메뉴 건너뛰기




Volumn 8, Issue 5, 2013, Pages

Assessing the Amount of Quadruplex Structures Present within G2-Tract Synthetic Random-Sequence DNA Libraries

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; GUANINE; DNA; GUANINE QUADRUPLEX;

EID: 84878159703     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0064131     Document Type: Article
Times cited : (13)

References (53)
  • 1
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
    • Tuerk C, Gold L, (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505-510.
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 2
    • 0025074907 scopus 로고
    • In vitro selection of RNA molecules that bind specific ligands
    • Ellington AD, Szostak JW, (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818-822.
    • (1990) Nature , vol.346 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 3
    • 66249097058 scopus 로고    scopus 로고
    • Functional nucleic acid sensors
    • Liu J, Cao Z, Lu Y, (2009) Functional nucleic acid sensors. Chem Rev 109: 1948-1998.
    • (2009) Chem Rev , vol.109 , pp. 1948-1998
    • Liu, J.1    Cao, Z.2    Lu, Y.3
  • 4
    • 79551660563 scopus 로고    scopus 로고
    • Functional Nucleic Acids as Molecular Recognition Elements for Small Organic and Biological Molecules
    • Lau PS, Li Y, (2011) Functional Nucleic Acids as Molecular Recognition Elements for Small Organic and Biological Molecules. Curr Org Chem 15: 557-575.
    • (2011) Curr Org Chem , vol.15 , pp. 557-575
    • Lau, P.S.1    Li, Y.2
  • 5
    • 0028965943 scopus 로고
    • A DNA aptamer that binds adenosine and ATP
    • Huizenga DE, Szostak JW, (1995) A DNA aptamer that binds adenosine and ATP. Biochemistry 34: 656-665.
    • (1995) Biochemistry , vol.34 , pp. 656-665
    • Huizenga, D.E.1    Szostak, J.W.2
  • 6
    • 15444375312 scopus 로고    scopus 로고
    • In vitro selection of structure-switching signaling aptamers
    • Nutiu R, Li Y, (2005) In vitro selection of structure-switching signaling aptamers. Angew Chem Int Ed 44: 1061-1065.
    • (2005) Angew Chem Int Ed , vol.44 , pp. 1061-1065
    • Nutiu, R.1    Li, Y.2
  • 7
    • 0035498871 scopus 로고    scopus 로고
    • In vitro evolution suggests multiple origins for the hammerhead ribozyme
    • Salehi-Ashtiani K, Szostak JW, (2001) In vitro evolution suggests multiple origins for the hammerhead ribozyme. Nature 414: 82-84.
    • (2001) Nature , vol.414 , pp. 82-84
    • Salehi-Ashtiani, K.1    Szostak, J.W.2
  • 8
    • 0030498356 scopus 로고    scopus 로고
    • The Ca2+ Ion as a Cofactor for a Novel RNA-Cleaving Deoxyribozyme
    • Faulhammer D, Famulok M, (1996) The Ca2+ Ion as a Cofactor for a Novel RNA-Cleaving Deoxyribozyme. Angew Chem Int Ed 35: 2837-2841.
    • (1996) Angew Chem Int Ed , vol.35 , pp. 2837-2841
    • Faulhammer, D.1    Famulok, M.2
  • 9
    • 0030898510 scopus 로고    scopus 로고
    • A general purpose RNA-cleaving DNA enzyme
    • Santoro SW, Joyce GF, (1997) A general purpose RNA-cleaving DNA enzyme. Proc Natl Acad Sci U S A 94: 4262-4266.
    • (1997) Proc Natl Acad Sci U S A , vol.94 , pp. 4262-4266
    • Santoro, S.W.1    Joyce, G.F.2
  • 10
    • 0034650291 scopus 로고    scopus 로고
    • In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme
    • Li J, Zheng W, Kwon AH, Lu Y, (2000) In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme. Nucleic Acids Res 28: 481-488.
    • (2000) Nucleic Acids Res , vol.28 , pp. 481-488
    • Li, J.1    Zheng, W.2    Kwon, A.H.3    Lu, Y.4
  • 11
    • 3342955521 scopus 로고    scopus 로고
    • Tracing sequence diversity change of RNA-cleaving deoxyribozymes under increasing selection pressure during in vitro selection
    • Schlosser K, Li Y, (2004) Tracing sequence diversity change of RNA-cleaving deoxyribozymes under increasing selection pressure during in vitro selection. Biochemistry 43: 9695-9707.
    • (2004) Biochemistry , vol.43 , pp. 9695-9707
    • Schlosser, K.1    Li, Y.2
  • 12
    • 1142281951 scopus 로고    scopus 로고
    • Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme
    • Cruz RP, Withers JB, Li Y, (2004) Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme. Chem Biol 11: 57-67.
    • (2004) Chem Biol , vol.11 , pp. 57-67
    • Cruz, R.P.1    Withers, J.B.2    Li, Y.3
  • 13
    • 33847622949 scopus 로고    scopus 로고
    • Multiple occurrences of an efficient self-phosphorylating deoxyribozyme motif
    • McManus SA, Li Y, (2007) Multiple occurrences of an efficient self-phosphorylating deoxyribozyme motif. Biochemistry 46: 2198-2204.
    • (2007) Biochemistry , vol.46 , pp. 2198-2204
    • McManus, S.A.1    Li, Y.2
  • 15
    • 0024787884 scopus 로고
    • Monovalent cation-induced structure of telomeric DNA: the G-quartet model
    • Williamson JR, Raghuraman MK, Cech TR, (1989) Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell 59: 871-880.
    • (1989) Cell , vol.59 , pp. 871-880
    • Williamson, J.R.1    Raghuraman, M.K.2    Cech, T.R.3
  • 16
    • 0023788886 scopus 로고
    • Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis
    • Sen D, 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
  • 17
    • 0024788528 scopus 로고
    • Structure and function of telomeres
    • Zakian VA, (1989) Structure and function of telomeres. Annu Rev Genet 23: 579-604.
    • (1989) Annu Rev Genet , vol.23 , pp. 579-604
    • Zakian, V.A.1
  • 18
    • 31944444804 scopus 로고    scopus 로고
    • An intramolecular G-quadruplex structure with mixed parallel/antiparallel G-strands formed in the human BCL-2 promoter region in solution
    • Dai J, Dexheimer TS, Chen D, Carver M, Ambrus A, et al. (2006) An intramolecular G-quadruplex structure with mixed parallel/antiparallel G-strands formed in the human BCL-2 promoter region in solution. J Am Chem Soc 128: 1096-1098.
    • (2006) J Am Chem Soc , vol.128 , pp. 1096-1098
    • Dai, J.1    Dexheimer, T.S.2    Chen, D.3    Carver, M.4    Ambrus, A.5
  • 19
    • 23044485047 scopus 로고    scopus 로고
    • Putative DNA quadruplex formation within the human c-kit oncogene
    • Rankin S, Reszka AP, Huppert J, Zloh M, Parkinson GN, et al. (2005) Putative DNA quadruplex formation within the human c-kit oncogene. J Am Chem Soc 127: 10584-10589.
    • (2005) J Am Chem Soc , vol.127 , pp. 10584-10589
    • Rankin, S.1    Reszka, A.P.2    Huppert, J.3    Zloh, M.4    Parkinson, G.N.5
  • 20
    • 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 CL, Bearss DJ, Hurley LH, (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
  • 21
    • 0034176194 scopus 로고    scopus 로고
    • G-quadruplex DNA: a potential target for anti-cancer drug design
    • Han H, Hurley LH, (2000) G-quadruplex DNA: a potential target for anti-cancer drug design. Trends Pharmacol Sci 21: 136-142.
    • (2000) Trends Pharmacol Sci , vol.21 , pp. 136-142
    • Han, H.1    Hurley, L.H.2
  • 22
    • 0026575221 scopus 로고
    • Selection of single-stranded DNA molecules that bind and inhibit human thrombin
    • Bock LC, Griffin LC, Latham JA, Vermaas EH, Toole JJ, (1992) Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 355: 564-566.
    • (1992) Nature , vol.355 , pp. 564-566
    • Bock, L.C.1    Griffin, L.C.2    Latham, J.A.3    Vermaas, E.H.4    Toole, J.J.5
  • 23
    • 0029964978 scopus 로고    scopus 로고
    • Inhibition of the human immunodeficiency virus type 1 integrase by guanosine quartet structures
    • Mazumder A, Neamati N, Ojwang JO, Sunder S, Rando RF, et al. (1996) Inhibition of the human immunodeficiency virus type 1 integrase by guanosine quartet structures. Biochemistry 35: 13762-13771.
    • (1996) Biochemistry , vol.35 , pp. 13762-13771
    • Mazumder, A.1    Neamati, N.2    Ojwang, J.O.3    Sunder, S.4    Rando, R.F.5
  • 24
    • 0030954291 scopus 로고    scopus 로고
    • Toward an efficient DNAzyme
    • Li Y, Sen D, (1997) Toward an efficient DNAzyme. Biochemistry 36: 5589-5599.
    • (1997) Biochemistry , vol.36 , pp. 5589-5599
    • Li, Y.1    Sen, D.2
  • 26
    • 0347089036 scopus 로고    scopus 로고
    • A deoxyribozyme that harnesses light to repair thymine dimers in DNA
    • Chinnapen DJ, Sen D, (2004) A deoxyribozyme that harnesses light to repair thymine dimers in DNA. Proc Natl Acad Sci U S A 101: 65-69.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 65-69
    • Chinnapen, D.J.1    Sen, D.2
  • 27
    • 37349013529 scopus 로고    scopus 로고
    • A deoxyribozyme with a novel guanine quartet-helix pseudoknot structure
    • McManus SA, Li Y, (2008) A deoxyribozyme with a novel guanine quartet-helix pseudoknot structure. J Mol Biol 375: 960-968.
    • (2008) J Mol Biol , vol.375 , pp. 960-968
    • McManus, S.A.1    Li, Y.2
  • 29
    • 0037462083 scopus 로고    scopus 로고
    • Structure-switching signaling aptamers
    • Nutiu R, Li Y, (2003) Structure-switching signaling aptamers. J Am Chem Soc 125: 4771-4778.
    • (2003) J Am Chem Soc , vol.125 , pp. 4771-4778
    • Nutiu, R.1    Li, Y.2
  • 30
    • 24644478623 scopus 로고    scopus 로고
    • Label-free electronic detection of thrombin in blood serum by using an aptamer-based sensor
    • Xiao Y, Lubin AA, Heeger AJ, Plaxco KW, (2005) Label-free electronic detection of thrombin in blood serum by using an aptamer-based sensor. Angew Chem Int Ed 44: 5456-5459.
    • (2005) Angew Chem Int Ed , vol.44 , pp. 5456-5459
    • Xiao, Y.1    Lubin, A.A.2    Heeger, A.J.3    Plaxco, K.W.4
  • 31
    • 0037021521 scopus 로고    scopus 로고
    • A novel potassium sensing in aqueous media with a synthetic oligonucleotide derivative. Fluorescence resonance energy transfer associated with Guanine quartet-potassium ion complex formation
    • Ueyama H, Takagi M, Takenaka S, (2002) A novel potassium sensing in aqueous media with a synthetic oligonucleotide derivative. Fluorescence resonance energy transfer associated with Guanine quartet-potassium ion complex formation. J Am Chem Soc 124: 14286-14287.
    • (2002) J Am Chem Soc , vol.124 , pp. 14286-14287
    • Ueyama, H.1    Takagi, M.2    Takenaka, S.3
  • 32
    • 33746928345 scopus 로고    scopus 로고
    • Aptamer conformational switch as sensitive electrochemical biosensor for potassium ion recognition
    • Radi AE, O'Sullivan CK, (2006) Aptamer conformational switch as sensitive electrochemical biosensor for potassium ion recognition. Chem Commun 32: 3432-3434.
    • (2006) Chem Commun , vol.32 , pp. 3432-3434
    • Radi, A.E.1    O'Sullivan, C.K.2
  • 33
    • 70349898026 scopus 로고    scopus 로고
    • Reversible Cell-Specific Drug Delivery with Aptamer-Functionalized Liposomes
    • Cao Z, Tong R, Mishra A, Xu W, Wong GCL, et al. (2009) Reversible Cell-Specific Drug Delivery with Aptamer-Functionalized Liposomes. Angew Chem Int Ed 48: 6494-6498.
    • (2009) Angew Chem Int Ed , vol.48 , pp. 6494-6498
    • Cao, Z.1    Tong, R.2    Mishra, A.3    Xu, W.4    Wong, G.C.L.5
  • 34
    • 21844467243 scopus 로고    scopus 로고
    • In vitro RNA random pools are not structurally diverse: a computational analysis
    • Gevertz J, Gan HH, Schlick T, (2005) In vitro RNA random pools are not structurally diverse: a computational analysis. RNA 11: 853-863.
    • (2005) RNA , vol.11 , pp. 853-863
    • Gevertz, J.1    Gan, H.H.2    Schlick, T.3
  • 35
    • 0037015034 scopus 로고    scopus 로고
    • Isolation of high-affinity GTP aptamers from partially structured RNA libraries
    • Davis JH, Szostak JW, (2002) Isolation of high-affinity GTP aptamers from partially structured RNA libraries. Proc Natl Acad Sci U S A 99: 11616-11621.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 11616-11621
    • Davis, J.H.1    Szostak, J.W.2
  • 36
    • 77955791967 scopus 로고    scopus 로고
    • Enhanced functional potential of nucleic acid aptamer libraries patterned to increase secondary structure
    • Ruff KM, Snyder TM, Liu DR, (2010) Enhanced functional potential of nucleic acid aptamer libraries patterned to increase secondary structure. J Am Chem Soc 132: 9453-9464.
    • (2010) J Am Chem Soc , vol.132 , pp. 9453-9464
    • Ruff, K.M.1    Snyder, T.M.2    Liu, D.R.3
  • 37
    • 78149314215 scopus 로고    scopus 로고
    • Computational approaches toward the design of pools for the in vitro selection of complex aptamers
    • Luo X, McKeague M, Pitre S, Dumontier M, Green J, et al. (2010) Computational approaches toward the design of pools for the in vitro selection of complex aptamers. RNA 16: 2252-2262.
    • (2010) RNA , vol.16 , pp. 2252-2262
    • Luo, X.1    McKeague, M.2    Pitre, S.3    Dumontier, M.4    Green, J.5
  • 38
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker M, (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 40
    • 38849085810 scopus 로고    scopus 로고
    • A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA G-quadruplexes
    • Bugaut A, Balasubramanian S, (2008) A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA G-quadruplexes. Biochemistry 47: 689-697.
    • (2008) Biochemistry , vol.47 , pp. 689-697
    • Bugaut, A.1    Balasubramanian, S.2
  • 41
    • 3042671689 scopus 로고    scopus 로고
    • Influence of loop size on the stability of intramolecular DNA quadruplexes
    • Risitano A, Fox KR, (2004) Influence of loop size on the stability of intramolecular DNA quadruplexes. Nucleic Acids Res 32: 2598-2606.
    • (2004) Nucleic Acids Res , vol.32 , pp. 2598-2606
    • Risitano, A.1    Fox, K.R.2
  • 43
    • 34547646128 scopus 로고    scopus 로고
    • Intramolecular DNA quadruplexes with different arrangements of short and long loops
    • Rachwal PA, Findlow IS, Werner JM, Brown T, Fox KR, (2007) Intramolecular DNA quadruplexes with different arrangements of short and long loops. Nucleic Acids Res 35: 4214-4222.
    • (2007) Nucleic Acids Res , vol.35 , pp. 4214-4222
    • Rachwal, P.A.1    Findlow, I.S.2    Werner, J.M.3    Brown, T.4    Fox, K.R.5
  • 44
    • 0038202304 scopus 로고    scopus 로고
    • Small change in a G-rich sequence, a dramatic change in topology: new dimeric G-quadruplex folding motif with unique loop orientations
    • Crnugelj M, Sket P, Plavec J, (2003) Small change in a G-rich sequence, a dramatic change in topology: new dimeric G-quadruplex folding motif with unique loop orientations. J Am Chem Soc 125: 7866-7871.
    • (2003) J Am Chem Soc , vol.125 , pp. 7866-7871
    • Crnugelj, M.1    Sket, P.2    Plavec, J.3
  • 45
    • 37249066753 scopus 로고    scopus 로고
    • Geometric formalism for DNA quadruplex folding
    • Webba da Silva M, (2007) Geometric formalism for DNA quadruplex folding. Chemistry 13: 9738-9745.
    • (2007) Chemistry , vol.13 , pp. 9738-9745
    • Webba da Silva, M.1
  • 49
    • 80155214231 scopus 로고    scopus 로고
    • Topological characterization of nucleic acid G-quadruplexes by UV absorption and circular dichroism
    • Karsisiotis AI, Hessari NM, Novellino E, Spada GP, Randazzo A, et al. (2011) Topological characterization of nucleic acid G-quadruplexes by UV absorption and circular dichroism. Angew Chem Int Ed 50: 10645-10648.
    • (2011) Angew Chem Int Ed , vol.50 , pp. 10645-10648
    • Karsisiotis, A.I.1    Hessari, N.M.2    Novellino, E.3    Spada, G.P.4    Randazzo, A.5
  • 50
    • 0032508468 scopus 로고    scopus 로고
    • Following G-quartet formation by UV-spectroscopy
    • Mergny JL, Phan AT, Lacroix L, (1998) Following G-quartet formation by UV-spectroscopy. FEBS Lett 435: 74-78.
    • (1998) FEBS Lett , vol.435 , pp. 74-78
    • Mergny, J.L.1    Phan, A.T.2    Lacroix, L.3
  • 51
    • 35448944443 scopus 로고    scopus 로고
    • Quadruplex melting
    • Rachwal PA, Fox KR, (2007) Quadruplex melting. Methods 43: 291-301.
    • (2007) Methods , vol.43 , pp. 291-301
    • Rachwal, P.A.1    Fox, K.R.2
  • 53
    • 0041620271 scopus 로고    scopus 로고
    • Regulatory sequence analysis tools
    • van Helden J, (2003) Regulatory sequence analysis tools. Nucleic Acids Res 31: 3593-3596.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3593-3596
    • van Helden, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.