Expanding the recognition of the minor groove of DNA by incorporation of β-alanine in hairpin polyamides
Abstract
In order to expand the recognition code by hairpin polyamides to include DNA sequences of the type 5′-CWWC-3′ two polyamides, PyPyPyPy-(R)^(H_2^N)γ-ImPyPyIm-β-Dp (1) and PyPyPyPy-(R)^(H_2^N)γ-ImPy-β-Im-β-Dp (2) were synthesized which have in common an Py/Im pair in the terminal position for targeting C·G but differ with respect to internal placement of a β-alanine residue. The equilibrium association constants (K_a) were determined at four DNA sites which differ at a single common position, 5′-TNTACA-3′ (N=T, A, G, C). Quantitative DNase I footprint titration experiments reveal that the eight-ring hairpin PyPyPyPy-(R)^(H_2^N)γ-ImPyPyIm-β-Dp (1) binds the four binding sites with similar affinities, K_a=1.3–1.9×10^(10) M^(−1) indicating that there is no preference for the position N. In contrast, a redesigned polyamide PyPyPyPy-(R)^(H_2^N)γ-ImPy-β-Im-β-Dp (2) that places an internal flexible aliphatic β-alanine to the 5′-side of a key imidazole group bound the match site 5′-TCTACA-3′ with high affinity and good sequence discrimination (K_a(match)=4.9×10^(10) M^(−1) and the single base pair mismatch sites with 5- to 25-fold lower affinity). These results expand the repertoire of sequences targetable by hairpins and emphasize the importance of β-alanine as a key element for minor groove recognition.
Additional Information
© 2001 Elsevier Science Ltd. Received 9 August 2000; accepted 16 October 2000. We are grateful to the National Institutes of Health (GM-27681) for research support, the Knut and Alice Wallenberg Foundation for a post-doctoral fellowship to U.E. and the National Institutes of Health for a research traineeship award (GM 08501) to C.C.C.W. We thank G. M. Hathaway for MALDI-TOF mass spectrometry.Additional details
- Eprint ID
- 66827
- Resolver ID
- CaltechAUTHORS:20160510-082733090
- NIH
- GM-27681
- Knut and Alice Wallenberg Foundation
- NIH Predoctoral Fellowship
- GM-08501
- Created
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2016-05-18Created from EPrint's datestamp field
- Updated
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2021-11-11Created from EPrint's last_modified field