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Albany 2001

category image Biomolecular
Stereodynamics
SUNY at Albany
June 19-23, 2001

Sequence and Salt Effects on Methylene Blue Binding to DNA with Alternating GC and AT Base Sequences

Methylene blue (MB), an efficient singlet oxygen generating photoactive dye, binds to DNA and induces photosensitized reactions which can be used for sequence-specific cleavage of the DNA backbone. Intercalation and groove binding are possible binding modes of the dye depending on base sequences and environmental conditions. In this modeling study using the JUMNA (Junction Minimization of Nucleic Acids) algorithm [1], we have analyzed and compared the stability of complexes formed by MB and DNA decamers with alternating GC and AT base sequences. The energetic analysis of the model structures includes an electrostatic continuum treatment of solvent and salt effects [2-3]. For each sequence, a search of the conformational space resulted in six model structures which were selected by the criterion of lowest total energies. Symmetric and asymmetric intercalation structures, both at the 5'-YpR-3' and 5'-RpY-3' steps, have been located and compared with the lowest energy structures obtained for minor and major groove binding. At low salt concentration, symmetric intercalation for alternating GC, at either the 5'-CpG-3' or the 5'-GpC-3' site [4], and minor groove binding for alternating AT are predicted as the predominant binding modes. Binding of the positively charged MB reduces the total charge of the complexes compared to the free DNA by one unit. Thus, the stabilizing effect of salt is higher for free DNA than for the complexes, resulting in decreasing binding energies with increasing ionic strength [5]. Due to the higher stabilizing effect of salt for groove binding compared to intercalation, the stability is shifted towards minor groove binding with increasing salt concentration. In the case of GC sequence, the higher stabilization of groove binding complexes leads to comparable binding energies for symmetric intercalation and minor groove binding at high salt concentration. The qualitative behavior of the model structures seems to be in good agreement with the data obtained experimentally [6]. The predicted structures may therefore be useful for a more detailed interpretation of experimental results. Moreover, they could serve as starting points of molecular dynamics simulations and for studying base sequence effects in view of photochemical applications of MB.

References and Footnotes
  1. Lavery, R.; Zakrzewska, K.; Sklenar, H. Comp. Phys. Com. 1995, 91, 135-158
  2. Gilson, M.K.; Sharp, K.A.; Honig, B.H. J. Comp. Chem. 1988, 9, 327-335
  3. Davis, M.; Madura, J.D.; Luty, B.; McCammon, J.A. Comp. Phys. Com. 1991, 62, 187-198
  4. Rohs, R.; Sklenar, H.; Lavery, R.; Röder, B. J. Am. Chem. Soc. 2000, 122, 2860-2866
  5. Rohs, R.; Sklenar, H. Indian J. Biochem. Biophys. 2001, 38, 1-6
  6. Tuite, E.M.; Nordén, B. J. Am. Chem. Soc. 1994, 116, 7548-7556

Remo Rohs and Heinz Sklenar

Theoretical Biophysics Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, D-13092 Berlin, Germany
Phone: +49 30 9406 3713; Fax: +49 30 9406 2548; rohs@mdc-berlin.de