메뉴 건너뛰기




Volumn 7409 LNBI, Issue , 2012, Pages 49-60

RNA folding algorithms with G-quadruplexes

Author keywords

Dynamic programming; RNA folding; ViennaRNA Package

Indexed keywords

COMBINATORIAL THEORY; DYNAMIC PROGRAMMING ALGORITHM; ENERGY MODEL; ENERGY PARAMETERS; G-QUADRUPLEXES; HUMAN GENOMES; RNA FOLDING; RNA SECONDARY STRUCTURE PREDICTION; RNA STRUCTURES; SECONDARY STRUCTURES; STRUCTURAL ELEMENTS; VIENNARNA PACKAGE;

EID: 84865601895     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-31927-3_5     Document Type: Conference Paper
Times cited : (13)

References (47)
  • 1
    • 80052788094 scopus 로고    scopus 로고
    • An RNA G-quadruplex in the 3′ UTR of the proto-oncogene PIM1 represses translation
    • Arora, A., Suess, B.: An RNA G-quadruplex in the 3′ UTR of the proto-oncogene PIM1 represses translation. RNA Biology 8, 802-805 (2011)
    • (2011) RNA Biology , vol.8 , pp. 802-805
    • Arora, A.1    Suess, B.2
  • 3
    • 77957058196 scopus 로고    scopus 로고
    • 5′-UTR G-quadruplex structures acting as translational repressors
    • Beaudoin, J.D., Perreault, J.P.: 5′-UTR G-quadruplex structures acting as translational repressors. Nucleic Acids Res. 38, 7022-7036 (2010)
    • (2010) Nucleic Acids Res. , vol.38 , pp. 7022-7036
    • Beaudoin, J.D.1    Perreault, J.P.2
  • 4
    • 62549119174 scopus 로고    scopus 로고
    • FRAXE-associated mental retardation protein (FMR2) is an RNA-binding protein with high affinity for G-quartet RNA forming structure
    • Bensaid, M., Melko, M., Bechara, E.G., Davidovic, L., Berretta, A., Catania, M.V., Gecz, J., Lalli, E., Bardoni, B.: FRAXE-associated mental retardation protein (FMR2) is an RNA-binding protein with high affinity for G-quartet RNA forming structure. Nucleic Acids Res. 37, 1269-1279 (2009)
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1269-1279
    • Bensaid, M.1    Melko, M.2    Bechara, E.G.3    Davidovic, L.4    Berretta, A.5    Catania, M.V.6    Gecz, J.7    Lalli, E.8    Bardoni, B.9
  • 6
    • 0023984838 scopus 로고
    • An improved algorithm for nucleic acid secondary structure display
    • Bruccoleri, R.E., Heinrich, G.: An improved algorithm for nucleic acid secondary structure display. Computer Appl. Biosci. 4, 167-173 (1988)
    • (1988) Computer Appl. Biosci. , vol.4 , pp. 167-173
    • Bruccoleri, R.E.1    Heinrich, G.2
  • 7
    • 38849085810 scopus 로고    scopus 로고
    • A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA Gquadruplexes
    • Bugaut, A., Balasubramanian, S.: A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA Gquadruplexes. Biochemistry 47, 689-697 (2008)
    • (2008) Biochemistry , vol.47 , pp. 689-697
    • Bugaut, A.1    Balasubramanian, S.2
  • 8
    • 84862229118 scopus 로고    scopus 로고
    • 5'-UTR RNA G-quadruplexes: Translation regulation and targeting
    • doi: 10.1093/nar/gks068
    • Bugaut, A., Balasubramanian, S.: 5'-UTR RNA G-quadruplexes: translation regulation and targeting. Nucleic Acids Res. (2012), doi: 10.1093/nar/gks068
    • (2012) Nucleic Acids Res.
    • Bugaut, A.1    Balasubramanian, S.2
  • 9
    • 33747874580 scopus 로고    scopus 로고
    • CONTRAfold: RNA secondary structure prediction without physics-based models
    • Do, C.B., Woods, D.A., Batzoglou, S.: CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics 22(14), e90-e98 (2006)
    • (2006) Bioinformatics , vol.22 , Issue.14
    • Do, C.B.1    Woods, D.A.2    Batzoglou, S.3
  • 10
    • 33748519569 scopus 로고    scopus 로고
    • Gene function correlates with potential for G4 DNA formation in the human genome
    • Eddy, J., Maizels, N.: Gene function correlates with potential for G4 DNA formation in the human genome. Nucleic Acids Res. 34, 3887-3896 (2006)
    • (2006) Nucleic Acids Res. , vol.34 , pp. 3887-3896
    • Eddy, J.1    Maizels, N.2
  • 13
    • 54349124117 scopus 로고    scopus 로고
    • G-Quadruplex formation interferes with P1 helix formation in the RNA component of telomerase hTERC
    • Gros, J., Guédin, A., Mergny, J.L., Lacroix, L.: G-Quadruplex formation interferes with P1 helix formation in the RNA component of telomerase hTERC. Chem-BioChem 9, 2075-2079 (2008)
    • (2008) Chem-BioChem , vol.9 , pp. 2075-2079
    • Gros, J.1    Guédin, A.2    Mergny, J.L.3    Lacroix, L.4
  • 14
    • 43049132871 scopus 로고    scopus 로고
    • Sequence effects in single-base loops for quadruplexes
    • Guédin, A., De Cian, A., Gros, J., Lacroix, L., Mergny, J.L.: Sequence effects in single-base loops for quadruplexes. Biochimie 90, 686-696 (2008)
    • (2008) Biochimie , vol.90 , pp. 686-696
    • Guédin, A.1    De Cian, A.2    Gros, J.3    Lacroix, L.4    Mergny, J.L.5
  • 15
    • 78649850820 scopus 로고    scopus 로고
    • How long is too long? Effects of loop size on G-quadruplex stability
    • Guédin, A., Gros, J., Patrizia, A., Mergny, J.L.: How long is too long? Effects of loop size on G-quadruplex stability. Nucleic Acids Res. 38, 7858-7868 (2010)
    • (2010) Nucleic Acids Res. , vol.38 , pp. 7858-7868
    • Guédin, A.1    Gros, J.2    Patrizia, A.3    Mergny, J.L.4
  • 16
    • 0036301332 scopus 로고    scopus 로고
    • Secondary structure prediction for aligned RNA sequences
    • Hofacker, I.L., Fekete, M., Stadler, P.F.: Secondary structure prediction for aligned RNA sequences. J. Mol. Biol. 319, 1059-1066 (2002)
    • (2002) J. Mol. Biol. , vol.319 , pp. 1059-1066
    • Hofacker, I.L.1    Fekete, M.2    Stadler, P.F.3
  • 17
    • 1042304206 scopus 로고    scopus 로고
    • Prediction of locally stable RNA secondary structures for genome-wide surveys
    • Hofacker, I.L., Priwitzer, B., Stadler, P.F.: Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics 20, 191-198 (2004)
    • (2004) Bioinformatics , vol.20 , pp. 191-198
    • Hofacker, I.L.1    Priwitzer, B.2    Stadler, P.F.3
  • 18
    • 20144364292 scopus 로고    scopus 로고
    • Prevalence of quadruplexes in the human genome
    • Huppert, J.L., Balasubramanian, S.: Prevalence of quadruplexes in the human genome. Nucleic Acids Res. 33, 2908-2916 (2005)
    • (2005) Nucleic Acids Res. , vol.33 , pp. 2908-2916
    • Huppert, J.L.1    Balasubramanian, S.2
  • 20
    • 81855190848 scopus 로고    scopus 로고
    • Inhibition of translation by small RNA-stabilized mRNA structures in human cells
    • Ito, K., Go, S., Komiyama, M., Xu, Y.: Inhibition of translation by small RNA-stabilized mRNA structures in human cells. J. Am. Chem. Soc. 133, 19153-19159 (2011)
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 19153-19159
    • Ito, K.1    Go, S.2    Komiyama, M.3    Xu, Y.4
  • 21
    • 84856801825 scopus 로고    scopus 로고
    • Potential G-quadruplexes in the human long non-coding transcriptome
    • Jayaraj, G.G., Pandey, S., Scaria, V., Maiti, S.: Potential G-quadruplexes in the human long non-coding transcriptome. RNA Biolog. 9, 81-86 (2012)
    • (2012) RNA Biolog. , vol.9 , pp. 81-86
    • Jayaraj, G.G.1    Pandey, S.2    Scaria, V.3    Maiti, S.4
  • 22
    • 69949186768 scopus 로고    scopus 로고
    • A comparison of DNA and RNA quadruplex structures and stabilities
    • Joachimi, A., Benz, A., Hartig, J.S.: A comparison of DNA and RNA quadruplex structures and stabilities. Bioorg. Med. Chem. 17, 6811-6815 (2009)
    • (2009) Bioorg. Med. Chem. , vol.17 , pp. 6811-6815
    • Joachimi, A.1    Benz, A.2    Hartig, J.S.3
  • 23
    • 47649105111 scopus 로고    scopus 로고
    • In vivo veritas: Using yeast to probe the biological functions of G-quadruplexes
    • Johnson, J.E., Smith, J.S., Kozak, M.L., Johnson, F.B.: In vivo veritas: using yeast to probe the biological functions of G-quadruplexes. Biochimie 90, 1250-1263 (2008)
    • (2008) Biochimie , vol.90 , pp. 1250-1263
    • Johnson, J.E.1    Smith, J.S.2    Kozak, M.L.3    Johnson, F.B.4
  • 24
    • 33747860882 scopus 로고    scopus 로고
    • QGRS mapper: A web-based server for predicting G-quadruplexes in nucleotide sequences
    • Kikin, O., D'Antonio, L., Bagga, P.S.: QGRS mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res. 34, W676-W682 (2006)
    • (2006) Nucleic Acids Res. , vol.34
    • Kikin, O.1    D'Antonio, L.2    Bagga, P.S.3
  • 25
    • 33947310727 scopus 로고    scopus 로고
    • An RNA Gquadruplex in the 5′UTR of the NRAS proto-oncogene modulates translation
    • Kumari, S., Bugaut, A., Huppert, J.L., Balasubramanian, S.: An RNA Gquadruplex in the 5′UTR of the NRAS proto-oncogene modulates translation. Nat. Chem. Biol. 3, 218-221 (2007)
    • (2007) Nat. Chem. Biol. , vol.3 , pp. 218-221
    • Kumari, S.1    Bugaut, A.2    Huppert, J.L.3    Balasubramanian, S.4
  • 26
    • 0029138009 scopus 로고
    • RNA aptamers that bind flavin and nicotinamide redox cofactors
    • Lauhon, C.T., Szostak, J.W.: RNA aptamers that bind flavin and nicotinamide redox cofactors. J. Am. Chem. Soc. 117, 1246-1257 (1995)
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 1246-1257
    • Lauhon, C.T.1    Szostak, J.W.2
  • 28
    • 69849104275 scopus 로고    scopus 로고
    • TERRA: Telomeric repeat-containing RNA
    • Luke, B., Lingner, J.: TERRA: telomeric repeat-containing RNA. EMBO J. 28, 2503-2510 (2009)
    • (2009) EMBO J. , vol.28 , pp. 2503-2510
    • Luke, B.1    Lingner, J.2
  • 29
    • 2442626706 scopus 로고    scopus 로고
    • Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    • Mathews, D.H., Disney, M.D., Childs, J.L., Schroeder, S.J., Zuker, M., Turner, D.H.: Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA 101, 7287-7292 (2004)
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 7287-7292
    • Mathews, D.H.1    Disney, M.D.2    Childs, J.L.3    Schroeder, S.J.4    Zuker, M.5    Turner, D.H.6
  • 30
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • McCaskill, J.S.: The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29, 1105-1119 (1990)
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1
  • 31
    • 34548726219 scopus 로고    scopus 로고
    • Interactions of the G quartet forming semaphorin 3F RNA with the RGG box domain of the fragile X protein family
    • Menon, L., Mihailescu, M.R.: Interactions of the G quartet forming semaphorin 3F RNA with the RGG box domain of the fragile X protein family. Nucleic Acids Res. 35, 5379-5392 (2007)
    • (2007) Nucleic Acids Res. , vol.35 , pp. 5379-5392
    • Menon, L.1    Mihailescu, M.R.2
  • 33
    • 67049134254 scopus 로고    scopus 로고
    • An unusually stable G-quadruplex within the 5′-UTR of the MT3 matrix metalloproteinase mRNA represses translation in eukaryotic cells
    • Morris, M.J., Basu, S.: An unusually stable G-quadruplex within the 5′-UTR of the MT3 matrix metalloproteinase mRNA represses translation in eukaryotic cells. Biochemistry 48, 5313-5319 (2009)
    • (2009) Biochemistry , vol.48 , pp. 5313-5319
    • Morris, M.J.1    Basu, S.2
  • 35
    • 27144451010 scopus 로고    scopus 로고
    • Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo
    • Paeschke, K., Simonsson, T., Postberg, J., Rhodes, D., Lipps, H.J.: Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo. Nature Struct. Mol. Biol. 12, 847-854 (2005)
    • (2005) Nature Struct. Mol. Biol. , vol.12 , pp. 847-854
    • Paeschke, K.1    Simonsson, T.2    Postberg, J.3    Rhodes, D.4    Lipps, H.J.5
  • 36
    • 0028196714 scopus 로고
    • From sequences to shapes and back: A case study in RNA secondary structures
    • Schuster, P., Fontana, W., Stadler, P.F., Hofacker, I.L.: From sequences to shapes and back: A case study in RNA secondary structures. Proc. Roy. Soc. Lond. B 255, 279-284 (1994)
    • (1994) Proc. Roy. Soc. Lond. B , vol.255 , pp. 279-284
    • Schuster, P.1    Fontana, W.2    Stadler, P.F.3    Hofacker, I.L.4
  • 37
    • 37249066753 scopus 로고    scopus 로고
    • Geometric formalism for DNA quadruplex folding
    • Webba da Silva, M.: Geometric formalism for DNA quadruplex folding. Chemistry 13, 9738-9745 (2007)
    • (2007) Chemistry , vol.13 , pp. 9738-9745
    • Webba Da Silva, M.1
  • 39
    • 35448996964 scopus 로고    scopus 로고
    • Bioinformatics approaches to quadruplex sequence location
    • Todd, A.K.: Bioinformatics approaches to quadruplex sequence location. Methods 43, 246-251 (2007)
    • (2007) Methods , vol.43 , pp. 246-251
    • Todd, A.K.1
  • 41
    • 34447541999 scopus 로고    scopus 로고
    • RNA quadruplex-based modulation of gene expression
    • Wieland, M., Hartig, J.S.: RNA quadruplex-based modulation of gene expression. Chem. Biol. 14, 757-763 (2007)
    • (2007) Chem. Biol. , vol.14 , pp. 757-763
    • Wieland, M.1    Hartig, J.S.2
  • 43
    • 80051739988 scopus 로고    scopus 로고
    • A sequence-independent analysis of the loop length dependence of intramolecular RNA G-quadruplex stability and topology
    • Zhang, A.Y., Bugaut, A., Balasubramanian, S.: A sequence-independent analysis of the loop length dependence of intramolecular RNA G-quadruplex stability and topology. Biochemistry 50, 7251-7258 (2011)
    • (2011) Biochemistry , vol.50 , pp. 7251-7258
    • Zhang, A.Y.1    Bugaut, A.2    Balasubramanian, S.3
  • 44
    • 77952870567 scopus 로고    scopus 로고
    • Monomorphic RNA G-quadruplex and polymorphic DNA G-quadruplex structures responding to cellular environmental factors
    • Zhang, D.H., Fujimoto, T., Saxena, S., Yu, H.Q., Miyoshi, D., Sugimoto, N.: Monomorphic RNA G-quadruplex and polymorphic DNA G-quadruplex structures responding to cellular environmental factors. Biochemistry 49, 4554-4563 (2010)
    • (2010) Biochemistry , vol.49 , pp. 4554-4563
    • Zhang, D.H.1    Fujimoto, T.2    Saxena, S.3    Yu, H.Q.4    Miyoshi, D.5    Sugimoto, N.6
  • 45
    • 77957334049 scopus 로고    scopus 로고
    • Structure monomorphism of RNA G-quadruplex that is independent of surrounding condition
    • Zhang, D.H., Zhi, G.Y.: Structure monomorphism of RNA G-quadruplex that is independent of surrounding condition. J. Biotechnol. 150, 6-10 (2010)
    • (2010) J. Biotechnol. , vol.150 , pp. 6-10
    • Zhang, D.H.1    Zhi, G.Y.2
  • 46
    • 34247645020 scopus 로고    scopus 로고
    • Extensive selection for the enrichment of G4 DNA motifs in transcriptional regulatory regions of warm blooded animals
    • Zhao, Y., Du, Z., Li, N.: Extensive selection for the enrichment of G4 DNA motifs in transcriptional regulatory regions of warm blooded animals. FEBS Letters 581, 1951-1956 (2007)
    • (2007) FEBS Letters , vol.581 , pp. 1951-1956
    • Zhao, Y.1    Du, Z.2    Li, N.3
  • 47
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker, M., Stiegler, P.: Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9, 133-148 (1981)
    • (1981) Nucleic Acids Res. , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.