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Volumn 11, Issue 6, 2005, Pages 853-863

In vitro RNA random pools are not structurally diverse: A computational analysis

Author keywords

Graph theory; In vitro selection; Random pool; RNA pool design; RNA secondary structure; RNA topology

Indexed keywords

APTAMER; RNA;

EID: 21844467243     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.7271405     Document Type: Article
Times cited : (72)

References (48)
  • 2
    • 1942489258 scopus 로고    scopus 로고
    • Informational complexity and functional activity of RNA structures
    • Carothers, J.M., Oestreich, S.C., Davis, J.H., and Szostak, J.W. 2004. Informational complexity and functional activity of RNA structures. J. Am. Chem. Soc. 126: 5130-5137.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 5130-5137
    • Carothers, J.M.1    Oestreich, S.C.2    Davis, J.H.3    Szostak, J.W.4
  • 3
    • 84968468352 scopus 로고
    • Diameters and eigenvalues
    • Chung, F.R.K. 1989. Diameters and eigenvalues. J. Am. Math. Soc. 2: 487-492.
    • (1989) J. Am. Math. Soc. , vol.2 , pp. 487-492
    • Chung, F.R.K.1
  • 5
    • 0037015034 scopus 로고    scopus 로고
    • Isolation of high-affinity GTP aptamers from partially structured RNA libraries
    • Davis, J.H. and Szostak, J.W. 2002. Isolation of high-affinity GTP aptamers from partially structured RNA libraries. Proc. Natl. Acad. Sci. 99: 11616-11621.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 11616-11621
    • Davis, J.H.1    Szostak, J.W.2
  • 7
    • 0042566833 scopus 로고
    • Laplacian of graphs and algebraic connectivity
    • Banach Center Publications, Warsaw
    • Fiedler, M. 1989. Laplacian of graphs and algebraic connectivity. In Combinatorics and graph theory, pp. 57-70. Banach Center Publications, Warsaw.
    • (1989) Combinatorics and Graph Theory , pp. 57-70
    • Fiedler, M.1
  • 9
    • 0037033435 scopus 로고    scopus 로고
    • In vitro selection and evaluation of RNA aptamers that recognize arginine-rich-motif model peptide on a quartz-crystal microbalance
    • Fukusho, S., Furusawa, H., and Okahata, Y. 2002. In vitro selection and evaluation of RNA aptamers that recognize arginine-richmotif model peptide on a quartz-crystal microbalance. Chem. Commun. (Camb.) 1: 88-89.
    • (2002) Chem. Commun. (Camb.) , vol.1 , pp. 88-89
    • Fukusho, S.1    Furusawa, H.2    Okahata, Y.3
  • 10
    • 0038606979 scopus 로고    scopus 로고
    • Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design
    • Gan, H.H., Pasquali, S., and Schlick, T. 2003. Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. Nucleic Acids Res. 31: 2926-2943.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 2926-2943
    • Gan, H.H.1    Pasquali, S.2    Schlick, T.3
  • 12
    • 0003780715 scopus 로고
    • Addison-Wesley, Reading, MA
    • Harary, F. 1969. Graph theory. Addison-Wesley, Reading, MA.
    • (1969) Graph Theory
    • Harary, F.1
  • 13
    • 51249194815 scopus 로고
    • The number of homeomorphically irreducible trees and other species
    • Harary, F. and Prins, G. 1959. The number of homeomorphically irreducible trees and other species. Acta Math. 101: 141-162.
    • (1959) Acta Math. , vol.101 , pp. 141-162
    • Harary, F.1    Prins, G.2
  • 14
    • 0002304830 scopus 로고
    • RNA secondary structure - A comparison of real and random sequences
    • Higgs, P.G. 1993. RNA secondary structure - A comparison of real and random sequences. J. Physique I 3: 43-59.
    • (1993) J. Physique I , vol.3 , pp. 43-59
    • Higgs, P.G.1
  • 15
    • 37049089723 scopus 로고
    • Thermodynamic properties of transfer-RNA - A computational study
    • _. 1995. Thermodynamic properties of transfer-RNA - A computational study. J. Chem. Soc. Faraday Trans. 91: 2531-2540.
    • (1995) J. Chem. Soc. Faraday Trans. , vol.91 , pp. 2531-2540
  • 16
    • 0347133523 scopus 로고    scopus 로고
    • Mechanistic studies on acyltransferase ribozymes and beyond
    • Hodgson, D.R. and Suga, H. 2004. Mechanistic studies on acyltransferase ribozymes and beyond. Biopolymers 73: 130-150.
    • (2004) Biopolymers , vol.73 , pp. 130-150
    • Hodgson, D.R.1    Suga, H.2
  • 17
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker, I.L. 2003. Vienna RNA secondary structure server. Nucleic Acids Res. 31: 3429-3431.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 18
    • 0036226352 scopus 로고    scopus 로고
    • Design, construction, and analysis of a novel class of self-folding RNA
    • Ikawa, Y., Fukada, K., Watanabe, S., Shiraishi, H., and Inoue, T. 2002. Design, construction, and analysis of a novel class of self-folding RNA. Structure 10: 527-534.
    • (2002) Structure , vol.10 , pp. 527-534
    • Ikawa, Y.1    Fukada, K.2    Watanabe, S.3    Shiraishi, H.4    Inoue, T.5
  • 19
    • 0033592981 scopus 로고    scopus 로고
    • A complex ligase ribozyme evolved in vitro from a group I ribozyme domain
    • Jaeger, L., Wright, M.C., and Joyce, G.F. 1999. A complex ligase ribozyme evolved in vitro from a group I ribozyme domain. Proc. Natl. Acad. Sci. 96: 14712-14717.
    • (1999) Proc. Natl. Acad. Sci. , vol.96 , pp. 14712-14717
    • Jaeger, L.1    Wright, M.C.2    Joyce, G.F.3
  • 20
    • 0035863772 scopus 로고    scopus 로고
    • TectoRNA: Modular assembly units for the construction of RNA nano-objects
    • Jaeger, L., Westhof, E., and Leontis, N.B. 2001. TectoRNA: Modular assembly units for the construction of RNA nano-objects. Nucleic Acids Res. 29: 455-463.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 455-463
    • Jaeger, L.1    Westhof, E.2    Leontis, N.B.3
  • 21
    • 0036888921 scopus 로고    scopus 로고
    • Characterization of RNA determinants recognized by the arginine- and proline-rich region of Us11, a herpes simplex virus type 1-encoded double-stranded RNA binding protein that prevents PKR activation
    • Khoo, D., Perez, C., and Mohr, I. 2002. Characterization of RNA determinants recognized by the arginine- and proline-rich region of Us11, a herpes simplex virus type 1-encoded double-stranded RNA binding protein that prevents PKR activation. J. Virol. 76: 11971-11981.
    • (2002) J. Virol. , vol.76 , pp. 11971-11981
    • Khoo, D.1    Perez, C.2    Mohr, I.3
  • 23
    • 0037388109 scopus 로고    scopus 로고
    • Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures
    • Kitagawa, J., Futamura, Y., and Yamamoto, K. 2003. Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures. Nucleic Acids Res. 31: 2006-2013.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 2006-2013
    • Kitagawa, J.1    Futamura, Y.2    Yamamoto, K.3
  • 24
    • 0037319334 scopus 로고    scopus 로고
    • Finding specific RNA motifs: Function in a zeptomole world?
    • Knight, R. and Yarus, M. 2003. Finding specific RNA motifs: Function in a zeptomole world? RNA 9: 218-230.
    • (2003) RNA , vol.9 , pp. 218-230
    • Knight, R.1    Yarus, M.2
  • 25
    • 0037162407 scopus 로고    scopus 로고
    • In vitro selection of hairpin ribozymes activated with short oligonucleotides
    • Komatsu, Y., Nobuoka, K., Karino-Abe, N., Matsuda, A., and Ohtsuka, E. 2002. In vitro selection of hairpin ribozymes activated with short oligonucleotides. Biochemistry 41: 9090-9098.
    • (2002) Biochemistry , vol.41 , pp. 9090-9098
    • Komatsu, Y.1    Nobuoka, K.2    Karino-Abe, N.3    Matsuda, A.4    Ohtsuka, E.5
  • 27
    • 0024386096 scopus 로고
    • Tree graphs of RNA secondary structures and their comparisons
    • Le, S.Y., Nussinov, R., and Maizel, J.V. 1989. Tree graphs of RNA secondary structures and their comparisons. Comput. Biomed. Res. 22: 461-473.
    • (1989) Comput. Biomed. Res. , vol.22 , pp. 461-473
    • Le, S.Y.1    Nussinov, R.2    Maizel, J.V.3
  • 29
    • 0037646509 scopus 로고    scopus 로고
    • In vitro selection of adenine-dependent hairpin ribozymes
    • Meli, M., Vergne, J., and Maurel, M.C. 2003. In vitro selection of adenine-dependent hairpin ribozymes. J. Biol. Chem. 278: 9835-9842.
    • (2003) J. Biol. Chem. , vol.278 , pp. 9835-9842
    • Meli, M.1    Vergne, J.2    Maurel, M.C.3
  • 30
    • 0001216057 scopus 로고
    • The Laplacian spectrum of graphs
    • eds. Y. Alavi et al., Wiley, New York
    • Mohar, B. 1991. The Laplacian spectrum of graphs. In Graph theory, combinatorics, and applications (eds. Y. Alavi et al.), pp. 871-899. Wiley, New York.
    • (1991) Graph Theory, Combinatorics, and Applications , pp. 871-899
    • Mohar, B.1
  • 32
    • 0346422450 scopus 로고    scopus 로고
    • Artificial modules for enhancing rate constants of a group I intron ribozyme without a P4-P6 core element
    • _. 2004. Artificial modules for enhancing rate constants of a group I intron ribozyme without a P4-P6 core element. J. Biol. Chem. 279: 540-546.
    • (2004) J. Biol. Chem. , vol.279 , pp. 540-546
  • 33
    • 0033524952 scopus 로고    scopus 로고
    • A dynamic programming algorithm for RNA structure prediction including pseudoknots
    • Rivas, E. and Eddy, S.R. 1999. A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol. 285: 2053-2068.
    • (1999) J. Mol. Biol. , vol.285 , pp. 2053-2068
    • Rivas, E.1    Eddy, S.R.2
  • 34
    • 0031259915 scopus 로고    scopus 로고
    • Accessing rare activities from random RNA sequences: The importance of the length of molecules in the starting pool
    • Sabeti, P.C., Unrau, P.J., and Bartel, D.P. 1997. Accessing rare activities from random RNA sequences: The importance of the length of molecules in the starting pool. Chem. Biol. 4: 767-774.
    • (1997) Chem. Biol. , vol.4 , pp. 767-774
    • Sabeti, P.C.1    Unrau, P.J.2    Bartel, D.P.3
  • 35
    • 0035498871 scopus 로고    scopus 로고
    • In vitro evolution suggests multiple origins for the hammerhead ribozyme
    • Salehi-Ashtiani, K. and Szostak, J.W. 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
  • 36
    • 0034698298 scopus 로고    scopus 로고
    • One sequence, two ribozymes: Implications for the emergence of new ribozyme folds
    • Schultes, E.A. and Bartel, D.P. 2000. One sequence, two ribozymes: Implications for the emergence of new ribozyme folds. Science 289: 448-452.
    • (2000) Science , vol.289 , pp. 448-452
    • Schultes, E.A.1    Bartel, D.P.2
  • 37
    • 0030759786 scopus 로고    scopus 로고
    • Global similarities in nucleotide base composition among disparate functional classes of single-stranded RNA imply adaptive evolutionary convergence
    • Schultes, E., Hraber, P.T., and LaBean, T.H. 1997. Global similarities in nucleotide base composition among disparate functional classes of single-stranded RNA imply adaptive evolutionary convergence. RNA 3: 792-806.
    • (1997) RNA , vol.3 , pp. 792-806
    • Schultes, E.1    Hraber, P.T.2    LaBean, T.H.3
  • 40
    • 0033119454 scopus 로고    scopus 로고
    • mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences
    • Seffens, W. and Digby, D. 1999. mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res. 27: 1578-1584.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 1578-1584
    • Seffens, W.1    Digby, D.2
  • 41
    • 0025187499 scopus 로고
    • Comparing multiple RNA secondary structures using tree comparisons
    • Shapiro, B.A. and Zhang, K.Z. 1990. Comparing multiple RNA secondary structures using tree comparisons. Comput. Appl. Biosci. 6: 309-318.
    • (1990) Comput. Appl. Biosci. , vol.6 , pp. 309-318
    • Shapiro, B.A.1    Zhang, K.Z.2
  • 42
    • 0037012440 scopus 로고    scopus 로고
    • Characterization of an RNA active site: Interactions between a Diels-Alderase ribozyme and its substrates and products
    • Stuhlmann, F. and Jaschke, A. 2002. Characterization of an RNA active site: Interactions between a Diels-Alderase ribozyme and its substrates and products. J. Am. Chem. Soc. 124: 3238-3244.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 3238-3244
    • Stuhlmann, F.1    Jaschke, A.2
  • 43
    • 0037665961 scopus 로고    scopus 로고
    • Functional information: Molecular messages
    • Szostak, J.W. 2003. Functional information: Molecular messages. Nature 423: 689.
    • (2003) Nature , vol.423 , pp. 689
    • Szostak, J.W.1
  • 44
    • 0037036390 scopus 로고    scopus 로고
    • In vitro selection of RNA aptamers that bind to cell adhesion receptors of Trypanosoma cruzi and inhibit cell invasion
    • Ulrich, H., Magdesian, M.H., Alves, M.J., and Colli, W. 2002. In vitro selection of RNA aptamers that bind to cell adhesion receptors of Trypanosoma cruzi and inhibit cell invasion. J. Biol. Chem. 277: 20756-20762.
    • (2002) J. Biol. Chem. , vol.277 , pp. 20756-20762
    • Ulrich, H.1    Magdesian, M.H.2    Alves, M.J.3    Colli, W.4
  • 46
    • 0032853242 scopus 로고    scopus 로고
    • In vitro selection of functional nucleic acids
    • Wilson, D.S. and Szostak, J.W. 1999. In vitro selection of functional nucleic acids. Annu. Rev. Biochem. 68: 611-647.
    • (1999) Annu. Rev. Biochem. , vol.68 , pp. 611-647
    • Wilson, D.S.1    Szostak, J.W.2
  • 47
    • 9344227328 scopus 로고    scopus 로고
    • Generation of a catalytic module on a self-folding RNA
    • Yoshioka, W., Ikawa, Y., Jaeger, L., Shiraishi, H., and Inoue, T. 2004. Generation of a catalytic module on a self-folding RNA. RNA 10: 1900-1906.
    • (2004) RNA , vol.10 , pp. 1900-1906
    • Yoshioka, W.1    Ikawa, Y.2    Jaeger, L.3    Shiraishi, H.4    Inoue, T.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.