MOLECULAR
DYNAMICS SIMULATIONS OF DNA TRIPLEXES CONTAINING MODIFIED HOOGSTEEN STRANDS -
POTENTIAL CANDIDATES FOR ANTIGENE THERAPY
IVAN BARVÍK jr.
Institute of Physics, Charles
University, Ke Karlovu 5, 12116 Prague, Czech Republic
The concept of
“antisense” and “antigene” nucleic
acids represents a
perspective approach in chemotherapy, promising to
inhibit selectively unwanted gene expression by creation of a helical complex with target mRNA or DNA
(carrying “sense” genetic
information) [1]. The
oligonucleotides with natural chemical composition have been, however, found as
unsuitable for in vivo applications because of their insufficient resistance
against nucleases. That is why numerous novel-type nucleotide analogs are
designed, synthesized and tested [1-6].
A number of phosphonate-based
mononucleotide analogs containing an O-(phosphono)methyl group instead of
the natural phosphonomonoester one were found
to be potent antivirals: this indicated enzyme stability of the
phosphonate -O-P-CH2-O- bond [7]. Several
types of isopolar modified oligothymidylates and oligoadenylates (15 mers) with
the phosphonate -O-P-CH2-O- internucleotide linkage were prepared. The modified
oligonucleotides were subjected to the study of their hybridization properties,
resistance against nucleases, and the ability to elicit RNase H activity [2]. Impact of the internucleoside linkage
modification by inserting a methylene group on the ability of the modified
oligonucleotide to hybridize with a natural DNA and RNA strand was studied by
fully solvated molecular dynamics (MD) simulations [3-6].
Triplex forming
oligodeoxynucleotides have attracted a great deal of attention because of their
potential use in gene therapy. In inter molecular triplexes, third strand of
ODN binds to the major groove of the DNA. However, in general, the binding of a
third-strand ODN to a target DNA duplex is thermodynamically weaker than duplex
formation itself. Thus much effort has been made to increase the affinity of
the third strand for its target. ODN analogues carrying various aminoalkyl
linkers have been synthesized, some of which have been shown to increase the
thermal stability of triplexes [8]. The
thermal stabilization can be explained by an electrostatic interaction between
the positively charged aminoalkyl residue of the nucleosides and a pro-R oxygen
of a negatively charged phosphate at the second strand of the target DNA.
The present work deals with
the phosphonate analog of the natural phosphodiester internucleoside linkage in
conjunction with various aminoalkyl-linkers. Several triple helical structures
consisting of a natural Watson-Crick duplex and a modified Hoogsteen thymidine
strand were used as model systems. Impact of the sugar phosphate backbone
modifications on the ability of the modified oligonucleotides to hybridize with
a nautral duplex, was studied by molecular dynamics simulations. The nucleic
acids were surrounded by a periodic box of ~10000 TIP3P water atoms. Fully
solvated trajectories were computed using the AMBER 5.0 software package. The
implemented force field doesn’t contain force constants needed to describe the
modified parts of the phosphonate analogs
[9]. The completion was made on the
base of ab initio calculations [3].
In acknowledgments, this work
was supported by the Grant of the Ministry of Education, Youth and Sports of
the Czech Republic (project No. VS 97113) and the Grant Agency of the Czech
Republic (project No. 203/01/1166 and No. 202/02/D114). Results have been
partially obtained using computer facilities of the MetaCentrum of the Czech
Universities in Brno.
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