메뉴 건너뛰기




Volumn 3, Issue , 2014, Pages

A Kinetic Model Explains Why Shorter and Less Affine Enzyme-recruiting Oligonucleotides Can Be More Potent

Author keywords

kinetic model; oligonucleotide affinity; potency

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; OLIGONUCLEOTIDE; RIBONUCLEASE H; RNA; SMALL INTERFERING RNA; MICRORNA;

EID: 84894522337     PISSN: None     EISSN: 21622531     Source Type: Journal    
DOI: 10.1038/mtna.2013.72     Document Type: Article
Times cited : (40)

References (38)
  • 1
    • 0024041180 scopus 로고
    • Role of RNase H in hybrid-arrested translation by antisense oligonucleotides
    • Walder, RY and Walder, JA (1988). Role of RNase H in hybrid-arrested translation by antisense oligonucleotides. Proc Natl Acad Sci USA 85: 5011-5015.
    • (1988) Proc Natl Acad Sci USA , vol.85 , pp. 5011-5015
    • Walder, R.Y.1    Walder, J.A.2
  • 2
    • 0014682495 scopus 로고
    • Enzyme from calf thymus degrading the RNA moiety of DNA-RNA Hybrids: Effect on DNA-dependent RNA polymerase
    • Stein, H and Hausen, P (1969). Enzyme from calf thymus degrading the RNA moiety of DNA-RNA Hybrids: effect on DNA-dependent RNA polymerase. Science 166: 393-395.
    • (1969) Science , vol.166 , pp. 393-395
    • Stein, H.1    Hausen, P.2
  • 4
    • 77949512140 scopus 로고    scopus 로고
    • RNA targeting therapeutics: Molecular mechanisms of antisense oligonucleotides as a therapeutic platform
    • Bennett, CF and Swayze, EE (2010). RNA targeting therapeutics: molecular mechanisms of antisense oligonucleotides as a therapeutic platform. Annu Rev Pharmacol Toxicol 50: 259-293.
    • (2010) Annu Rev Pharmacol Toxicol , vol.50 , pp. 259-293
    • Bennett, C.F.1    Swayze, E.E.2
  • 5
    • 0030862285 scopus 로고    scopus 로고
    • 3-endo sugar puckering
    • PII S0040403997103227
    • Obika, S, Nanbu, D, Hari, Y, Morio, K, In, Y, Ishida, T et al. (1997). Synthesis of 2-O, 4-C-methyleneuridine and-cytidine. Novel bicyclic nucleosides having a fxed C3,-endo sugar puckering. Tet Lett 38, 8735-8738. (Pubitemid 27504436)
    • (1997) Tetrahedron Letters , vol.38 , Issue.50 , pp. 8735-8738
    • Obika, S.1    Nanbu, D.2    Hari, Y.3    Morio, K.-I.4    In, Y.5    Ishida, T.6    Imanishi, T.7
  • 6
    • 0032473890 scopus 로고    scopus 로고
    • LNA (Locked Nucleic Acids): Synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition
    • DOI 10.1016/S0040-4020(98)00094-5, PII S0040402098000945
    • Koshkin, AA, Singh, SK, Nielsen, P, Rajwanshi, VK, Kumar, R, Meldgaard, M et al. (1998). LNA (Locked Nucleic Acids): synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron 54, 3607-3630. (Pubitemid 28108183)
    • (1998) Tetrahedron , vol.54 , Issue.14 , pp. 3607-3630
    • Koshkin, A.A.1    Singh, S.K.2    Nielsen, P.3    Rajwanshi, V.K.4    Kumar, R.5    Meldgaard, M.6    Olsen, C.E.7    Wengel, J.8
  • 8
    • 78649877710 scopus 로고    scopus 로고
    • Short locked nucleic acid antisense oligonucleotides potently reduce apolipoprotein B mRNA and serum cholesterol in mice and non-human primates
    • Straarup, EM, Fisker, N, Hedtjärn, M, Lindholm, M W, Rosenbohm, C, Aarup, V et al. (2010). Short locked nucleic acid antisense oligonucleotides potently reduce apolipoprotein B mRNA and serum cholesterol in mice and non-human primates. Nucleic Acids Res 38: 7100-7111.
    • (2010) Nucleic Acids Res , vol.38 , pp. 7100-7111
    • Straarup, E.M.1    Fisker, N.2    Hedtjärn, M.3    Lindholm, M.W.4    Rosenbohm, C.5    Aarup, V.6
  • 9
    • 0032750621 scopus 로고    scopus 로고
    • 2'-carbohydrate modifcations in antisense oligonucleotide therapy: Importance of conformation, confguration and conjugation
    • Manoharan, M (1999). 2'-carbohydrate modifcations in antisense oligonucleotide therapy: importance of conformation, confguration and conjugation. Biochim Biophys Acta 1489: 117-130.
    • (1999) Biochim Biophys Acta , vol.1489 , pp. 117-130
    • Manoharan, M.1
  • 10
  • 11
    • 84894521728 scopus 로고    scopus 로고
    • The medicinal chemistry of oligonucleotides
    • Crooke, ST (ed.) CRC: Boca Raton, FL
    • Swayze, EE and Bhat, B (2007). The medicinal chemistry of oligonucleotides. In: Crooke, ST (ed.). Antisense Drug Technology. CRC: Boca Raton, FL.
    • (2007) Antisense Drug Technology
    • Swayze, E.E.1    Bhat, B.2
  • 12
    • 59449093219 scopus 로고    scopus 로고
    • Short antisense oligonucleotides with novel 2'-4' conformationaly restricted nucleoside analogues show improved potency without increased toxicity in animals
    • Seth, P P, Siwkowski, A, Allerson, CR, Vasquez, G, Lee, S, Prakash, TP et al. (2009). Short antisense oligonucleotides with novel 2'-4' conformationaly restricted nucleoside analogues show improved potency without increased toxicity in animals. J Med Chem 52: 10-13.
    • (2009) J Med Chem , vol.52 , pp. 10-13
    • Seth, P.P.1    Siwkowski, A.2    Allerson, C.R.3    Vasquez, G.4    Lee, S.5    Prakash, T.P.6
  • 14
    • 0025850802 scopus 로고
    • Implications of ribozyme kinetics for targeting the cleavage of specific RNA molecules in vivo: More isn't always better
    • Herschlag, D (1991). Implications of ribozyme kinetics for targeting the cleavage of specifc RNA molecules in vivo: more isn't always better. Proc Natl Acad Sci USA 88: 6921-6925. (Pubitemid 21915061)
    • (1991) Proceedings of the National Academy of Sciences of the United States of America , vol.88 , Issue.16 , pp. 6921-6925
    • Herschlag, D.1
  • 15
    • 78449310037 scopus 로고    scopus 로고
    • MRNA turnover rate limits siRNA and microRNA effcacy
    • Larsson, E, Sander, C and Marks, D (2010). mRNA turnover rate limits siRNA and microRNA effcacy. Mol Syst Biol 6: 433.
    • (2010) Mol Syst Biol , vol.6 , pp. 433
    • Larsson, E.1    Sander, C.2    Marks, D.3
  • 16
    • 25844526639 scopus 로고    scopus 로고
    • Molecular and cellular barriers limiting the effectiveness of antisense oligonucleotides
    • DOI 10.1529/biophysj.104.054080
    • Roth, CM (2005). Molecular and cellular barriers limiting the effectiveness of antisense oligonucleotides. Biophys J 89: 2286-2295. (Pubitemid 41401020)
    • (2005) Biophysical Journal , vol.89 , Issue.4 , pp. 2286-2295
    • Roth, C.M.1
  • 17
    • 42749109054 scopus 로고    scopus 로고
    • Statistical mechanical approaches to models with many poorly known parameters
    • Brown, KS and Sethna, JP (2003). Statistical mechanical approaches to models with many poorly known parameters. Phys Rev E Stat Nonlin Soft Matter Phys 68(2 Pt 1): 021904.
    • (2003) Phys Rev e Stat Nonlin Soft Matter Phys , vol.68 , Issue.2 PART 1 , pp. 021904
    • Brown, K.S.1    Sethna, J.P.2
  • 20
    • 0026621339 scopus 로고
    • Implication of RNA structure on antisense oligonucleotide hybridization kinetics
    • DOI 10.1021/bi00163a013
    • Lima, W F, Monia, B P, Ecker, DJ and Freier, SM (1992). Implication of RNA structure on antisense oligonucleotide hybridization kinetics. Biochemistry 31: 12055-12061. (Pubitemid 23011348)
    • (1992) Biochemistry , vol.31 , Issue.48 , pp. 12055-12061
    • Lima, W.F.1    Monia, B.P.2    Ecker, D.J.3    Freier, S.M.4
  • 21
    • 0342547300 scopus 로고    scopus 로고
    • Theoretical and experimental selection parameters for HBV-Directed antisense RNA are related to increased RNA-RNA annealing
    • Patzel, V, zu Putlitz, J, Wieland, S, Blum, HE and Sczakiel, G (1997). Theoretical and experimental selection parameters for HBV-directed antisense RNA are related to increased RNA-RNA annealing. Biol Chem 378: 539-543. (Pubitemid 27296329)
    • (1997) Biological Chemistry , vol.378 , Issue.6 , pp. 539-543
    • Patzel, V.1    Zu Putlitz, J.2    Wieland, S.3    Blum, H.E.4    Sczakiel, G.5
  • 22
    • 67349125445 scopus 로고    scopus 로고
    • Single-fuorophore monitoring of DNA hybridization for investigating the effect of secondary structure on the nucleation step
    • Jo, JJ, Kim, MJ, Son, J T, Kim, J and Shin, JS (2009). Single-fuorophore monitoring of DNA hybridization for investigating the effect of secondary structure on the nucleation step. Biochem Biophys Res Commun 385: 88-93.
    • (2009) Biochem Biophys Res Commun , vol.385 , pp. 88-93
    • Jo, J.J.1    Kim, M.J.2    Son, J.T.3    Kim, J.4    Shin, J.S.5
  • 24
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie, DT (1977). Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81: 2340-2361.
    • (1977) J Phys Chem , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 25
    • 0024296609 scopus 로고
    • Physicochemical properties of phosphorothioate oligodeoxynucleotides
    • Stein, CA, Subasinghe, C, Shinozuka, K and Cohen, JS (1988). Physicochemical properties of phosphorothioate oligodeoxynucleotides. Nucleic Acids Res 16: 3209-3221.
    • (1988) Nucleic Acids Res , vol.16 , pp. 3209-3221
    • Stein, C.A.1    Subasinghe, C.2    Shinozuka, K.3    Cohen, J.S.4
  • 29
    • 1542303744 scopus 로고    scopus 로고
    • Analysis of Thermal Melting Curves
    • DOI 10.1089/154545703322860825
    • Mergny, JL and Lacroix, L (2003). Analysis of thermal melting curves. Oligonucleotides 13: 515-537. (Pubitemid 38296149)
    • (2003) Oligonucleotides , vol.13 , Issue.6 , pp. 515-537
    • Mergny, J.-L.1    Lacroix, L.2
  • 30
    • 48249102785 scopus 로고    scopus 로고
    • Calorimetry and thermodynamics in drug design
    • Chaires, JB (2008). Calorimetry and thermodynamics in drug design. Annu Rev Biophys 37: 135-151.
    • (2008) Annu Rev Biophys , vol.37 , pp. 135-151
    • Chaires, J.B.1
  • 31
  • 32
    • 2442496406 scopus 로고    scopus 로고
    • Sequence-Dependent Thermodynamic Parameters for Locked Nucleic Acid (LNA)-DNA Duplex Formation
    • DOI 10.1021/bi035976d
    • McTigue, PM, Peterson, RJ and Kahn, JD (2004). Sequence-dependent thermodynamic parameters for locked nucleic acid (LNA)-DNA duplex formation. Biochemistry 43: 5388-5405. (Pubitemid 38620931)
    • (2004) Biochemistry , vol.43 , Issue.18 , pp. 5388-5405
    • McTigue, P.M.1    Peterson, R.J.2    Kahn, J.D.3
  • 33
    • 80055018807 scopus 로고    scopus 로고
    • Stability and mismatch discrimination of locked nucleic acid-DNA duplexes
    • Owczarzy, R, You, Y, Groth, CL and Tataurov, AV (2011). Stability and mismatch discrimination of locked nucleic acid-DNA duplexes. Biochemistry 50: 9352-9367.
    • (2011) Biochemistry , vol.50 , pp. 9352-9367
    • Owczarzy, R.1    You, Y.2    Groth, C.L.3    Tataurov, A.V.4
  • 34
    • 0032539693 scopus 로고    scopus 로고
    • A unifed view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • SantaLucia, J Jr (1998). A unifed view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 95: 1460-1465.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 1460-1465
    • Santalucia, Jr.J.1
  • 38
    • 0035868358 scopus 로고    scopus 로고
    • Stopped-flow kinetics of locked nucleic acid (LNA) - Oligonucleotide duplex formation: Studies of LNA-DNA and DNA-DNA interactions
    • DOI 10.1042/0264-6021:3540481
    • Christensen, U, Jacobsen, N, Rajwanshi, VK, Wengel, J and Koch, T (2001). Stopped-fow kinetics of locked nucleic acid (LNA)-oligonucleotide duplex formation: studies of LNA-DNA and DNA-DNA interactions. Biochem J 354(Pt 3): 481-484. (Pubitemid 32269710)
    • (2001) Biochemical Journal , vol.354 , Issue.3 , pp. 481-484
    • Christensen, U.1    Jacobsen, N.2    Rajwanshi, V.K.3    Wengel, J.4    Koch, T.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.