Abstract
Acid-induced catalysis of imino proton exchange in G.C pairs of DNA duplexes is surprisingly fast, being nearly as fast as for the isolated nucleoside, despite base-pair dissociation constants in the range of 10(-5) at neutral or basic pH. It is also observed in terminal G.C pairs of duplexes and in base pairs of drug-DNA complexes. We have measured imino proton exchange in deoxyguanosine and in the duplex (ATATAGATCTATAT) as a function of pH. We show that acid-induced exchange can be assigned to proton transfer from N7-protonated guanosine to cytidine in the open state of the pair. This is faster than transfer from neutral guanosine (the process of intrinsic catalysis previously characterized at neutral ph) due to the lower imino proton pK of the protonated form, 7.2 instead of 9.4. Other interpretations are excluded by a study of exchange catalysis by formiate and cytidine as exchange catalysts. The cross-over pH between the regimes of pH-independent and acid-induced exchange rates is more basic in the case of base pairs than in the mononucleoside, suggestive of an increase by one to two decades in the dissociation constant of the base pair upon N7 protonation of G. Acid-induced catalysis is much weaker in A.T base pairs, as expected in view of the low pK for protonation of thymidine.
Full Text
The Full Text of this article is available as a PDF (168.7 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Banville D. L., Marzilli L. G., Wilson W. D. NMR investigation of DNA conformational changes on base protonation: use of Cu2+ and pyrazole as probes. Biochemistry. 1986 Nov 18;25(23):7393–7401. doi: 10.1021/bi00371a022. [DOI] [PubMed] [Google Scholar]
- Guéron M., Kochoyan M., Leroy J. L. A single mode of DNA base-pair opening drives imino proton exchange. Nature. 1987 Jul 2;328(6125):89–92. doi: 10.1038/328089a0. [DOI] [PubMed] [Google Scholar]
- Leroy J. L., Gao X. L., Guéron M., Patel D. J. Proton exchange and internal motions in two chromomycin dimer-DNA oligomer complexes. Biochemistry. 1991 Jun 11;30(23):5653–5661. doi: 10.1021/bi00237a003. [DOI] [PubMed] [Google Scholar]
- Leroy J. L., Gao X. L., Misra V., Guéron M., Patel D. J. Proton exchange in DNA-luzopeptin and DNA-echinomycin bisintercalation complexes: rates and processes of base-pair opening. Biochemistry. 1992 Feb 11;31(5):1407–1415. doi: 10.1021/bi00120a017. [DOI] [PubMed] [Google Scholar]
- Leroy J. L., Gehring K., Kettani A., Guéron M. Acid multimers of oligodeoxycytidine strands: stoichiometry, base-pair characterization, and proton exchange properties. Biochemistry. 1993 Jun 15;32(23):6019–6031. doi: 10.1021/bi00074a013. [DOI] [PubMed] [Google Scholar]
- McConnell B., Politowski D. Buffer catalysis of amino proton exchange in compounds of adenosine, cytidine and their endocyclic N-methylated derivatives. Biophys Chem. 1984 Aug;20(1-2):135–148. doi: 10.1016/0301-4622(84)80013-7. [DOI] [PubMed] [Google Scholar]
- 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]