Abstract
Here, we study the metastable decay of 5′-d(TTGCTT) in the presence of 0–6 alkaline metal ions (Li+, Na+, K+, Rb+) and 0−3 alkaline earth metal ions (Mg2+ and Ca2 +), which replace the corresponding number of protons in the oligonucleotide. We find that all ions studied here stabilize the oligonucleotide with respect to simple 3′-C–O backbone cleavage, but at the same time these metal ions promote a central oligonucleotide deletion accompanied by a concomitant recombination of the terminal d(TT) groups. We find that the quenching of the 3′-C–O backbone cleavage is not ion specific, since it is due to the removal of the phosphate protons upon replacement with the respective metal ions. The central nucleotide deletion competes with the 3′-C–O backbone cleavage channels and is thus promoted through the replacement of the exchangeable protons against metal ions. However, with increasing positive charge density of the metal ions the yield of the central nucleotide deletion further increases. We attribute this effect to the necessity of sufficient proximity of the terminal d(TT) group to allow for their recombination on this reaction path. Hence, the formation of a reactive conformer is mediated by the metal ions.
Similar content being viewed by others
References
J. Müller, Metallomics 2, 318 (2010)
M.A. Young, B. Jayaram, D.L. Beveridge, J. Am. Chem. Soc. 119, 59 (1997)
X.Q. Shui, L. McFail-Isom, G.G. Hu, L.D. Williams, Biochemistry 37, 8341 (1998)
F.C. Marincola, V.P. Denisov, B. Halle, J. Am. Chem. Soc. 126, 6739 (2004)
N.B. Leontis, P. Ghosh, P.B. Moore, Biochemistry 25, 7386 (1986)
C.C. Correll, B. Freeborn, P.B. Moore, T.A. Steitz, Cell 91, 705 (1997)
M.J. Serra, J.D. Baird, T. Dale, B.L. Fey, K. Retatagos, E. Westhof, RNA 8, 307 (2002)
S. Basu, R.P. Rambo, J. Strauss-Soukup, J.H. Cate, A.R. Ferre-D’Amare, S.A. Strobel, J.A. Doudna, Nat. Struct. Biol. 5, 986 (1998)
D.M.J. Lilley, R.M. Clegg, Ann. Rev. Biophys. Biomol. Struct. 22, 299 (1993)
B. Lippert, D. Gupta, Dalton Trans. 24, 4619 (2009)
P. Schultze, N.V. Hud, F.W. Smith, J. Feigon, Nucleic Acids Res. 27, 3018 (1999)
P.W.K. Rothemund, Nature 440, 297 (2006)
A. Keller, I. Bald, A. Rotaru, E. Cauet, K.V. Gothelf, F. Besenbacher, ACS Nano 6, 4392 (2012)
J. Gidden, E.S. Baker, A. Ferzoco, M.T. Bowers, Int. J. Mass Spectrom. 240, 183 (2005)
V. Gabelica, E. De Pauw, J. Mass Spectrom. 36, 397 (2001)
P.D. Schnier, J.S. Klassen, E.E. Strittmatter, E.R. Williams, J. Am. Chem. Soc. 120, 9605 (1998)
F. Rosu, V. Gabelica, C. Houssier, P. Colson, E. De Pauw, Rapid Commun. Mass Spectrom. 16, 1729 (2002)
D.R. Goodlett, D.G. Camp, C.C. Hardin, M. Corregan, R.D. Smith, Biol. Mass Spectrom. 22, 181 (1993)
H.D. Flosadóttir, B. Omarsson, I. Bald, O. Ingólfsson, Eur. Phys. J. D 66, 13 (2012)
I. Bald, H.D. Flosadóttir, B. Omarsson, O. Ingólfsson, Int. J. Mass Spectrom. 313, 15 (2012)
H.D. Flosadóttir, K. Gislason, S.T. Sigurdsson, O. Ingólfsson, J. Am. Soc. Mass Spectrom. 23, 690 (2012)
H.D. Flosadóttir, M. Stano, O. Ingólfsson, J. Am. Soc. Mass Spectrom. 20, 689 (2009)
M. Stano, H.D. Flosadóttir, O. Ingólfsson, Rapid Commun. Mass Spectrom. 20, 3498 (2006)
R.D. Shannon, Acta Crystallogr. A 32, 751 (1976)
S.A. McLuckey, G.J. Vanberkel, G.L. Glish, J. Am. Soc. Mass Spectrom. 3, 60 (1992)
E.P.L. Hunter, S.G. Lias, J. Phys. Chem. Ref. Data 27, 413 (1998)
Author information
Authors and Affiliations
Corresponding authors
Rights and permissions
About this article
Cite this article
Piekarczyk, A., Bald, I., Flosadóttir, H. et al. Influence of metal ion complexation on the metastable fragmentation of DNA hexamers. Eur. Phys. J. D 68, 146 (2014). https://doi.org/10.1140/epjd/e2014-40838-7
Received:
Revised:
Published:
DOI: https://doi.org/10.1140/epjd/e2014-40838-7