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Volumn 7, Issue 2, 2001, Pages 314-327

Mapping of RNA accessible sites by extension of random oligonucleotide libraries with reverse transcriptase

Author keywords

Antisense; Extendible sites; Hybridization; ICAM 1; Invasive cleavage; RNA detection

Indexed keywords

ORYCTOLAGUS CUNICULUS;

EID: 0035261221     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838201001698     Document Type: Article
Times cited : (38)

References (57)
  • 1
    • 0028220670 scopus 로고
    • Inhibition of endothelial cell adhesion molecule expression with antisense oligonucleotides
    • Bennett CF, Condon TP, Grimm S, Chan H, Chiang MY. 1994. Inhibition of endothelial cell adhesion molecule expression with antisense oligonucleotides. J Immunol 152:3530-3540.
    • (1994) J Immunol , vol.152 , pp. 3530-3540
    • Bennett, C.F.1    Condon, T.P.2    Grimm, S.3    Chan, H.4    Chiang, M.Y.5
  • 2
    • 0030952735 scopus 로고    scopus 로고
    • Probing accessible sites for ribozymes on human acetylcholinesterase RNA
    • Birikh KR, Berlin YA, Soreq H, Eckstein F. 1997. Probing accessible sites for ribozymes on human acetylcholinesterase RNA, RNA 3:429-437.
    • (1997) RNA , vol.3 , pp. 429-437
    • Birikh, K.R.1    Berlin, Y.A.2    Soreq, H.3    Eckstein, F.4
  • 3
    • 0030887663 scopus 로고    scopus 로고
    • Control of complexity constraints on combinatorial screening for preferred oligonucleotide hybridization sites on structured RNA
    • Bruice TW, Lima WF. 1997. Control of complexity constraints on combinatorial screening for preferred oligonucleotide hybridization sites on structured RNA, Biochemistry 36:5004-5019.
    • (1997) Biochemistry , vol.36 , pp. 5004-5019
    • Bruice, T.W.1    Lima, W.F.2
  • 4
    • 0029348716 scopus 로고
    • Identification of ribozymes within a ribozyme library that efficiently cleave a long substrate RNA
    • Campbell TB, Cech TR. 1995. Identification of ribozymes within a ribozyme library that efficiently cleave a long substrate RNA. RNA 1:598-609.
    • (1995) RNA , vol.1 , pp. 598-609
    • Campbell, T.B.1    Cech, T.R.2
  • 5
    • 0026052924 scopus 로고
    • Antisense oligonucleotides inhibit intercellular adhesion molecule 1 expression by two distinct mechanisms
    • Chiang MY, Chan H, Zounes MA, Freier SM, Lima WF, Bennett CF. 1991. Antisense oligonucleotides inhibit intercellular adhesion molecule 1 expression by two distinct mechanisms. J Biol Chem 266:18162-18171.
    • (1991) J Biol Chem , vol.266 , pp. 18162-18171
    • Chiang, M.Y.1    Chan, H.2    Zounes, M.A.3    Freier, S.M.4    Lima, W.F.5    Bennett, C.F.6
  • 6
    • 0015223584 scopus 로고
    • Relaxation kinetics of dimer formation by self complementary oligonucleotides
    • Craig ME, Crothers DM, Doty P. 1971. Relaxation kinetics of dimer formation by self complementary oligonucleotides. J Mol Biol 62:383-401.
    • (1971) J Mol Biol , vol.62 , pp. 383-401
    • Craig, M.E.1    Crothers, D.M.2    Doty, P.3
  • 7
    • 0029619816 scopus 로고
    • Kinetic characteristics of Escherichia coli RNase H1: Cleavage of various antisense oligonucleotide - RNA duplexes
    • Crooke ST, Lemonidis KM, Neilson L, Griffey R, Lesnik EA, Monia BP. 1995. Kinetic characteristics of Escherichia coli RNase H1: Cleavage of various antisense oligonucleotide - RNA duplexes. Biochem J 312:599-608.
    • (1995) Biochem J , vol.312 , pp. 599-608
    • Crooke, S.T.1    Lemonidis, K.M.2    Neilson, L.3    Griffey, R.4    Lesnik, E.A.5    Monia, B.P.6
  • 8
    • 0028292570 scopus 로고
    • Inhibition of protein kinase C-alpha expression in human A549 cells by antisense oligonucleotides inhibits induction of intercellular adhesion molecule 1 (ICAM-1) mRNA by phorbol esters
    • Dean NM, McKay R, Condon TP, Bennett CF. 1994. Inhibition of protein kinase C-alpha expression in human A549 cells by antisense oligonucleotides inhibits induction of intercellular adhesion molecule 1 (ICAM-1) mRNA by phorbol esters. J Biol Chem 269:16416-16424.
    • (1994) J Biol Chem , vol.269 , pp. 16416-16424
    • Dean, N.M.1    McKay, R.2    Condon, T.P.3    Bennett, C.F.4
  • 9
    • 0017280567 scopus 로고
    • Transcription of single base oligonucleotides by ribonucleic acid-directed deoxyribonucleic acid polymerase
    • Falvey AK, Weiss GB, Krueger LJ, Kantor JA, Anderson WF. 1976. Transcription of single base oligonucleotides by ribonucleic acid-directed deoxyribonucleic acid polymerase. Nucleic Acids Res 3:79-88.
    • (1976) Nucleic Acids Res , vol.3 , pp. 79-88
    • Falvey, A.K.1    Weiss, G.B.2    Krueger, L.J.3    Kantor, J.A.4    Anderson, W.F.5
  • 10
    • 0019878376 scopus 로고
    • Equilibria and kinetics of lac represser-operator interactions by polyacrylamide gel electrophoresis
    • Fried M, Crothers DM. 1981. Equilibria and kinetics of lac represser-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res 9:6505-6525.
    • (1981) Nucleic Acids Res , vol.9 , pp. 6505-6525
    • Fried, M.1    Crothers, D.M.2
  • 11
    • 0015119212 scopus 로고
    • Distinguishing reverse transcriptase of an RNA tumor virus from other known DNA polymerases
    • Goodman NC, Spiegelman S. 1971. Distinguishing reverse transcriptase of an RNA tumor virus from other known DNA polymerases. Proc Natl Acad Sci USA 68:2203-2206.
    • (1971) Proc Natl Acad Sci USA , vol.68 , pp. 2203-2206
    • Goodman, N.C.1    Spiegelman, S.2
  • 13
    • 0003038882 scopus 로고    scopus 로고
    • Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries
    • Ho SP, Bao Y, Lesher T, Malhotra R, Ma LY, Fluharty S, Sakai R. 1998. Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries. Nat Biotechnol 16:59-63.
    • (1998) Nat Biotechnol , vol.16 , pp. 59-63
    • Ho, S.P.1    Bao, Y.2    Lesher, T.3    Malhotra, R.4    Ma, L.Y.5    Fluharty, S.6    Sakai, R.7
  • 14
    • 0029938209 scopus 로고    scopus 로고
    • Potent antisense oligonucleotides to the human multidrug resistance-1 mRNA are rationally selected by mapping RNA-accessible sites with oligonucleotide libraries
    • Ho SP, Britton DH, Stone BA, Behrens DL, Leffet LM, Hobbs FW, Miller JA, Trainor GL. 1996. Potent antisense oligonucleotides to the human multidrug resistance-1 mRNA are rationally selected by mapping RNA-accessible sites with oligonucleotide libraries. Nucleic Acids Res 24:1901-1907.
    • (1996) Nucleic Acids Res , vol.24 , pp. 1901-1907
    • Ho, S.P.1    Britton, D.H.2    Stone, B.A.3    Behrens, D.L.4    Leffet, L.M.5    Hobbs, F.W.6    Miller, J.A.7    Trainor, G.L.8
  • 15
    • 0014734641 scopus 로고
    • The stability of a codon transfer RNA complex
    • Hogenauer G. 1970. The stability of a codon transfer RNA complex. Eur J Biochem 12:527-532.
    • (1970) Eur J Biochem , vol.12 , pp. 527-532
    • Hogenauer, G.1
  • 18
    • 0033428098 scopus 로고    scopus 로고
    • Clinical, genetic, and pharmacogenetic applications of the Invader assay
    • Kwiatkowski RW, Lyamichev V, de Arruda M, Neri B. 1999. Clinical, genetic, and pharmacogenetic applications of the Invader assay. Mol Diagn 4:353-364.
    • (1999) Mol Diagn , vol.4 , pp. 353-364
    • Kwiatkowski, R.W.1    Lyamichev, V.2    De Arruda, M.3    Neri, B.4
  • 19
    • 0014935509 scopus 로고
    • Derivation of the secondary structure of 5s RNA from its binding of complementary oligonucleotides
    • Lewis JB, Doty P. 1970. Derivation of the secondary structure of 5S RNA from its binding of complementary oligonucleotides. Nature 225:510-512.
    • (1970) Nature , vol.225 , pp. 510-512
    • Lewis, J.B.1    Doty, P.2
  • 20
    • 0028943217 scopus 로고
    • Selection of efficient cleavage sites in target RNAs by using a ribozyme expression library
    • Lieber A, Strauss M. 1995. Selection of efficient cleavage sites in target RNAs by using a ribozyme expression library. Mol Cell Biol 15:540-551.
    • (1995) Mol Cell Biol , vol.15 , pp. 540-551
    • Lieber, A.1    Strauss, M.2
  • 21
    • 0031032603 scopus 로고    scopus 로고
    • Combinatorial screening and rational optimization for hybridization to folded hepatitis C virus RNA of oligonucleotides with biological antisense activity
    • Lima WF, Brown-Driver V, Fox M, Hanecak R, Bruice TW. 1997. Combinatorial screening and rational optimization for hybridization to folded hepatitis C virus RNA of oligonucleotides with biological antisense activity. J Biol Chem 272:626-638.
    • (1997) J Biol Chem , vol.272 , pp. 626-638
    • Lima, W.F.1    Brown-Driver, V.2    Fox, M.3    Hanecak, R.4    Bruice, T.W.5
  • 22
    • 0030735085 scopus 로고    scopus 로고
    • Cleavage of single strand RNA adjacent to RNA-DNA duplex regions by Escherichia coli RNase H1
    • Lima WF, Crooke ST. 1997. Cleavage of single strand RNA adjacent to RNA-DNA duplex regions by Escherichia coli RNase H1. J Biol Chem 272:27513-27516.
    • (1997) J Biol Chem , vol.272 , pp. 27513-27516
    • Lima, W.F.1    Crooke, S.T.2
  • 23
    • 0026621339 scopus 로고
    • Implication of RNA structure on antisense oligonucleotide hybridization kinetics
    • Lima WF, Monia BP, Ecker DJ, Freier SM. 1992. Implication of RNA structure on antisense oligonucleotide hybridization kinetics. Biochemistry 31:12055-12061.
    • (1992) Biochemistry , vol.31 , pp. 12055-12061
    • Lima, W.F.1    Monia, B.P.2    Ecker, D.J.3    Freier, S.M.4
  • 25
    • 0033028685 scopus 로고    scopus 로고
    • Comparison of the 5′ nuclease activities of Taq DNA polymerase and its isolated nuclease domain
    • Lyamichev V, Brow MA, Varvel VE, Dahlberg JE. 1999a. Comparison of the 5′ nuclease activities of Taq DNA polymerase and its isolated nuclease domain. Proc Natl Acad Sci USA 96:6143-6148.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 6143-6148
    • Lyamichev, V.1    Brow, M.A.2    Varvel, V.E.3    Dahlberg, J.E.4
  • 30
    • 0031574209 scopus 로고    scopus 로고
    • A rapid in vitro method for obtaining RNA accessibility patterns for complementary DNA probes: Correlation with an intracellular pattern and known RNA structures
    • Matveeva O, Felden B, Audlin S, Gesteland RF, Atkins JF. 1997. A rapid in vitro method for obtaining RNA accessibility patterns for complementary DNA probes: Correlation with an intracellular pattern and known RNA structures. Nucleic Acids Res 25:5010-5016.
    • (1997) Nucleic Acids Res , vol.25 , pp. 5010-5016
    • Matveeva, O.1    Felden, B.2    Audlin, S.3    Gesteland, R.F.4    Atkins, J.F.5
  • 32
    • 0030902471 scopus 로고    scopus 로고
    • Selecting effective antisense reagents on combinatorial oligonucleotide arrays
    • Milner N, Mir KU, Southern EM. 1997. Selecting effective antisense reagents on combinatorial oligonucleotide arrays. Nat Biotechnol 15:537-541.
    • (1997) Nat Biotechnol , vol.15 , pp. 537-541
    • Milner, N.1    Mir, K.U.2    Southern, E.M.3
  • 33
    • 0032857575 scopus 로고    scopus 로고
    • Determining the influence of structure on hybridization using oligonucleotide arrays
    • Mir KU, Southern EM. 1999. Determining the influence of structure on hybridization using oligonucleotide arrays. Nat Biotechnol 17:788-792.
    • (1999) Nat Biotechnol , vol.17 , pp. 788-792
    • Mir, K.U.1    Southern, E.M.2
  • 35
    • 0033570886 scopus 로고    scopus 로고
    • A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability
    • Patzel V, Steidl U, Kronenwett R, Haas R, Sczakiel G. 1999. A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability. Nucleic Acids Res 27:4328-4334.
    • (1999) Nucleic Acids Res , vol.27 , pp. 4328-4334
    • Patzel, V.1    Steidl, U.2    Kronenwett, R.3    Haas, R.4    Sczakiel, G.5
  • 36
    • 0015223587 scopus 로고
    • Co-operative non-enzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic-oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH
    • Porschke D, Eigen M. 1971. Co-operative non-enzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic-oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH. J Mol Biol 62:361-381.
    • (1971) J Mol Biol , vol.62 , pp. 361-381
    • Porschke, D.1    Eigen, M.2
  • 37
    • 0020597717 scopus 로고
    • Nucleotide sequence analysis of the T24 human bladder carcinoma oncogene
    • Reddy EP. 1983. Nucleotide sequence analysis of the T24 human bladder carcinoma oncogene. Science 220:1061-1063.
    • (1983) Science , vol.220 , pp. 1061-1063
    • Reddy, E.P.1
  • 40
    • 0027289572 scopus 로고
    • Computer-aided search for effective antisense RNA target sequences of the human immunodeficiency virus type 1
    • Sczakiel G, Homann M, Rittner K. 1993. Computer-aided search for effective antisense RNA target sequences of the human immunodeficiency virus type 1. Antisense Res Dev 3:45-52.
    • (1993) Antisense Res Dev , vol.3 , pp. 45-52
    • Sczakiel, G.1    Homann, M.2    Rittner, K.3
  • 41
    • 0032890879 scopus 로고    scopus 로고
    • The folding of large RNAs studied by hybridization to arrays of complementary oligonucle-otides
    • Sohail M, Akhtar S, Southern EM. 1999. The folding of large RNAs studied by hybridization to arrays of complementary oligonucle-otides. RNA 5:646-655.
    • (1999) RNA , vol.5 , pp. 646-655
    • Sohail, M.1    Akhtar, S.2    Southern, E.M.3
  • 43
    • 0032998423 scopus 로고    scopus 로고
    • Keeping the biotechnology of antisense in context
    • Stein CA. 1999. Keeping the biotechnology of antisense in context. Nat Biotechnol 17:209.
    • (1999) Nat Biotechnol , vol.17 , pp. 209
    • Stein, C.A.1
  • 44
    • 0027376439 scopus 로고
    • Antisense oligonucleotides as therapeutic agents - Is the bullet really magical?
    • Stein CA, Cheng YC. 1993. Antisense oligonucleotides as therapeutic agents - is the bullet really magical? Science 261:1004-1012.
    • (1993) Science , vol.261 , pp. 1004-1012
    • Stein, C.A.1    Cheng, Y.C.2
  • 45
    • 0026770701 scopus 로고
    • Predicting antisense oligonucleotide inhibitory efficacy: A computational approach using histograms and thermodynamic indices
    • Stull RA, Taylor LA, Szoka FC, Jr. 1992. Predicting antisense oligonucleotide inhibitory efficacy: A computational approach using histograms and thermodynamic indices. Nucleic Acids Res 20: 3501-3508.
    • (1992) Nucleic Acids Res , vol.20 , pp. 3501-3508
    • Stull, R.A.1    Taylor, L.A.2    Szoka F.C., Jr.3
  • 47
    • 0015505497 scopus 로고
    • Complementary oligonucleotide binding to transfer RNA
    • Uhlenbeck OC. 1972. Complementary oligonucleotide binding to transfer RNA. J Mol Biol 65:25-41.
    • (1972) J Mol Biol , vol.65 , pp. 25-41
    • Uhlenbeck, O.C.1
  • 48
    • 0014935515 scopus 로고
    • Complementary oligonucleotide binding to the anticodon loop of fMet-transfer RNA
    • Uhlenbeck OC, Baller J, Doty P. 1970. Complementary oligonucleotide binding to the anticodon loop of fMet-transfer RNA. Nature 225:508-510.
    • (1970) Nature , vol.225 , pp. 508-510
    • Uhlenbeck, O.C.1    Baller, J.2    Doty, P.3
  • 49
    • 0016741477 scopus 로고
    • Studies on reverse transcriptase of RNA tumor viruses III. Properties of purified moloney murine leukemia virus DNA polymerase and associated RNase H
    • Verma IM. 1975. Studies on reverse transcriptase of RNA tumor viruses III. Properties of purified Moloney murine leukemia virus DNA polymerase and associated RNase H. J Virol 15:843-854.
    • (1975) J Virol , vol.15 , pp. 843-854
    • Verma, I.M.1
  • 50
    • 0034653783 scopus 로고    scopus 로고
    • Effects of RNA secondary structure on cellular antisense activity
    • Vickers TA, Wyatt JR, Freier SM. 2000. Effects of RNA secondary structure on cellular antisense activity. Nucleic Acids Res 28: 1340-1347.
    • (2000) Nucleic Acids Res , vol.28 , pp. 1340-1347
    • Vickers, T.A.1    Wyatt, J.R.2    Freier, S.M.3
  • 51
    • 0028019410 scopus 로고
    • Gene inhibition using antisense oligodeoxynucleotides
    • Wagner RW. 1994. Gene inhibition using antisense oligodeoxynucleotides. Nature 372:333-335.
    • (1994) Nature , vol.372 , pp. 333-335
    • Wagner, R.W.1
  • 52
    • 0029943016 scopus 로고    scopus 로고
    • Potent and selective inhibition of gene expression by an antisense heptanucleotide
    • Wagner RW, Matteucci MD, Grant D, Huang T, Froehler BC. 1996. Potent and selective inhibition of gene expression by an antisense heptanucleotide. Nat Biotechnol 14:840-844.
    • (1996) Nat Biotechnol , vol.14 , pp. 840-844
    • Wagner, R.W.1    Matteucci, M.D.2    Grant, D.3    Huang, T.4    Froehler, B.C.5
  • 53
    • 0033527352 scopus 로고    scopus 로고
    • Prediction of antisense oligonucleotide binding affinity to a structured RNA target
    • Walton SP, Stephanopoulos GN, Yarmush ML, Roth CM. 1999. Prediction of antisense oligonucleotide binding affinity to a structured RNA target. Biotechnol Bioeng 65:1-9.
    • (1999) Biotechnol Bioeng , vol.65 , pp. 1-9
    • Walton, S.P.1    Stephanopoulos, G.N.2    Yarmush, M.L.3    Roth, C.M.4
  • 55
    • 0343963180 scopus 로고    scopus 로고
    • Mapping of accessible sites for oligonucleotide hybridization on hepatitis delta virus ribozymes
    • Wrzesinski J, Legiewicz M, Ciesiolka J. 2000. Mapping of accessible sites for oligonucleotide hybridization on hepatitis delta virus ribozymes. Nucleic Acids Res 28:1785-1793.
    • (2000) Nucleic Acids Res , vol.28 , pp. 1785-1793
    • Wrzesinski, J.1    Legiewicz, M.2    Ciesiolka, J.3
  • 57
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • Zuker M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244:48-52.
    • (1989) Science , vol.244 , pp. 48-52
    • Zuker, M.1


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