Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides
| Autor: | Moses Lee, Karen L. Buchmueller, Peter B. Uthe, Andrew M. Staples, Kari K. Cox, Cameron M. Howard, Suzanna L. Bailey, Binh Nguyen, W. David Wilson, Kimberly A. O. Pacheco, James A. Henry, Sarah M. Horick |
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| Rok vydání: | 2005 |
| Předmět: |
Circular dichroism
Stereochemistry Base pair Circular Dichroism Imidazoles DNA Biology Surface Plasmon Resonance Antiparallel (biochemistry) Nucleic Acid Denaturation Article chemistry.chemical_compound Nylons Molecular recognition chemistry Biochemistry Pairing Genetics Imidazole Pyrroles Binding site Base Pairing |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 |
| Popis: | Polyamides containing an N-terminal formamido (f) group bind to the minor groove of DNA as staggered, antiparallel dimers in a sequence-specific manner. The formamido group increases the affinity and binding site size, and it promotes the molecules to stack in a staggered fashion thereby pairing itself with either a pyrrole (Py) or an imidazole (Im). There has not been a systematic study on the DNA recognition properties of the f/Py and f/Im terminal pairings. These pairings were analyzed here in the context of f-ImPyPy, f-ImPyIm, f-PyPyPy and f-PyPyIm, which contain the central pairing modes, -ImPy- and -PyPy-. The specificity of these triamides towards symmetrical recognition sites allowed for the f/Py and f/Im terminal pairings to be directly compared by SPR, CD and DeltaT (M) experiments. The f/Py pairing, when placed next to the -ImPy- or -PyPy- central pairings, prefers A/T and T/A base pairs to G/C base pairs, suggesting that f/Py has similar DNA recognition specificity to Py/Py. With -ImPy- central pairings, f/Im prefers C/G base pairs (>10 times) to the other Watson-Crick base pairs; therefore, f/Im behaves like the Py/Im pair. However, the f/Im pairing is not selective for the C/G base pair when placed next to the -PyPy- central pairings. |
| Databáze: | OpenAIRE |
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