Cycle polyamide motif for recognition of the minor groove of DNA
Abstract
Motifs for covalent linkage of side-by-side complexes of pyrrole−imidazole (Py−Im) polyamides in the DNA minor groove provide for small molecules that specifically recognize predetermined sequences with subnanomolar affinity. Polyamide subunits linked by a turn-specific γ-aminobutyric acid (γ) residue form hairpin polyamide structures. Selective amino-substitution of the prochiral α-position of the γ-turn residue relocates the cationic charge from the hairpin C terminus. Here we report the synthesis of pyrrole resin as well as a solid-phase strategy for the preparation of cycle polyamides. The DNA binding properties of two eight-ring cycle polyamides were analyzed on a DNA restriction fragment containing six base pair match and mismatch binding sites. Quantitative footprint titrations demonstrate that a cycle polyamide of sequence composition cyclo-(γ-ImPyPyPy-(R)^(H2N)γ-ImPyPyPy-) binds a 5'-AGTACT-3' site with an equilibrium association constant K_a = 7.6 × 10^(10) M^(-1), a 3600-fold enhancement relative to the unlinked homodimer (ImPyPyPy-β-Dp)_2·5'-AGTACT-3', and an 8-fold enhancement relative to hairpin analogue ImPyPyPy-(R)^(H2N)γ-ImPyPyPy-C3−OH·5'-AGTACT-3'. Replacement of a single nitrogen atom with a C−H (Im→Py) regulates affinity and specificity of the cycle polyamide by 2 orders of magnitude. The results presented here suggest that addition of a chiral γ-turn combined with placement of a second γ-turn within the hairpin structure provides a cycle polyamide motif with favorable DNA binding properties.
Additional Information
© 1999 American Chemical Society. Received September 8, 1998. Publication Date (Web): January 27, 1999. We are grateful to the National Institutes of Health (GM-27681) for research support, the National Institutes of Health for a research service award to D.M.H., J. Edward Richter for an undergraduate fellowship to J.M.T., and the Howard Hughes Medical Institute for a predoctoral fellowship to E.E.B. We thank G.M. Hathaway for MALDI-TOF mass spectrometry.Attached Files
Supplemental Material - ja983206x_s.pdf
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Additional details
- Eprint ID
- 66855
- DOI
- 10.1021/ja983206x
- Resolver ID
- CaltechAUTHORS:20160510-092504987
- NIH
- GM-27681
- NIH Predoctoral Fellowship
- J. Edward Richter
- Howard Hughes Medical Institute (HHMI)
- Created
-
2016-05-10Created from EPrint's datestamp field
- Updated
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2021-11-11Created from EPrint's last_modified field