Aliphatic/Aromatic Amino Acid Pairings for Polyamide Recognition in the Minor Groove of DNA
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- 作者：James M. Turner ; Susanne E. Swalley ; Eldon E. Baird ; and Peter B. Dervan
- 刊名：Journal of the American Chemical Society
- 出版年：1998
- 出版时间：July 1, 1998
- 年：1998
- 卷：120
- 期：25
- 页码：6219 - 6226
- 全文大小：540K
- 年卷期：v.120,no.25(July 1, 1998)
- ISSN：1520-5126
文摘
Selective placement of an aliphatic 
-alanine () residuepaired side-by-side with either a pyrrole(Py) or imidazole (Im) aromatic amino acid is found to compensate forsequence composition effects forrecognition of the minor groove of DNA by hairpin pyrrole-imidazolepolyamides. A series of polyamideswere prepared which contain pyrrole and imidazole aromatic amino acids,as well as 
-aminobutyric acid ()"turn" and -alanine "spring" aliphatic amino acid residues.The binding affinities and specificities of thesepolyamides are regulated by the placement of paired /, Py/,and Im/ residues. Quantitative footprinttitrations demonstrate that replacing two Py/Py pairings in a 12-ringhairpin (6--6) with two Py/ pairingsaffords 10-fold enhanced affinity and similar sequence specificity foran 8-bp target sequence. The 6--6hairpin ImPyImPyPyPy--ImPyPyPyPyPy--Dp, which contains sixconsecutive amino acid pairings, is unableto discriminate a single-base-pair mismatch site5'-TGTTAACA-3' from a 5'-TGTGAACA-3' match site.Thehairpin polyamide Im--ImPyPyPy--ImPyPyPy--Py--Dp binds tothe 8-bp match sequence 5'-TGTGAACA-3' with an equilibrium association constant of Ka= 2.4 × 1010 M-1 and
48-fold specificity versus the 5'-TGTTAACA-3' single-base-pair mismatch site.Modeling indicates that the -alanine residue relaxesligandcurvature, providing for optimal hydrogen bond formation between thefloor of the minor groove and both Imresidues within the Im--Im polyamide subunit. This observationprovided the basis for design of a hairpinpolyamide, Im--ImPy--Im--ImPy--Dp, which incorporatesIm/ pairings to recognize a "problematic"5'-GCGC-3' sequence at subnanomolar concentrations. These resultsidentify Im/ and /Im pairings thatrespectively discriminate G·C and C·G fromA·T/T·A as well as Py/ and /Py pairings thatdiscriminateA·T/T·A from G·C/C·G. Thesealiphatic/aromatic amino acid pairings will facilitate the design ofhairpinpolyamides which recognize both a larger binding site size as well as amore diverse sequence repertoire.
-alanine () residuepaired side-by-side with either a pyrrole(Py) or imidazole (Im) aromatic amino acid is found to compensate forsequence composition effects forrecognition of the minor groove of DNA by hairpin pyrrole-imidazolepolyamides. A series of polyamideswere prepared which contain pyrrole and imidazole aromatic amino acids,as well as -aminobutyric acid ()"turn" and -alanine "spring" aliphatic amino acid residues.The binding affinities and specificities of thesepolyamides are regulated by the placement of paired /, Py/,and Im/ residues. Quantitative footprinttitrations demonstrate that replacing two Py/Py pairings in a 12-ringhairpin (6--6) with two Py/ pairingsaffords 10-fold enhanced affinity and similar sequence specificity foran 8-bp target sequence. The 6--6hairpin ImPyImPyPyPy--ImPyPyPyPyPy--Dp, which contains sixconsecutive amino acid pairings, is unableto discriminate a single-base-pair mismatch site5'-TGTTAACA-3' from a 5'-TGTGAACA-3' match site.Thehairpin polyamide Im--ImPyPyPy--ImPyPyPy--Py--Dp binds tothe 8-bp match sequence 5'-TGTGAACA-3' with an equilibrium association constant of Ka= 2.4 × 1010 M-1 and48-fold specificity versus the 5'-TGTTAACA-3' single-base-pair mismatch site.Modeling indicates that the -alanine residue relaxesligandcurvature, providing for optimal hydrogen bond formation between thefloor of the minor groove and both Imresidues within the Im--Im polyamide subunit. This observationprovided the basis for design of a hairpinpolyamide, Im--ImPy--Im--ImPy--Dp, which incorporatesIm/ pairings to recognize a "problematic"5'-GCGC-3' sequence at subnanomolar concentrations. These resultsidentify Im/ and /Im pairings thatrespectively discriminate G·C and C·G fromA·T/T·A as well as Py/ and /Py pairings thatdiscriminateA·T/T·A from G·C/C·G. Thesealiphatic/aromatic amino acid pairings will facilitate the design ofhairpinpolyamides which recognize both a larger binding site size as well as amore diverse sequence repertoire.