Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides.
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.
Buchmueller
Karen L
KL
Department of Chemistry, Furman University, Greenville, SC 29613, USA.
Staples
Andrew M
AM
Uthe
Peter B
PB
Howard
Cameron M
CM
Pacheco
Kimberly A O
KA
Cox
Kari K
KK
Henry
James A
JA
Bailey
Suzanna L
SL
Horick
Sarah M
SM
Nguyen
Binh
B
Wilson
W David
WD
Lee
Moses
M
D020029:Base Pairing; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D007093:Imidazoles / Q000737:chemistry*; D009691:Nucleic Acid Denaturation; D009757:Nylons / Q000737:chemistry*; D011758:Pyrroles / Q000737:chemistry*; D020349:Surface Plasmon Resonance
D007093:Imidazoles; D009757:Nylons; D011758:Pyrroles; D004247:DNA