Sequence selective recognition in the minor groove of dsDNA by pyrrole, imidazole-substituted bis-benzimidazole conjugates.
A series of pyrrole, imidazole-substituted bis-benzimidazole conjugates, Py-Py-Im-gamma-biBenz, Py-Py-gamma-biBenz, Py-Im-gamma-biBenz, and Im-Py-gamma-biBenz (1-4), were prepared in an attempt to target dsDNA sequences possessing both A/T and G/C bps. The dsDNA interactions and sequence specificity of the conjugates have been characterized via spectrofluorometric titrations and thermal melting studies. All conjugates form 1:1 complexes with dsDNA at subnanomolar concentrations. The Im moiety selectively recognizes a G/C bp embedded in the A/T-rich binding site. This represents the first clear example of sequence selective recognition in a 1:1 motif.(1) The equilibrium association constant (K(1)) for complexation of a specific nine-bp dsDNA site, 5'-gcggTATGAAATTcgacg-3', by conjugate 1 is approximately 2.6 x 10(9) M(-1). Displacement of the G/C position or G/C-->A/T substitution within the nine-bp site decreases the K(1) by approximately 8-fold, whereas two continuous G/C bps decrease the K(1) by approximately 50-fold magnitude. The K(1) values for seven-bp dsDNA, 5'-gcggtaTGAAATTcgacg-3' and 5'-gcggtaCAAAATTcgacg-3', binding sites by conjugates Py-Im-gamma-biBenz (3) and Im-Py-gamma-biBenz (4) are approximately 2.3 x 10(9) and approximately 1.2 x 10(9) M(-1), respectively. However, the conjugates with no Im moiety, Py-Py-gamma-biBenz (2) and Py-Py-Py-gamma-biBenz (5 and 6), are specific for seven- to nine-bp A/T-rich sites and single A/T-->G/C bp substitution within the binding site decreases the K(1) values by 1-2 orders of magnitude.
Reddy
Putta Mallikarjuna
PM
Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106, USA.
Jindra
Peter T
PT
Satz
Alexander L
AL
Bruice
Thomas C
TC
D001562:Benzimidazoles / Q000737:chemistry*; D003432:Cross-Linking Reagents / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D005470:Fluorometry; D006885:Hydroxybutyrates / Q000737:chemistry; D007093:Imidazoles / Q000737:chemistry; D007700:Kinetics; D009690:Nucleic Acid Conformation; D011758:Pyrroles / Q000737:chemistry*; D017186:Titrimetry
D001562:Benzimidazoles; D003432:Cross-Linking Reagents; D006885:Hydroxybutyrates; D007093:Imidazoles; D011758:Pyrroles; C111420:4-hydroxybutyric acid; D004247:DNA