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Tethered imidazole mediated duplex stabilization and its potential for aptamer stabilization

(2018) NUCLEIC ACIDS RESEARCH. 46(22). p.11671-11686
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Abstract
Previous investigations of the impact of an imidazole-tethered thymidine in synthetic DNA duplexes, monitored using UV and NMR spectroscopy, revealed a base context dependent increase in thermal stability of these duplexes and a striking correlation with the imidazolium pK(a). Unrestrained molecular dynamics (MD) simulations demonstrated the existence of a hydrogen bond between the imidazolium and theHoogsteen side of a nearby guanosine which, together with electrostatic interactions, form the basis of the so-called pK(a)-motif responsible for these duplex-stabilizing and pK(a)-modulating properties. Here, the robustness and utility of this pK(a)-motif was explored by introducing multiple imidazoletethered thymidines at different positions on the same dsDNA duplex. For all constructs, sequence based expectations as to pK(a)-motif formation were supported by MD simulations and experimentally validated using NOESY. Based on the analysis of the pK(a) values and melting temperatures, guidelines are formulated to assist in the rational design of oligonucleotides modified with imidazoliumtethered thymidines for increased thermal stability that should be generally applicable, as demonstrated through a triply modified construct. In addition, a proof-of-principle study demonstrating enhanced stability of the L-argininamide binding aptamer modified with an imidazole-tethered thymidine in the presence and absence of ligand, demonstrates its potential for the design of more stable aptamers.
Keywords
MOLECULAR-DYNAMICS SIMULATIONS, CATIONIC 3-AMINOPROPYL CHAIN, IN-VITRO SELECTION, DNA APTAMERS, NMR-SPECTROSCOPY, CLEAVING DNA, RNA, BINDING, DNAZYME, ACID

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Citation

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MLA
Verdonck, Lars et al. “Tethered Imidazole Mediated Duplex Stabilization and Its Potential for Aptamer Stabilization.” NUCLEIC ACIDS RESEARCH 46.22 (2018): 11671–11686. Print.
APA
Verdonck, Lars, Buyst, D., de Vries, A.-M., Gheerardijn, V., Madder, A., & Martins, J. (2018). Tethered imidazole mediated duplex stabilization and its potential for aptamer stabilization. NUCLEIC ACIDS RESEARCH, 46(22), 11671–11686.
Chicago author-date
Verdonck, Lars, Dieter Buyst, Anne-Mare de Vries, Vicky Gheerardijn, Annemieke Madder, and José Martins. 2018. “Tethered Imidazole Mediated Duplex Stabilization and Its Potential for Aptamer Stabilization.” Nucleic Acids Research 46 (22): 11671–11686.
Chicago author-date (all authors)
Verdonck, Lars, Dieter Buyst, Anne-Mare de Vries, Vicky Gheerardijn, Annemieke Madder, and José Martins. 2018. “Tethered Imidazole Mediated Duplex Stabilization and Its Potential for Aptamer Stabilization.” Nucleic Acids Research 46 (22): 11671–11686.
Vancouver
1.
Verdonck L, Buyst D, de Vries A-M, Gheerardijn V, Madder A, Martins J. Tethered imidazole mediated duplex stabilization and its potential for aptamer stabilization. NUCLEIC ACIDS RESEARCH. 2018;46(22):11671–86.
IEEE
[1]
L. Verdonck, D. Buyst, A.-M. de Vries, V. Gheerardijn, A. Madder, and J. Martins, “Tethered imidazole mediated duplex stabilization and its potential for aptamer stabilization,” NUCLEIC ACIDS RESEARCH, vol. 46, no. 22, pp. 11671–11686, 2018.
@article{8580819,
  abstract     = {Previous investigations of the impact of an imidazole-tethered thymidine in synthetic DNA duplexes, monitored using UV and NMR spectroscopy, revealed a base context dependent increase in thermal stability of these duplexes and a striking correlation with the imidazolium pK(a). Unrestrained molecular dynamics (MD) simulations demonstrated the existence of a hydrogen bond between the imidazolium and theHoogsteen side of a nearby guanosine which, together with electrostatic interactions, form the basis of the so-called pK(a)-motif responsible for these duplex-stabilizing and pK(a)-modulating properties. Here, the robustness and utility of this pK(a)-motif was explored by introducing multiple imidazoletethered thymidines at different positions on the same dsDNA duplex. For all constructs, sequence based expectations as to pK(a)-motif formation were supported by MD simulations and experimentally validated using NOESY. Based on the analysis of the pK(a) values and melting temperatures, guidelines are formulated to assist in the rational design of oligonucleotides modified with imidazoliumtethered thymidines for increased thermal stability that should be generally applicable, as demonstrated through a triply modified construct. In addition, a proof-of-principle study demonstrating enhanced stability of the L-argininamide binding aptamer modified with an imidazole-tethered thymidine in the presence and absence of ligand, demonstrates its potential for the design of more stable aptamers.},
  author       = {Verdonck, Lars and Buyst, Dieter and de Vries, Anne-Mare and Gheerardijn, Vicky and Madder, Annemieke and Martins, José},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keywords     = {MOLECULAR-DYNAMICS SIMULATIONS,CATIONIC 3-AMINOPROPYL CHAIN,IN-VITRO SELECTION,DNA APTAMERS,NMR-SPECTROSCOPY,CLEAVING DNA,RNA,BINDING,DNAZYME,ACID},
  language     = {eng},
  number       = {22},
  pages        = {11671--11686},
  title        = {Tethered imidazole mediated duplex stabilization and its potential for aptamer stabilization},
  url          = {http://dx.doi.org/10.1093/nar/gky1062},
  volume       = {46},
  year         = {2018},
}

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