References and Footnotes
- Soyfer , V. N. and Potaman , V. N. 1996 . Triple-Helical Nucleic Acids 100 – 219 . (a) Springer: New York, (b). R.R. Sinden, DNA Structure and Function, Academic Press: San Diego, pp. 219–258 (1994); (c). N.T. Thuong and C. Hélène, Angew.Chemie, 32, 666–690 (1993); (d). E. Palecek, Crit.Rev.Biochem.Mol.Biol. 26, 151–226 (1991)
- 1991 . Anticancer Drug Des. , 6 : 569 – 584 . (a) C. Hélène; (b). L.J. Maher, B. Wold and P.B. Dervan, Science, 231, 725–730 (1989)
- Beal , P. A. and Dervan , P. B. 1992 . Nucleic Acids Res. , 20 : 2773 – 2779 .
- Thomas , T. and Thomas , T. J. 1993 . Biochemistry , 32 : 14068 – 14074 .
- Sabat , M. and Lippert , B. 1996 . Metal Ions in Biological Systems Edited by: Sigel , A. and Sigel , H. Vol. 33 , 143 – 176 . New York : Marcel Dekker .
- Marzilli , L. G. 1981 . Advances in Inorganic Biochemistry, Vol. 3, Metal Ions in Genetic Information Transfer Edited by: Eichhorn , G. L. and Marzilli , L. G. 47 – 85 . New York : Elsevier-North Holland .
- Malkov , V. A. , Voloshin , O. N. , Soyfer , V. N. and Frank-Kamenetskii , M. D. 1993 . Nucleic Acids Res. , 21 : 585 – 591 .
- Potaman , V. N. and Soyfer , V. N. 1994 . J. Biomol. Struct. Dynamics , 11 : 1035 – 1040 .
- Basch , H. , Krauss , M. and Stevens , W. J. 1985 . J. Am.Chem.Soc. , 107 : 7267 – 7271 . (a) (b). E.H.S. Anwander, M.M. Probstand B.M. Rode,. Biopolymers 29, 757–769 (1990);(c). J. Šponer, J.V. Burda, P. Mejzlik, J. Leszczynski and P. Hobza, J. Biomol. Struct. Dynamics 14, 613–628 (1997)
- The systems optimized by using gradient geometry methods within the Hartree-Fock (HF) approximation included the reverse Hoogsteen G•G•C and A•A•T H-bonded base triplets interacting with a divalent metal cation (Mg2+, Zn2+) surrounded by a complete water shell (five water molecules). Initially, the cations were allowed to interact with the N7 atom of the third-Strand purine. The standard split-valence 6–31G* basis set was applied for the H, C, N, O, and Mg2+atoms, while Zn2+ was described by the Christiansen relativistic pseudopotential11 as in our previous studies (12). The interaction energies were evaluated for the HF-optimized geometries by using the full second-order Moeller-Plesset perturbational method (MP2). The main task of the present study was to estimate the influence of the solvated metal cation on the stability of the purine-purine base pairs. Therefore, the remote pyrimidine base was neglected in the calculation of interaction energies, as this base does not have any significant effect on the purine-purine interaction. The cation with its hydration sphere was considered as one subsystem. Thus, the energy calculations were performed for the purine-purine-hydrated cation “trimer”. The energy of interactions within the trimer was decomposed into the individual pair wise contributions and a three-body term. (9c, 12b,c). The interaction energies were corrected for the basis set superposition error (13) in the trimer-centered basis set. All of the calculations were done by using the Gaussian 94 suite of programs (14)
- Ross , R. B. , Powers , J. M. , Atashroo , T. , Ermler , W. C. , LaJohn , L. A. and Christiansen , P. A. 1990 . J. Chem. Phys. , 93 : 6654 – 6670 . and references therein
- Burda , J. V. , Sponer , J. and Hobza , P. 1996 . J. Phys. Chem. , 100 : 7250 – 7255 . (a) (b). J.V. Burda, J. Sponer, J. Leszczynski and P. Hobza, J. Phys. Chem. B, 101, 9670–9677 (1997); (c). J. Sponer, J.V. Burda, M. Sabat, J. Leszczynski and P. Hobza, J. Phys.Chem. A, 102, 5951- 5957(1998)
- Boys , S. F. and Bernardi , F. 1970 . Mol. Phys. , 19 : 553 – 566 . Basis set superposition error (BSSE) is a computational artifact resulting from the finite size of the basis set of atomic orbitals. It can be corrected by using the counterpoise procedure (see). In order to provide an estimate of the BSSE in our systems we evaluated interaction energies for the GG—;Mg (H2O)5 2+ system without inclusion of the BSSE corrections. The uncorrected value of the interaction energy is −147.4 kcal/mol, ca.18 kcal/mol lower than the BSSE-corrected value in Table I. Thus, in contrast to the popular belief that BSSE is quite negligible for ionic systems, the correction is quite significant and we recommend correcting all data for larger systems by applying the countepoise procedure
- Frisch , M. J. , Trucks , G. W. , Schlegel , H. B. , Gill , P. M.W. , Johnson , B. G. , Robb , M. A. , Cheeseman , J. R. , Keith , T. , Petersson , G. A. , Montgomery , J. A. , Raghavachari , K. , Al-Laham , M. A. , Zakrzewski , W. G. , Ortiz , J. V. , Foresman , J. B. , Peng , C. Y. , Ayala , P. Y. , Chen , W. , Wong , M. W. , Andres , L. J. , Replogle , E. S. , Gomperts , R. , Martin , R. L , Fox , D. J. , Binkley , J. S. , Defrees , D. J. , Baker , J. , Stewart , J. P. , Head-Gordon , M. , Gonzalez , C. and Pople , J. A. 1995 . Pittsburgh , PA : Gaussian Inc. .
- The constraint has been applied for the following reason: during the optimization the structure was essentially planar for approximately 20 cycles, followed by a rotation and pyramidalization of the proximal amino group with a subsequent very fast disruption of the AA base pairving in the A.AT triplet. The unconstrained optimization was then terminated because the resulting structure was not compatible with the H-bonded arrangement of bases in the triplet. (Similar behavior was observed for unconstrained optimizations of the bare metal ion—;AA rH systems).9c
- Šponer , J. and Hobza , P. 1994 . J. Am. Chem. Soc. , 116 : 709 – 714 . (a) (b). B. Luisi, M. Orozco, J. Sponer, F.J. Luque and Z. Shakked. J. Mol.Biol. in press
- This difference is compensated for by the many-body term leading to similar Pu1—;Mhydr contributions. For more details see ref. 12c
- Garmer , D. R. and Gresh , N. 1994 . J. Am.Chem.Soc. , 116 : 3556 – 3567 . (a) (b). N. Gresh and D.R. Darmer, J. Comput. Chem. 17, 1481–1491 (1996)