Alteration of A•T base-pair opening kinetics by the ammonium cation in DNA A-tracts

K. Snoussi, Jeal Louis Leroy

Research output: Contribution to journalArticle

Abstract

We have investigated by NMR the effects of NH4+ on the chemical shifts, on the structure, and on the imino proton exchange kinetics of two duplexes containing an A-tract, [d(CGCGAATTCGCG)]2 and [d(GCA4T4GC)]2, and of a B-DNA duplex, [d(CGCGATCGCG)]2. Upon NH4+ addition to [d(CGC-GAATTCGCG)]2, the adenosine H2 protons, the thymidine imino protons, and the guanosine imino proton of the adjacent G•C pair show unambiguous chemical shifts. Similar shifts are observed in the A-tract of [d(GCA4T4GC)]2 and for the A5(H2) proton of the B DNA duplex [d(CGCGATCGCG)]2. The localization of the shifted protons suggests an effect related to NH4+ binding in the minor groove. The cross-peak intensities of the NOESY spectra collected at low and high NH4+ concentrations are comparable, and the COSY spectra do not show any change of the sugar pucker. This indicates a modest effect of ammonium binding on the duplex structures. Nevertheless, the imino proton exchange catalysis by ammonia provides evidence for a substantial effect of NH4+ binding on the A•T base-pair kinetics in the A-tracts. Proton exchange experiments performed at high and low NH4+ concentrations show the occurrence of two native conformations in proportions depending on the NH4+ concentration. The base-pair lifetimes and the open-state lifetimes of each conformation are distinct. Exchange from each conformation proceeds via a single open state. But if, and only if, the NH4+ concentration is kept larger than 1 M, the A•T imino proton exchange times of A-tract sequences exhibit a linear dependence versus the inverse of the NH3 proton acceptor concentration. This had been interpreted as an indication for two distinct base-pair opening modes (Wärmländer, S., Sen, A., and Leijon, M. (2000) Biochemistry 39, 607-615).

Original languageEnglish (US)
Pages (from-to)12467-12474
Number of pages8
JournalBiochemistry®
Volume41
Issue number41
DOIs
StatePublished - Oct 15 2002
Externally publishedYes

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Ammonium Compounds
Base Pairing
Cations
Protons
Kinetics
DNA
Conformations
Chemical shift
B-Form DNA
Biochemistry
Guanosine
Catalysis
Ammonia
Sugars
Adenosine
Thymidine
Ion exchange
Nuclear magnetic resonance

ASJC Scopus subject areas

  • Biochemistry

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Alteration of A•T base-pair opening kinetics by the ammonium cation in DNA A-tracts. / Snoussi, K.; Leroy, Jeal Louis.

In: Biochemistry®, Vol. 41, No. 41, 15.10.2002, p. 12467-12474.

Research output: Contribution to journalArticle

Snoussi, K. ; Leroy, Jeal Louis. / Alteration of A•T base-pair opening kinetics by the ammonium cation in DNA A-tracts. In: Biochemistry®. 2002 ; Vol. 41, No. 41. pp. 12467-12474.
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abstract = "We have investigated by NMR the effects of NH4+ on the chemical shifts, on the structure, and on the imino proton exchange kinetics of two duplexes containing an A-tract, [d(CGCGAATTCGCG)]2 and [d(GCA4T4GC)]2, and of a B-DNA duplex, [d(CGCGATCGCG)]2. Upon NH4+ addition to [d(CGC-GAATTCGCG)]2, the adenosine H2 protons, the thymidine imino protons, and the guanosine imino proton of the adjacent G•C pair show unambiguous chemical shifts. Similar shifts are observed in the A-tract of [d(GCA4T4GC)]2 and for the A5(H2) proton of the B DNA duplex [d(CGCGATCGCG)]2. The localization of the shifted protons suggests an effect related to NH4+ binding in the minor groove. The cross-peak intensities of the NOESY spectra collected at low and high NH4+ concentrations are comparable, and the COSY spectra do not show any change of the sugar pucker. This indicates a modest effect of ammonium binding on the duplex structures. Nevertheless, the imino proton exchange catalysis by ammonia provides evidence for a substantial effect of NH4+ binding on the A•T base-pair kinetics in the A-tracts. Proton exchange experiments performed at high and low NH4+ concentrations show the occurrence of two native conformations in proportions depending on the NH4+ concentration. The base-pair lifetimes and the open-state lifetimes of each conformation are distinct. Exchange from each conformation proceeds via a single open state. But if, and only if, the NH4+ concentration is kept larger than 1 M, the A•T imino proton exchange times of A-tract sequences exhibit a linear dependence versus the inverse of the NH3 proton acceptor concentration. This had been interpreted as an indication for two distinct base-pair opening modes (W{\"a}rml{\"a}nder, S., Sen, A., and Leijon, M. (2000) Biochemistry 39, 607-615).",
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N2 - We have investigated by NMR the effects of NH4+ on the chemical shifts, on the structure, and on the imino proton exchange kinetics of two duplexes containing an A-tract, [d(CGCGAATTCGCG)]2 and [d(GCA4T4GC)]2, and of a B-DNA duplex, [d(CGCGATCGCG)]2. Upon NH4+ addition to [d(CGC-GAATTCGCG)]2, the adenosine H2 protons, the thymidine imino protons, and the guanosine imino proton of the adjacent G•C pair show unambiguous chemical shifts. Similar shifts are observed in the A-tract of [d(GCA4T4GC)]2 and for the A5(H2) proton of the B DNA duplex [d(CGCGATCGCG)]2. The localization of the shifted protons suggests an effect related to NH4+ binding in the minor groove. The cross-peak intensities of the NOESY spectra collected at low and high NH4+ concentrations are comparable, and the COSY spectra do not show any change of the sugar pucker. This indicates a modest effect of ammonium binding on the duplex structures. Nevertheless, the imino proton exchange catalysis by ammonia provides evidence for a substantial effect of NH4+ binding on the A•T base-pair kinetics in the A-tracts. Proton exchange experiments performed at high and low NH4+ concentrations show the occurrence of two native conformations in proportions depending on the NH4+ concentration. The base-pair lifetimes and the open-state lifetimes of each conformation are distinct. Exchange from each conformation proceeds via a single open state. But if, and only if, the NH4+ concentration is kept larger than 1 M, the A•T imino proton exchange times of A-tract sequences exhibit a linear dependence versus the inverse of the NH3 proton acceptor concentration. This had been interpreted as an indication for two distinct base-pair opening modes (Wärmländer, S., Sen, A., and Leijon, M. (2000) Biochemistry 39, 607-615).

AB - We have investigated by NMR the effects of NH4+ on the chemical shifts, on the structure, and on the imino proton exchange kinetics of two duplexes containing an A-tract, [d(CGCGAATTCGCG)]2 and [d(GCA4T4GC)]2, and of a B-DNA duplex, [d(CGCGATCGCG)]2. Upon NH4+ addition to [d(CGC-GAATTCGCG)]2, the adenosine H2 protons, the thymidine imino protons, and the guanosine imino proton of the adjacent G•C pair show unambiguous chemical shifts. Similar shifts are observed in the A-tract of [d(GCA4T4GC)]2 and for the A5(H2) proton of the B DNA duplex [d(CGCGATCGCG)]2. The localization of the shifted protons suggests an effect related to NH4+ binding in the minor groove. The cross-peak intensities of the NOESY spectra collected at low and high NH4+ concentrations are comparable, and the COSY spectra do not show any change of the sugar pucker. This indicates a modest effect of ammonium binding on the duplex structures. Nevertheless, the imino proton exchange catalysis by ammonia provides evidence for a substantial effect of NH4+ binding on the A•T base-pair kinetics in the A-tracts. Proton exchange experiments performed at high and low NH4+ concentrations show the occurrence of two native conformations in proportions depending on the NH4+ concentration. The base-pair lifetimes and the open-state lifetimes of each conformation are distinct. Exchange from each conformation proceeds via a single open state. But if, and only if, the NH4+ concentration is kept larger than 1 M, the A•T imino proton exchange times of A-tract sequences exhibit a linear dependence versus the inverse of the NH3 proton acceptor concentration. This had been interpreted as an indication for two distinct base-pair opening modes (Wärmländer, S., Sen, A., and Leijon, M. (2000) Biochemistry 39, 607-615).

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