D., Jones, R.A. and Yang, D. (2007) Structure of the intramolecular human telomeric G-quadruplex in potassium solution: a novel adenine triple formation. Nucleic Acids Res., 35, 2440-2450.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 2440-2450
    • Dai, J.1    Punchihewa, C.2    Ambrus, A.3    Chen, D.4    Jones, R.A.5    Yang, D.6
  • 8
    • 33746600695 scopus 로고    scopus 로고
    • Structure of the human telomere in K+solution: An intramolecular (3+1) G-quadruplex scaffold
    • Luu, K.N., Phan, A.T., Kuryavyi, V., Lacroix,L. and Patel, D.J. (2006) Structure of the human telomere in K+solution: an intramolecular (3+1) G-quadruplex scaffold. J. Am. Chem. Soc., 128, 9963-9970.
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 9963-9970
    • Luu, K.N.1    Phan, A.T.2    Kuryavyi, V.3    Lacroix, L.4    Patel, D.J.5
  • 9
    • 36148991081 scopus 로고    scopus 로고
    • Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+solution
    • Phan, A.T., Kuryavyi, V., Luu, K.N. and Patel, D.J. (2007) Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+solution. Nucleic Acids Res., 35, 6517-6525.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 6517-6525
    • Phan, A.T.1    Kuryavyi, V.2    Luu, K.N.3    Patel, D.J.4
  • 10
    • 0027918585 scopus 로고
    • Solution structure of the human telomeric repeat d[AG3(T2AG3) 3] G-tetraplex
    • Wang,Y. and Patel, D.J. (1993) Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex. Structure, 1, 263-282.
    • (1993) Structure , vol.1 , pp. 263-282
    • Wang, Y.1    Patel, D.J.2
  • 11
    • 67749124298 scopus 로고    scopus 로고
    • Structure of the human telomere in K+solution: A stable basket-type G-quadruplex with only two G-tetrad layers
    • Lim, K.W., Amrane, S., Bouaziz, S., Xu, W., Mu, Y., Patel, D.J., Luu, K.N. and Phan, A.T. (2009) Structure of the human telomere in K+solution: a stable basket-type G-quadruplex with only two G-tetrad layers. J. Am. Chem. Soc., 131, 4301-4309.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 4301-4309
    • Lim, K.W.1    Amrane, S.2    Bouaziz, S.3    Xu, W.4    Mu, Y.5    Patel, D.J.6    Luu, K.N.7    Phan, A.T.8
  • 12
    • 34548550548 scopus 로고    scopus 로고
    • Structure of the Hybrid-2 type intramolecular human telomeric G-quadruplex in K+solution: Insights into structure polymorphism of the human telomeric sequence
    • Dai, J., Carver, M., Punchihewa, C., Jones, R.A. and Yang, D. (2007) Structure of the Hybrid-2 type intramolecular human telomeric G-quadruplex in K+solution: insights into structure polymorphism of the human telomeric sequence. Nucleic Acids Res., 35, 4927-4940.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 4927-4940
    • Dai, J.1    Carver, M.2    Punchihewa, C.3    Jones, R.A.4    Yang, D.5
  • 13
    • 0041822089 scopus 로고    scopus 로고
    • Cell biology: Join the crowd
    • Ellis, R.J. and Minton, A.P. (2003) Cell biology: join the crowd. Nature, 425, 27-28.
    • (2003) Nature , vol.425 , pp. 27-28
    • Ellis, R.J.1    Minton, A.P.2
  • 14
    • 78650109518 scopus 로고    scopus 로고
    • Hydration is a major determinant of the G-quadruplex stability and conformation of the human telomere 30 sequence of d(AG3(TTAG3)3)
    • Miller, M.C., Buscaglia, R., Chaires, J.B., Lane, A.N. and Trent, J.O. (2010) Hydration is a major determinant of the G-quadruplex stability and conformation of the human telomere 30 sequence of d(AG3(TTAG3)3). J. Am. Chem. Soc., 132, 17105-17107.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 17105-17107
    • Miller, M.C.1    Buscaglia, R.2    Chaires, J.B.3    Lane, A.N.4    Trent, J.O.5
  • 15
    • 84857799908 scopus 로고    scopus 로고
    • The parallel G-quadruplex structure of vertebrate telomeric repeat sequences is not the preferred folding topology under physiological conditions
    • Hãnsel, R., Löhr, F., Trant?́rková, S.F., Bamberg, E., Trant?́rek,L. and Dötsch, V. (2011) The parallel G-quadruplex structure of vertebrate telomeric repeat sequences is not the preferred folding topology under physiological conditions. Nucleic Acids Res., 3, 1-8.
    • (2011) Nucleic Acids Res. , vol.3 , pp. 1-8
    • Hãnsel, R.1
  • 16
    • 84865089860 scopus 로고    scopus 로고
    • Studying the effect of crowding and dehydration on DNA G-quadruplexes
    • Petraccone, L., Pagano,B. and Giancola, C. (2012) Studying the effect of crowding and dehydration on DNA G-quadruplexes. Methods, 57, 76-83.
    • (2012) Methods , vol.57 , pp. 76-83
    • Petraccone, L.1    Pagano, B.2    Giancola, C.3
  • 17
    • 84874437147 scopus 로고    scopus 로고
    • Thermodynamics-hydration relationships within loops that affect G-quadruplexes under molecular crowding conditions
    • Fujimoto, T., Nakano,S.-i., Sugimoto,N. and Miyoshi, D. (2012) Thermodynamics-hydration relationships within loops that affect G-quadruplexes under molecular crowding conditions. J. Phys. Chem. B, 117, 963-972.
    • (2012) J. Phys. Chem. B , vol.117 , pp. 963-972
    • Fujimoto, T.1    Nakano, S.-I.2    Sugimoto, N.3    Miyoshi, D.4
  • 18
    • 33646943863 scopus 로고    scopus 로고
    • Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution
    • Ambrus, A., Chen, D., Dai, J., Bialis, T., Jones, R.A. and Yang, D. (2006) Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution. Nucleic Acids Res., 34, 2723-2735.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 2723-2735
    • Ambrus, A.1    Chen, D.2    Dai, J.3    Bialis, T.4    Jones, R.A.5    Yang, D.6
  • 21
    • 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
  • 22
    • 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
  • 26
    • 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
  • 27
    • 84864453805 scopus 로고    scopus 로고
    • Click chemistry assisted single-molecule fingerprinting reveals a 3D biomolecular folding funnel
    • Yu, Z., Koirala, D., Cui, Y., Easterling, L.F., Zhao,Y. and Mao, H. (2012) Click chemistry assisted single-molecule fingerprinting reveals a 3D biomolecular folding funnel. J. Am. Chem. Soc., 134, 12338-12341.
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 12338-12341
    • Yu, Z.1    Koirala, D.2    Cui, Y.3    Easterling, L.F.4    Zhao, Y.5    Mao, H.6
  • 28
    • 0000096835 scopus 로고    scopus 로고
    • Click chemistry: Diverse chemical function from a few good reactions
    • Kolb, H.C., Finn, M.G. and Sharpless, K.B. (2001) Click chemistry: diverse chemical function from a few good reactions. Angew. Chem. Int. Ed. Engl., 40, 2004-2021.
    • (2001) Angew. Chem. Int. Ed. Engl. , vol.40 , pp. 2004-2021
    • Kolb, H.C.1    Finn, M.G.2    Sharpless, K.B.3
  • 29
    • 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. Sens. Actuat. B, 129, 764-771.
    • (2008) Sens. Actuat. B , vol.129 , pp. 764-771
    • Mao, H.1    Luchette, P.2
  • 30
    • 0030024985 scopus 로고    scopus 로고
    • Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules
    • Smith, S.B., Cui, Y.J. and Bustamante, C. (1996) Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science, 271, 795-799.
    • (1996) Science , vol.271 , pp. 795-799
    • Smith, S.B.1    Cui, Y.J.2    Bustamante, C.3
  • 31
    • 0033534516 scopus 로고    scopus 로고
    • Flexibility of single-stranded DNA: Use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA)
    • Mills, J.B., Vacano,E. and Hagerman, P.J. (1999) Flexibility of single-stranded DNA: use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA). J. Mol. Biol., 285, 245-257.
    • (1999) J. Mol. Biol. , vol.285 , pp. 245-257
    • Mills, J.B.1    Vacano, E.2    Hagerman, P.J.3
  • 32
    • 0031238076 scopus 로고    scopus 로고
    • Persistence length of single-stranded DNA
    • Tinland, B., Pluen, A., Sturm,J. and Weill, G. (1997) Persistence length of single-stranded DNA. Macromolecules, 30, 5763-5765.
    • (1997) Macromolecules , vol.30 , pp. 5763-5765
    • Tinland, B.1    Pluen, A.2    Sturm, J.3    Weill, G.4
  • 33
    • 0017820499 scopus 로고
    • Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The roles of ion association or release, screening, and ion effects on water activity
    • Record, M.T.J., Anderson, C.F. and Lohman, T.M. (1978) Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Quart. Rev. Biophys., 11, 103-178.
    • (1978) Quart. Rev. Biophys. , vol.11 , pp. 103-178
    • Record, M.T.J.1    Anderson, C.F.2    Lohman, T.M.3
  • 34
    • 28444431959 scopus 로고    scopus 로고
    • Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins
    • Laurence, T.A., Kong, X., Jager,M. and Weiss, S. (2005) Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins. Proc. Natl Acad. Sci. USA, 102, 17348-17353.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 17348-17353
    • Laurence, T.A.1    Kong, X.2    Jager, M.3    Weiss, S.4
  • 36
    • 38849204944 scopus 로고    scopus 로고
    • Direct observation of hierarchical folding in single riboswitch aptamers
    • 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.
    • (2008) Science , vol.319 , pp. 630-633
    • Greenleaf, W.J.1    Frieda, K.L.2    Foster, D.A.3    Woodside, M.T.4    Block, S.M.5
  • 37
    • 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
  • 38
    • 80053144268 scopus 로고    scopus 로고
    • Single-base pair unwinding and asynchronous RNA release by the hepatitis C virus NS3 helicase
    • Cheng, W., Arunajadai, S.G., Moffitt, J.R., Tinoco,I. Jr and Bustamante, C. (2011) Single-base pair unwinding and asynchronous RNA release by the hepatitis C virus NS3 helicase. Science, 333, 1746-1749.
    • (2011) Science , vol.333 , pp. 1746-1749
    • Cheng, W.1    Arunajadai, S.G.2    Moffitt, J.R.3    Tinoco Jr., I.4    Bustamante, C.5
  • 39
    • 31944436148 scopus 로고    scopus 로고
    • Protein structure by mechanical triangulation
    • Dietz,H. and Rief, M. (2006) Protein structure by mechanical triangulation. Proc. Natl Acad. Sci. USA, 103, 1244-1247.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 1244-1247
    • Dietz, H.1    Rief, M.2
  • 40
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium equality for free energy differences
    • Jarzynski, C. (1997) Nonequilibrium equality for free energy differences. Phys. Rev. Lett., 78, 2690-2693.
    • (1997) Phys. Rev. Lett. , vol.78 , pp. 2690-2693
    • Jarzynski, C.1
  • 41
    • 79961120537 scopus 로고    scopus 로고
    • Improving free-energy estimates from unidirectional work measurements: Theory and experiment
    • Palassini,M. and Ritort, F. (2011) Improving free-energy estimates from unidirectional work measurements: theory and experiment. Phys. Rev. Lett., 107, 060601.
    • (2011) Phys. Rev. Lett. , vol.107 , pp. 060601
    • Palassini, M.1    Ritort, F.2
  • 42
    • 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
  • 43
    • 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
  • 44
    • 79952379785 scopus 로고    scopus 로고
    • Human telomeric G-quadruplexes undergo dynamic conversion in a molecular crowding environment
    • Xu, L., Feng,S. and Zhou, X. (2011) Human telomeric G-quadruplexes undergo dynamic conversion in a molecular crowding environment. Chem. Commun., 47, 3517-3519.
    • (2011) Chem. Commun. , vol.47 , pp. 3517-3519
    • Xu, L.1    Feng, S.2    Zhou, X.3
  • 45
    • 34548762534 scopus 로고    scopus 로고
    • Human telomeric DNA forms parallel-stranded intramolecular G-Quadruplex in K+ solution under molecular crowding condition
    • Xue, Y., Kan, Z., Wang, Q., Yao, Y., Liu, J., Hao,Y. and Tan, Z. (2007) Human telomeric DNA forms parallel-stranded intramolecular G-Quadruplex in K+ solution under molecular crowding condition. J. Am. Chem. Soc., 129, 11185-11191.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 11185-11191
    • Xue, Y.1    Kan, Z.2    Wang, Q.3    Yao, Y.4    Liu, J.5    Hao, Y.6    Tan, Z.7
  • 46
    • 0041931122 scopus 로고    scopus 로고
    • Macromolecular crowding: Qualitative and semiquantitative successes, quantitative challenges
    • Hall,D. and Minton, A.P. (2003) Macromolecular crowding: qualitative and semiquantitative successes, quantitative challenges. Biochim. Biophys. Acta, 1649, 127-139.
    • (2003) Biochim. Biophys. Acta , vol.1649 , pp. 127-139
    • Hall, D.1    Minton, A.P.2
  • 47
    • 0037036070 scopus 로고    scopus 로고
    • Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality
    • Liphardt, J., Dumont, S., Smith, S.B., Tinoco,I. Jr and Bustamante, C. (2002) Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality. Science, 296, 1832-1835.
    • (2002) Science , vol.296 , pp. 1832-1835
    • Liphardt, J.1    Dumont, S.2    Smith, S.B.3    Tinoco Jr., I.4    Bustamante, C.5
  • 48
    • 67749110113 scopus 로고    scopus 로고
    • Hydration of Watson Crick base pairs and dehydration of hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions
    • Miyoshi, D., Nakamura, K., Tateishi-Karimata, H., Ohmichi,T. and Sugimoto, N. (2009) Hydration of Watson Crick base pairs and dehydration of hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions. J. Am. Chem. Soc., 131, 3522-3531.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 3522-3531
    • Miyoshi, D.1    Nakamura, K.2    Tateishi-Karimata, H.3    Ohmichi, T.4    Sugimoto, N.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.