Recognition by nonaromatic and stereochemical subunit-containing polyamides of the four Watson-Crick base pairs in the DNA minor groove.

In order to develop an optimal subunit as a T-recognition element in hairpin polyamides, 15 novel chirality-modified polyamides containing (R)-a,beta-diaminopropionic acid (R beta?a-NH?2), (S)-a,beta-diaminopropionic acid (S beta?a-NH?2), (1R,3S)-3-aminocyclopentanecarboxylic acid (RSCp), (1S,3R)-3-amino-cyclopentanecarboxylic acid (RSCp), (1R,3R)-3-aminocyclopentanecarboxylic acid (RRCp) and (1S,3S)-3-amino-cyclopentanecarboxylic acid (SSCp) residues were synthesized. Their binding characteristics to DNA sequences 5'-TGCNCAT-3'/3'-ACGN'GTA-5' (N.N'=A.T, T.A, G.C and C.G) were systemically studied by surface plasmon resonance (SPR) and molecular simulation (MSim) techniques. SPR showed that polyamide 4, AcIm-S beta?a-NH?2-ImPy-?-ImPy-beta-Py-beta Dp (beta/S beta?a-NH?2 pair), bound to a DNA sequence containing a core binding site of 5'-TGCACAT-3' with a dissociation equilibrium constant (KD) of 4.5 x 10(-8)?m. This was a tenfold improvement in specificity over 5'-TGCTCAT-3' (KD=4.5 x 10(-7)?M). MSim studies supported the SPR results. More importantly, for the first time, we found that chiral 3-aminocyclopentanecarboxylic acids in polyamides can be employed as base readers with only a small decrease in binding affinity to DNA. In particular, SPR showed that polyamide 9 (RRCp/beta pair) had a 15-fold binding preference for 5'-TGCTCAT-3' over 5'-TGCACAT-3'. A large difference in standard free energy change for A.T over T.A was determined (??Go=5.9 kJ?mol-1), as was a twofold decrease in interaction energy by MSim. Moreover, a 1:1 stoichiometry (9 to 5'-TGCTCAT-3'/3'-ACGAGTA-5') was shown by MSim to be optimal for the chiral five-membered cycle to fit the minor groove. Collectively, the study suggests that the (S)-a-amino-beta-aminopropionic acid and (1R,3R)-3-aminocyclopentanecarboxylic acid can serve as a T-recognition element, and the stereochemistry and the nature of these subunits significantly influence binding properties in these recognition events. Subunit (1R,3R)-3-aminocyclopentanecarboxylic acid broadens our scope to design novel polyamides.