Nucleic Acids Research, Vol 26, Issue 3 831-838, Copyright © 1998 by Oxford University Press
S Kumar, MW Reed, HB Gamper Jr, VV Gorn, EA Lukhtanov, M Foti, J West, RB Meyer Jr and BI Schweitzer
The tripeptide 1,2-dihydro-(3 H )-pyrrolo[3,2- e ]indole-7-carboxylate
(CDPI3) binds to the minor groove of DNA with high affinity. When this
minor groove binder is conjugated to the 5'-end of short oligonucleotides
the conjugates form unusually stable hybrids with complementary DNA and
thus may have useful diagnostic and/or therapeutic applications. In order
to gain an understanding of the structural interactions between the
CDPI3minor groove binding moiety and the DNA, we have determined and
compared the solution structure of a duplex consisting of
oligodeoxyribonucleotide 5'-TGATTATCTG-3' conjugated at the 5'-end to CDPI3
and its complementary strand to an unmodified control duplex of the same
sequence using nuclear magnetic resonance techniques. Thermal denaturation
studies indicated that the hybrid of this conjugate with its complementary
strand had a melting temperature that was 30 degrees C higher compared with
the unmodified control duplex. Following restrained molecular dynamics and
relaxation matrix refinement, the solution structure of the
CDPI3-conjugated DNA duplex demonstrated that the overall shape of the
duplex was that of a straight B-type helix and that the CDPI3moiety was
bound snugly in the minor groove, where it was stabilized by extensive van
der Waal's interactions.
ARTICLES
Solution structure of a highly stable DNA duplex conjugated to a minor groove binder
Walt Disney Memorial Cancer Institute at Florida Hospital, 12722 Research Parkway, Orlando, FL 32826, USA.
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