NDI and DAN DNA: Nucleic Acid-Directed
Assembly of
NDI and DAN
- Publication date
- Publisher
Abstract
Two novel DNA base
surrogate phosphoramidites <b>1</b> and <b>2</b>, based
upon relatively electron-rich 1,5-dialkoxynaphthalene
(DAN) and relatively electron-deficient 1,4,5,8-naphthalenetetracarboxylic
diimide (NDI), respectively, were designed, synthesized, and incorporated
into DNA oligonucleotide strands. The DAN and NDI artificial DNA bases
were inserted within a three-base-pair region within the interior
of a 12-mer oligonucleotide duplex in various sequential arrangements
and investigated with CD spectroscopy and UV melting curve analysis.
The CD spectra of the modified duplexes indicated B-form DNA topology.
Melting curve analyses revealed trends in DNA duplex stability that
correlate with the known association of DAN and NDI moieties in aqueous
solution as well as the known favorable interactions between NDI and
natural DNA base pairs. This demonstrates that DNA duplex stability
and specificity can be driven by the electrostatic complementarity
between DAN and NDI. In the most favorable case, an NDI–DAN–NDI
arrangement in the middle of the DNA duplex was found to be approximately
as stabilizing as three A–T base pairs