2 research outputs found
Threading Polyintercalators with Extremely Slow Dissociation Rates and Extended DNA Binding Sites
The
development of small molecules that bind DNA sequence specifically
has the potential to modulate gene expression in a general way. One
mode of DNA binding is intercalation, or the insertion of molecules
between DNA base pairs. We have developed a modular polyintercalation
system in which intercalating naphthalene diimide (NDI) units are
connected by flexible linkers that alternate between the minor and
major grooves of DNA when bound. We recently reported a threading
tetraintercalator with a dissociation half-life of 16 days, the longest
reported to date, from its preferred 14 bp binding site. Herein, three
new tetraintercalator derivatives were synthesized with one, two,
and three additional methylene units in the central major groove-binding
linker. These molecules displayed dissociation half-lives of 57, 27,
and 18 days, respectively, from the 14 bp site. The optimal major
groove-binding linker was used in the design of an NDI hexaintercalator
that was analyzed by gel-shift assays, DNase I footprinting, and UV–vis
spectroscopy. The hexaintercalator bound its entire 22 bp binding
site, the longest reported specific binding site for a synthetic,
non-nucleic acid-based DNA binding molecule, but with a significantly
faster dissociation rate compared to the tetraintercalators
Subtle Recognition of 14-Base Pair DNA Sequences via Threading Polyintercalation
Small molecules that bind DNA in a sequence-specific
manner could
act as antibiotic, antiviral, or anticancer agents because of their
potential ability to manipulate gene expression. Our laboratory has
developed threading polyintercalators based on 1,4,5,8-naphthalene
diimide (NDI) units connected in a head-to-tail fashion by flexible
peptide linkers. Previously, a threading tetraintercalator composed
of alternating minor–major–minor groove-binding modules
was shown to bind specifically to a 14 bp DNA sequence with a dissociation
half-life of 16 days [Holman, G. G., et al. (2011) <i>Nat. Chem.
3</i>, 875–881]. Herein are described new NDI-based tetraintercalators
with a different major groove-binding module and a reversed N to C
directionality of one of the minor groove-binding modules. DNase I
footprinting and kinetic analyses revealed that these new tetraintercalators
are able to discriminate, by as much as 30-fold, 14 bp DNA binding
sites that differ by 1 or 2 bp. Relative affinities were found to
correlate strongly with dissociation rates, while overall <i>C</i><sub>2</sub> symmetry in the DNA-binding molecule appeared
to contribute to enhanced association rates