메뉴 건너뛰기




Volumn 18, Issue 4, 2005, Pages 318-326

Investigation of potential RNA bulge stabilizing elements

Author keywords

2 O alkyl RNA; Nucleic acid hybridization; RNA bulges; RNA recognition

Indexed keywords

OLIGONUCLEOTIDE; RIBONUCLEASE; RIBONUCLEOSIDE; RNA;

EID: 23044465203     PISSN: 09523499     EISSN: None     Source Type: Journal    
DOI: 10.1002/jmr.736     Document Type: Article
Times cited : (5)

References (41)
  • 5
    • 0033990403 scopus 로고    scopus 로고
    • Progress in antisense technology: The end of the beginning
    • Crooke ST. 2000. Progress in antisense technology: the end of the beginning. Meth. Enzymol. 313: 3-45.
    • (2000) Meth. Enzymol. , vol.313 , pp. 3-45
    • Crooke, S.T.1
  • 6
    • 0030856838 scopus 로고    scopus 로고
    • Binding of Hoechst 33258 to the TAR RNA of HIV-1. Recognition of a pyrimidine bulge-dependent structure
    • Dassonneville L, Hamyl F, Colson P, Houssier C, Bailly C. 1997. Binding of Hoechst 33258 to the TAR RNA of HIV-1. Recognition of a pyrimidine bulge-dependent structure. Nucl. Acids Res. 25: 4487-4492.
    • (1997) Nucl. Acids Res. , vol.25 , pp. 4487-4492
    • Dassonneville, L.1    Hamyl, F.2    Colson, P.3    Houssier, C.4    Bailly, C.5
  • 7
    • 0442323636 scopus 로고    scopus 로고
    • Two sides of the coin: Affinity and specificity of nucleic interactions
    • Demidov VV, Frank-Kemenetskii. 2004. Two sides of the coin: affinity and specificity of nucleic interactions. Trends Biochem. Sci. 29: 62-71.
    • (2004) Trends Biochem. Sci. , vol.29 , pp. 62-71
    • Demidov, V.V.1    Frank-Kemenetskii2
  • 8
    • 0032041954 scopus 로고    scopus 로고
    • PNA, antisense, and antimicrobials
    • Ecker DJ, Freier SM. 1998. PNA, antisense, and antimicrobials. Nat. Biotechnol. 16: 332-332.
    • (1998) Nat. Biotechnol. , vol.16 , pp. 332-332
    • Ecker, D.J.1    Freier, S.M.2
  • 9
    • 0000117791 scopus 로고    scopus 로고
    • Structural aspects of nucleic acid analogs and antisense oligonucleotides
    • Egli M. 1996. Structural aspects of nucleic acid analogs and antisense oligonucleotides. Angew. Chem. Int. Edn. Engl. 35: 1894-1909.
    • (1996) Angew. Chem. Int. Edn. Engl. , vol.35 , pp. 1894-1909
    • Egli, M.1
  • 10
    • 0029956116 scopus 로고    scopus 로고
    • RNA hydration: A detailed look
    • Egli M, Portman S, Usman N. 1996. RNA hydration: a detailed look. Biochemistry 35: 8489-8494.
    • (1996) Biochemistry , vol.35 , pp. 8489-8494
    • Egli, M.1    Portman, S.2    Usman, N.3
  • 11
    • 0033150948 scopus 로고    scopus 로고
    • Oligonucelotide aptamers that recognize small molecules
    • Famulok M. 1999. Oligonucelotide aptamers that recognize small molecules. Curr. Opin. Struct. Biol. 9: 324-329.
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 324-329
    • Famulok, M.1
  • 12
    • 0015526994 scopus 로고
    • Free energy of imperfect nucleic acid helices. I. The bulge defect
    • Fink TR, Crothers DM. 1972. Free energy of imperfect nucleic acid helices. I. The bulge defect. J. Mol. Biol. 66: 1-12.
    • (1972) J. Mol. Biol. , vol.66 , pp. 1-12
    • Fink, T.R.1    Crothers, D.M.2
  • 13
    • 0016469299 scopus 로고
    • The enthalpy of the 'bulge' defect of imperfect nucleic acid helices
    • Fink TR, Krakauer H. 1975. The enthalpy of the 'bulge' defect of imperfect nucleic acid helices. Biopolymers 14: 433-436.
    • (1975) Biopolymers , vol.14 , pp. 433-436
    • Fink, T.R.1    Krakauer, H.2
  • 14
    • 0030727765 scopus 로고    scopus 로고
    • The ups and downs of nucleic acid duplex stability: Structure-stability studies on chemically-modified DNA:RNA duplexes
    • Freier SM, Altmann KH. 1997. The ups and downs of nucleic acid duplex stability: structure-stability studies on chemically-modified DNA:RNA duplexes. Nucl. Acids Res. 25: 4429-4443.
    • (1997) Nucl. Acids Res. , vol.25 , pp. 4429-4443
    • Freier, S.M.1    Altmann, K.H.2
  • 15
    • 4243477595 scopus 로고
    • The tetraisopropyl-1.3-diyl: A versatile protecting group for the synthesis of adenylyl-(2′,5′)-adenylyl-(2′,5′)-adenosine (2-5A core)
    • Gioeli S, Kwiatkowski M, Öberg B, Chattopadhyaya JB. 1981. The tetraisopropyl-1.3-diyl: a versatile protecting group for the synthesis of adenylyl-(2′,5′)-adenylyl-(2′,5′)-adenosine (2-5A core). Tetrahedron Lett. 22: 1741-1744.
    • (1981) Tetrahedron Lett. , vol.22 , pp. 1741-1744
    • Gioeli, S.1    Kwiatkowski, M.2    Öberg, B.3    Chattopadhyaya, J.B.4
  • 16
    • 0024579255 scopus 로고
    • Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide
    • Groebe DR, Uhlenbeck OC. 1989. Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide. Biochemistry 28: 742-747.
    • (1989) Biochemistry , vol.28 , pp. 742-747
    • Groebe, D.R.1    Uhlenbeck, O.C.2
  • 17
    • 0019332380 scopus 로고
    • Nucleoside conformation is determined by the electronegativity of the sugar substituent
    • Guschlbauer W, Jankowski K. 1980. Nucleoside conformation is determined by the electronegativity of the sugar substituent. Nucl. Acids Res. 8: 1421-1433.
    • (1980) Nucl. Acids Res. , vol.8 , pp. 1421-1433
    • Guschlbauer, W.1    Jankowski, K.2
  • 18
    • 0029792376 scopus 로고    scopus 로고
    • Towards artificial ribonucleases: The sequence-specific cleavage of RNA in a duplex
    • Hall J, Huesken D, Häner R. 1996. Towards artificial ribonucleases: the sequence-specific cleavage of RNA in a duplex. Nucl. Acids Res. 24: 3522-3526.
    • (1996) Nucl. Acids Res. , vol.24 , pp. 3522-3526
    • Hall, J.1    Huesken, D.2    Häner, R.3
  • 20
    • 0034743058 scopus 로고    scopus 로고
    • The cleavage of phosphodiester bonds within small RNA bulges in the presence and absence of metal ion catalysts
    • Kaukinen U, Bielecki L, Mikkola S, Adamiak RW, Lönnberg H. 2001. The cleavage of phosphodiester bonds within small RNA bulges in the presence and absence of metal ion catalysts. J. Chem. Soc., Perkin Trans. 2: 1024-1031.
    • (2001) J. Chem. Soc., Perkin Trans. , vol.2 , pp. 1024-1031
    • Kaukinen, U.1    Bielecki, L.2    Mikkola, S.3    Adamiak, R.W.4    Lönnberg, H.5
  • 21
    • 0025186882 scopus 로고
    • Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides
    • Longfellow CE, Kierzek R, Turner DH. 1990. Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides. Biochemistry 29: 278-285.
    • (1990) Biochemistry , vol.29 , pp. 278-285
    • Longfellow, C.E.1    Kierzek, R.2    Turner, D.H.3
  • 22
    • 0030874397 scopus 로고    scopus 로고
    • Solution conformation of a five-nucleotide RNA bulge loop from a group I intron
    • Luebke KJ, Landry SM, Tinoco I Jr. 1997. Solution conformation of a five-nucleotide RNA bulge loop from a group I intron. Biochemistry 36: 10246-10255.
    • (1997) Biochemistry , vol.36 , pp. 10246-10255
    • Luebke, K.J.1    Landry, S.M.2    Tinoco Jr., I.3
  • 23
    • 0344443727 scopus 로고    scopus 로고
    • Stabilisation of RNA bulges by oligonucleotide complements containing an adenosine analogue
    • Madder A, Ehrl R, Strömberg R. 2003. Stabilisation of RNA bulges by oligonucleotide complements containing an adenosine analogue. Chem. Biol. Chem. 4: 1194-1200.
    • (2003) Chem. Biol. Chem. , vol.4 , pp. 1194-1200
    • Madder, A.1    Ehrl, R.2    Strömberg, R.3
  • 24
    • 0035230816 scopus 로고    scopus 로고
    • The effect of secondary structure on the cleavage of the phosphodiester bonds of RNA
    • Mikkola S, Kaukinen U, Lönnberg H. 2001. The effect of secondary structure on the cleavage of the phosphodiester bonds of RNA. Cell Biochem. Biophys. 34: 95-119.
    • (2001) Cell Biochem. Biophys. , vol.34 , pp. 95-119
    • Mikkola, S.1    Kaukinen, U.2    Lönnberg, H.3
  • 25
    • 0019764554 scopus 로고
    • DNA and RNA oligomer thermodynamics: The effect of mismatched bases on double-helix stability
    • Nelson JW, Martin FH, Tinoco I Jr. 1981. DNA and RNA oligomer thermodynamics: the effect of mismatched bases on double-helix stability. Biopolymers 20: 2509-2531.
    • (1981) Biopolymers , vol.20 , pp. 2509-2531
    • Nelson, J.W.1    Martin, F.H.2    Tinoco Jr., I.3
  • 26
    • 0031152065 scopus 로고    scopus 로고
    • Aptamers as therapeutic and diagnostic reagents: Problems and prospects
    • Osborne SE, Matsumura I, Ellington AD. 1997. Aptamers as therapeutic and diagnostic reagents: problems and prospects. Curr. Opin. Chem. Biol. 1: 5-9.
    • (1997) Curr. Opin. Chem. Biol. , vol.1 , pp. 5-9
    • Osborne, S.E.1    Matsumura, I.2    Ellington, A.D.3
  • 27
    • 0029051383 scopus 로고
    • The crystal structure of r(CCCCGGGG) in two distinct lattices
    • Portmann S, Usman N, Egli M. 1995. The crystal structure of r(CCCCGGGG) in two distinct lattices. Biochemistry 34: 7569-7575.
    • (1995) Biochemistry , vol.34 , pp. 7569-7575
    • Portmann, S.1    Usman, N.2    Egli, M.3
  • 28
    • 0030090986 scopus 로고    scopus 로고
    • Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage
    • Portmann S, Grimm S, Workman C, Usman N, Egli M. 1996. Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage. Chem. Biol. 3: 173-184.
    • (1996) Chem. Biol. , vol.3 , pp. 173-184
    • Portmann, S.1    Grimm, S.2    Workman, C.3    Usman, N.4    Egli, M.5
  • 31
    • 0142011647 scopus 로고    scopus 로고
    • Targeting RNA with small molecules
    • Tor Y. 2003. Targeting RNA with small molecules. Chem. Biol. Chem. 4: 998-1007.
    • (2003) Chem. Biol. Chem. , vol.4 , pp. 998-1007
    • Tor, Y.1
  • 32
    • 0015243953 scopus 로고
    • Synthesis of some pyrimidine 2′-amino-2′-deoxynucleosides
    • Verheyden JPH, Wagner D, Moffatt JG. 1971. Synthesis of some pyrimidine 2′-amino-2′-deoxynucleosides. J. Org. Chem. 36: 250-254.
    • (1971) J. Org. Chem. , vol.36 , pp. 250-254
    • Verheyden, J.P.H.1    Wagner, D.2    Moffatt, J.G.3
  • 33
    • 0034886697 scopus 로고    scopus 로고
    • Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site
    • Vicens Q, Westhof E. 2001. Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site. Structure 9: 647-658.
    • (2001) Structure , vol.9 , pp. 647-658
    • Vicens, Q.1    Westhof, E.2
  • 34
    • 0142106950 scopus 로고    scopus 로고
    • RNA as a drug target: The case of aminoglycosides
    • Vicens Q, Westhof E. 2003. RNA as a drug target: the case of aminoglycosides. Chem. Bio. Chem. 4: 1018-1023.
    • (2003) Chem. Bio. Chem. , vol.4 , pp. 1018-1023
    • Vicens, Q.1    Westhof, E.2
  • 35
    • 0036191824 scopus 로고    scopus 로고
    • Recognition of bulged DNA by a neocarzinostatin product via an induced fit mechanism
    • Yang CF, Jackson PJ, Xi Z, Goldberg IH. 2002. Recognition of bulged DNA by a neocarzinostatin product via an induced fit mechanism. Bioorg. Med. Chem. 10: 1329-1335.
    • (2002) Bioorg. Med. Chem. , vol.10 , pp. 1329-1335
    • Yang, C.F.1    Jackson, P.J.2    Xi, Z.3    Goldberg, I.H.4
  • 36
    • 0030475417 scopus 로고    scopus 로고
    • Deep penetration of an alpha-helix into a widened RNA major groove in the HIV-1 rev peptide-RNA aptamer complex
    • Ye X, Gorin A, Ellington AD, Patel DJ. 1996. Deep penetration of an alpha-helix into a widened RNA major groove in the HIV-1 rev peptide-RNA aptamer complex. Nat. Struct. Biol. 3: 1026-1033.
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 1026-1033
    • Ye, X.1    Gorin, A.2    Ellington, A.D.3    Patel, D.J.4
  • 37
    • 0041582974 scopus 로고
    • Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide
    • Zamecnik PC, Stephenson ML. 1978. Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide. Proc. Natl Acad. Sci. USA 75: 280-284.
    • (1978) Proc. Natl. Acad. Sci. USA , vol.75 , pp. 280-284
    • Zamecnik, P.C.1    Stephenson, M.L.2
  • 38
    • 0033619687 scopus 로고    scopus 로고
    • The effect of base sequence on the stability of RNA and DNA single base bulges
    • Zhu J, Wartell RM. 1999. The effect of base sequence on the stability of RNA and DNA single base bulges. Biochemistry 38: 15986-15993.
    • (1999) Biochemistry , vol.38 , pp. 15986-15993
    • Zhu, J.1    Wartell, R.M.2
  • 40
    • 17144452346 scopus 로고    scopus 로고
    • Synthesis of new OBANs and further studies on positioning of the catalytic group
    • Åström H, Strömberg R. 2004. Synthesis of new OBANs and further studies on positioning of the catalytic group. Org. Biomol. Chem. 2: 1901-1907.
    • (2004) Org. Biomol. Chem. , vol.2 , pp. 1901-1907
    • Åström, H.1    Strömberg, R.2
  • 41
    • 0141974888 scopus 로고    scopus 로고
    • Oligonucleotide based artificial nuclease (OBAN) systems. Bulge size dependence and positioning of catalytic group in cleavage of RNA-bulges
    • Åström H, Williams NH, Strömberg R. 2003. Oligonucleotide based artificial nuclease (OBAN) systems. Bulge size dependence and positioning of catalytic group in cleavage of RNA-bulges. Org. Biomol. Chem. 1: 1461-465.
    • (2003) Org. Biomol. Chem. , vol.1 , pp. 1461-1465
    • Åström, H.1    Williams, N.H.2    Strömberg, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.