9.
Impact of the internucleotide linkage modification by inserting a methylene group to the P-O bond (—O—PO
2
—
—O— chain changed for —O—PO
2
—
—CH
2—O—), on the modified oligonucleotide binding ability to the natural DNA strand was studied by molecular dynamics simulation. Complex of (dT)
11 with a deoxyadenosine undecamer containing alternating modified and natural internucleotide linkage was studied as a model system. The Amber force field was completed by a set of new parameters needed to model the modified part of the nucleotide. The simulations confirmed existence of a double-helical complex the melting point of which is considerably higher than 300 K. While the thymidine (unmodified) strand possesses a B-type secondary structure, the conformation of the adenosine (modified) strand is not stable at 300 K. The
-ggt conformation of the modified linkages is highly preferred, temporary jumps to the
-g-gt and
ggt conformations were, however, observed.
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