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Structural Effects on ss‐ and dsDNA Recognition by a β‐Hairpin Peptide
Author(s) -
Stewart Amanda L.,
Waters Marcey L.
Publication year - 2009
Publication title -
chembiochem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.05
H-Index - 126
eISSN - 1439-7633
pISSN - 1439-4227
DOI - 10.1002/cbic.200800524
Subject(s) - chemistry , dna , duplex (building) , chirality (physics) , biophysics , dissociation constant , dimer , folding (dsp implementation) , peptide , binding site , binding selectivity , plasma protein binding , stereochemistry , biochemistry , receptor , biology , chiral symmetry breaking , physics , organic chemistry , engineering , quantum mechanics , nambu–jona lasinio model , electrical engineering , quark
Form defines function : The effects of β‐hairpin structure on the binding affinity and selectivity for ssDNA versus dsDNA were investigated; this provided insights into the factors that contribute to the selective recognition of both ss‐ and dsDNA and suggested new approaches for designing biomimetic receptors. Binding studies showed that 1) folding is crucial for binding to both ss‐ and dsDNA, and 2) chirality affects binding for duplex but not for ssDNA.The interactions involved in the binding of a designed β‐hairpin dimer to single‐stranded and duplex DNA have been explored. Previously the peptide dimer had been found to bind ssDNA with a dissociation constant of 3 μ μ through a combination of aromatic and electrostatic interactions, whereas binding to duplex DNA was primarily driven by electrostatic interactions. In this report, the effects of folding and chirality were studied to determine the factors that contribute to affinity and selectivity for ssDNA versus dsDNA. Binding studies showed that 1) folding is crucial for binding to both ss‐ and dsDNA, and 2) chirality affects binding for duplex DNA but not for ssDNA. Taken together, these studies reveal different modes of binding for ss‐ and duplex DNA, with different driving forces, but in each case peptide structure contributes significantly to binding.