Premium
Molecular recognition between oligopeptides and nucleic acids. Sequence specific binding of (4S)‐(+)‐ and (4R)‐(−)‐dihydrokikumycin B to DNA deduced form 1 H NMR, footprinting studies and thermodynamic data
Author(s) -
Lee Moses,
Shea Regan G.,
Hartley John A.,
Lown J. Willliam,
Kissinger Koren,
Dabrowiak James C.,
Vesnaver Gorazd,
Breslauer Kenneth J.,
Pon Richard T.
Publication year - 1989
Publication title -
journal of molecular recognition
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.401
H-Index - 79
eISSN - 1099-1352
pISSN - 0952-3499
DOI - 10.1002/jmr.300020103
Subject(s) - footprinting , chemistry , enantiomer , stereochemistry , circular dichroism , dna , nuclear magnetic resonance spectroscopy , ligand (biochemistry) , crystallography , dna footprinting , biochemistry , dna binding protein , receptor , base sequence , transcription factor , gene
The sequence specific binding of the antibiotic (4S)‐(+)‐dihydrokikumycin B and its (4R)‐(−)enantiomer, [(S)‐I and (R)‐I, respectively] to DNA were characterized by DNase I and MPE footprinting, calorimetry, UV, spectroscopy, circular dichroism, and 1 H NMR studies. Footprinting analyses showed that both enantiomers [(S)‐I and (R)‐I] bind to AT‐rich regions of DNA. 1 H NMR studies (ligand induced chemical shift changes and NOE differences) of the dihydrokikumycins with d‐[CGCAATTGCG] 2 show unambiguously that the N to C termini of the ligands are bound to 5′‐A 5 T 6 T 7 ‐3′ reading from left to right. From quantitative 1D‐NOE studies, the AH2(5)‐ligand H7 distance of complex A [(S)‐I plus decamer (which is bound more strongely)] and complex B[(R)‐I and decamer] are estimated to be 3.8 ± 0.3 Å and 4.9 ± 0.4 Å, respectively. This difference in binding properties is reflected in the thermodynamic profiles of the two enantiomeric ligands determined by a combination of spectroscopic and calorimetric techniques. The binding freee energies (Δ G °) of (S)‐I and (R)‐I to poly d(AT)·poly d(AT) at 25°C are −31.8 and −29.3 kJ mol −1 , respectively while the corresponding binding enthalpies (Δ H °) are −11.3 and −0.8 kJ mol −1 . These data permit the construction of models for the binding of the enantiomeric dihydrokikumycins to DNA and account for the more efficient binding of the natural (S) isomer to DNA.