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. 2001 Dec;81(6):3422–3431. doi: 10.1016/S0006-3495(01)75974-7

Additional hydrogen bonds and base-pair kinetics in the symmetrical AMP-DNA aptamer complex.

S Nonin-Lecomte 1, C H Lin 1, D J Patel 1
PMCID: PMC1301798  PMID: 11721004

Abstract

The solution structure of an adenosine monophosphate (AMP)-DNA aptamer complex has been determined previously [Lin, C. H., and Patel, D. J. (1997) Chem. Biol. 4:817-832]. On a symmetrical aptamer complex containing the same binding loop, but with better resolved spectra, we have identified two additional hydrogen bond-mediated associations in the binding loop. One of these involves a rapidly exchanging G imino proton. The phosphate group of the AMP ligand was identified as the acceptor by comparison with other aptamer complexes. Imino proton exchange measurements also yielded the dissociation constants of the stem and binding loop base pairs. This study shows that nuclear magnetic resonance-based imino proton exchange is a good probe for detection of weak hydrogen-bond associations.

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Selected References

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  1. Dieckmann T., Suzuki E., Nakamura G. K., Feigon J. Solution structure of an ATP-binding RNA aptamer reveals a novel fold. RNA. 1996 Jul;2(7):628–640. [PMC free article] [PubMed] [Google Scholar]
  2. Dingley A. J., Masse J. E., Feigon J., Grzesiek S. Characterization of the hydrogen bond network in guanosine quartets by internucleotide 3hJ(NC)' and 2hJ(NN) scalar couplings. J Biomol NMR. 2000 Apr;16(4):279–289. doi: 10.1023/a:1008307115641. [DOI] [PubMed] [Google Scholar]
  3. Guéron M., Leroy J. L. Studies of base pair kinetics by NMR measurement of proton exchange. Methods Enzymol. 1995;261:383–413. doi: 10.1016/s0076-6879(95)61018-9. [DOI] [PubMed] [Google Scholar]
  4. Hermann T., Patel D. J. Adaptive recognition by nucleic acid aptamers. Science. 2000 Feb 4;287(5454):820–825. doi: 10.1126/science.287.5454.820. [DOI] [PubMed] [Google Scholar]
  5. Huizenga D. E., Szostak J. W. A DNA aptamer that binds adenosine and ATP. Biochemistry. 1995 Jan 17;34(2):656–665. doi: 10.1021/bi00002a033. [DOI] [PubMed] [Google Scholar]
  6. Jiang F., Kumar R. A., Jones R. A., Patel D. J. Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex. Nature. 1996 Jul 11;382(6587):183–186. doi: 10.1038/382183a0. [DOI] [PubMed] [Google Scholar]
  7. Lin C. H., Patel D. J. Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP. Chem Biol. 1997 Nov;4(11):817–832. doi: 10.1016/s1074-5521(97)90115-0. [DOI] [PubMed] [Google Scholar]
  8. Majumdar A., Kettani A., Skripkin E. Observation and measurement of internucleotide 2JNN coupling constants between 15N nuclei with widely separated chemical shifts. J Biomol NMR. 1999 May;14(1):67–70. doi: 10.1023/a:1008335502416. [DOI] [PubMed] [Google Scholar]
  9. Nonin S., Jiang F., Patel D. J. Imino proton exchange and base-pair kinetics in the AMP-RNA aptamer complex. J Mol Biol. 1997 May 2;268(2):359–374. doi: 10.1006/jmbi.1997.0986. [DOI] [PubMed] [Google Scholar]
  10. Nonin S., Leroy J. L., Gueron M. Acid-induced exchange of the imino proton in G.C pairs. Nucleic Acids Res. 1996 Feb 15;24(4):586–595. doi: 10.1093/nar/24.4.586. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Nonin S., Leroy J. L., Guéron M. Terminal base pairs of oligodeoxynucleotides: imino proton exchange and fraying. Biochemistry. 1995 Aug 22;34(33):10652–10659. doi: 10.1021/bi00033a041. [DOI] [PubMed] [Google Scholar]
  12. Nonin S., Phan A. T., Leroy J. L. Solution structure and base pair opening kinetics of the i-motif dimer of d(5mCCTTTACC): a noncanonical structure with possible roles in chromosome stability. Structure. 1997 Sep 15;5(9):1231–1246. doi: 10.1016/s0969-2126(97)00273-6. [DOI] [PubMed] [Google Scholar]
  13. Sassanfar M., Szostak J. W. An RNA motif that binds ATP. Nature. 1993 Aug 5;364(6437):550–553. doi: 10.1038/364550a0. [DOI] [PubMed] [Google Scholar]
  14. Zídek L., Stefl R., Sklenár V. NMR methodology for the study of nucleic acids. Curr Opin Struct Biol. 2001 Jun;11(3):275–281. doi: 10.1016/s0959-440x(00)00218-9. [DOI] [PubMed] [Google Scholar]

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