computational study on the structure of dna

computational study on the structure of dna

COMPUTATIONAL STUDY ON THE STRUCTURE OF DNA
M. Swart,a,b M.A. van Bochove,b M. Solàc and F.M. Bickelhauptb
a
b
c
ICREA Researcher at Institut de Química Computacional, Universitat de Girona,
Campus Montilivi, 17071 Girona, Spain
Theoretische Chemie, Vrije Universiteit Amsterdam, De Boelelaan 1083, NL-1081 HV
Amsterdam, The Netherlands
Institut de Química Computacional, Universitat de Girona, Campus Montilivi, 17071
Girona, Spain
We present here our first attempts to use QM, QM/MM and QM/QM methods to study the
structure of DNA oligomers, as well as the influence of the molecular environment on
them. For the hydrogen bonds between DNA base pairs, the latter influence was previously
shown to be of utmost importance for the comparison of experimental and theoretical
results for structures1 and NMR parameters.2 The DNA oligomer set consists among others
of all 10 possible base-pairing combinations (i.e. AA, AC, AG, AT, CA, CC, CG, GA, GC,
TA; see figure for GC dimer) for a DNA dimer3,4, whose structure is for all different
methods fully optimized (using a gradient convergence criterium of 1.0·10-5 a.u.).
G
C
In the QM/MM methods, only the most relevant parts of the system are described by DFT,
while the others are treated at a lower, yet sufficiently accurate, MM level; the QM/QM
method treats the complete system by QM methods, but different QM methods are used for
different regions of the system. All QM, QM/MM and QM/QM calculations have been
performed with the QUILD program,5 using the adapted delocalized coordinates6 to treat
strong and weak coordinates at the same footing, which enhances the convergence of the
optimization.
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2
3
4
5
6
Fonseca Guerra, C.; Bickelhaupt, F. M.; Snijders, J. G.; Baerends, E. J. J. Am. Chem. Soc. 2000,
122, 4117.
Swart, M.; Fonseca Guerra, C.; Bickelhaupt, F. M. J. Am. Chem. Soc. 2004, 126, 16718.
Franklin, R. E.; Gosling, R. G. Nature 1953, 171, 740.
Watson, J. D.; Crick, F. H. C. Nature 1953, 171, 737.
Swart, M.; Bickelhaupt, F. M. QUILD: QUantum-regions Interconnected by Local Descriptions.
Swart, M.; Bickelhaupt, F. M. Int. J. Quant. Chem. 2006, in press.