DNA Sequence Recognition in the Minor Groove by Crosslinked Polyamides: The Effect of N-Terminal Head Group and Linker Length on Binding Affinity and Specificity

Development of sequence-reading polyamides or "lexitropsins" with comparable DNA-binding affinities to cellular proteins raises the possibility of artificially regulated gene expression. Covalent linkage of polyamide ligands, with either a hairpin motif or crosslinking methylene bridge, ha...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2002-01, Vol.99 (1), p.72-77
Main Authors: O'Hare, C. Caroline, Mack, Darcy, Tandon, Manju, Sharma, Sanjay K., Lown, J. William, Kopka, Mary L., Dickerson, Richard E., Hartley, John A.
Format: Article
Language:English
Subjects:
Amides
Binding Sites
Biological Sciences
Biology
Chemistry
Cross-Linking Reagents - pharmacology
Deoxyribonuclease I - chemistry
Deoxyribonuclease I - metabolism
Deoxyribonucleic acid
Dimers
DNA
DNA - chemistry
DNA-Binding Proteins - chemistry
Gels
Genetics
Hydrocarbons
Hydrogen
Hydrogen Bonding
Imidazoles
Kinetics
lexitropsin
Ligands
Methane - analogs & derivatives
Methane - chemistry
Models, Chemical
Models, Statistical
Nucleic Acid Conformation
Nucleotide sequences
Nylons - chemistry
Oligomers
polyamides
Protein Binding
Proteins
Repetitive Sequences, Nucleic Acid
Studies
Thiazoles
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Summary:Development of sequence-reading polyamides or "lexitropsins" with comparable DNA-binding affinities to cellular proteins raises the possibility of artificially regulated gene expression. Covalent linkage of polyamide ligands, with either a hairpin motif or crosslinking methylene bridge, has greatly improved binding affinity by ensuring their side-by-side register. Whereas hairpin polyamides have been investigated extensively, the optimized structure of crosslinked polyamides remains to be determined. This study examines a series of thiazole-imidazole-pyrrole (TIP) monomers and crosslinked dimers to evaluate the effects on selectivity and binding affinity of different N-terminal head groups attached to the leading thiazole ring and differing methylene linker lengths. Quantitative footprinting of a DNA sequence, containing potential match and mismatch sites for both maximum overlap and one-residue stagger binding modes, allowed measurement of binding constants at each putative site. Within an N-terminal amino TIP series, C7 and C8-linked compounds bound most strongly to these sites, whereas maximum binding affinity was observed for a C6 linker with a formyl head group. A C5 linker gave weak binding with either head group. A hydrogen or acetyl head group abrogated binding. Binding was confirmed by gel shift analyses. The highest specificity for the maximum overlap site over the one-residue stagger was observed with TIP-C7-amino. Selectivity of the leading thiazole was modulated by the head group, with N-terminal formyl TIP exhibiting up to 3-fold specificity for AGT over TGT, suggesting that N-formyl-thiazole may provide sequence discrimination of adenine over thymine. Moreover, the leading head group and methylene linker length significantly influences the binding characteristics of crosslinked polyamides.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.012588799