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Published July 30, 1997 | public
Journal Article

Discrimination of 5'-GGGG-3',5'-GCGC-3', and 5'-GGCC-3' sequences in the minor groove of DNA by eight-ring hairpin polyamides

Abstract

Eight-ring hairpin polyamides which differ only by the linear arrangement of pyrrole (Py) and imidazole (Im) amino acids were designed for recognition of six base pair DNA sequences containing four contiguous G,C base pairs. The respective DNA binding properties of three polyamides, ImImPyPy-γ-ImImPyPy-β-Dp, ImPyImPy-γ-ImPyImPy-β-Dp, and ImImImIm-γ-PyPyPyPy-β-Dp, were analyzed by footprinting and affinity cleavage on a DNA fragment containing the respective match sites 5'-TGGCCA-3', 5'-TGCGCA-3', and 5'-TGGGGA-3'. Quantitative footprint titrations demonstrate that ImImPyPy-γ-ImImPyPy-β-Dp binds the designed match site 5'-TGGCCA-3' with an equilibrium association constant of Ka = 1 × 1010 M-1 and >250-fold specificity versus the mismatch sequences, 5'-TGCGCA-3' and 5'-TGGGGA-3'. The polyamides ImPyImPy-γ-ImPyImPy-β-Dp and ImImImIm-γ-PyPyPyPy-β-Dp recognize their respective 5'-TGCGCA-3' and 5'-TGGGGA-3' match sites with reduced affinity relative to ImImPyPy-γ-ImImPyPy-β-Dp, but again with high specificity with regard to mismatch sites. These results expand the DNA sequence repertoire targeted by pyrrole-imidazole polyamides and identify sequence composition effects which will guide further second-generation polyamide design for DNA recognition.

Additional Information

© 1997 American Chemical Society. Received April 14, 1997. Publication Date (Web): July 30, 1997. Abstract published in Advance ACS Abstracts, July 15, 1997. We are grateful to the National Institutes of Health (GM-2768) for research support, the National Institutes of Health for a research traineeship award (GM-08501) to S.E.S., and the Howard Hughes Medical Institute for a predoctoral fellowship to E.E.B. We thank G. M. Hathaway for MALDI-TOF mass spectrometry.

Additional details

Created:
August 19, 2023
Modified:
October 18, 2023