Quantitative Modeling of DNA-Mediated Electron Transfer between Metallointercalators

Abstract

The distance dependence of electron transfer (ET) rates between donors and acceptors in a DNA environment has been an area of intense research and heated discussion, especially with regard to the recent report of ultrafast ET over a separation of >40 Å. This paper is focused on quantitative modeling of the photodynamics and gel electrophoresis/photocleavage experiments of the untethered DNA/metallointercalator system. Simulations are compared to previously published experimental results in order to quantitatively examine the possible involvement of long-range ET and donor/acceptor clustering in the DNA-mediated ET between metallointercalators. Comparison of the simulation results with a broad range of experimental data strongly indicates that a fairly typical distance dependence for ET (β ≈ 1 Å -1 ) coupled to donor/acceptor clustering is able to account for all features in the data and for related photocleavage studies.

Solution Photoreactivity of Phenanthrenequinone Diimine Complexes of Rhodium and Correlations with DNA Photocleavage and Photooxidation

“…8,12 The experiments were performed in water, and the pH was adjusted by addition of 0.18 M HCl or 0.10 M NaOH unless otherwise noted. For experiments in acetonitrile, the protonated form of the Rh(III) complexes was precipitated from a pH 5.0 aqueous solution with ammonium hexafluorophosphate to obtain the PF 6 -salts of the complexes.…”

“…[1][2][3][4][5][6][7] Irradiation at higher energies (λ irr ) 313 nm) results in DNA photocleavage at the complex's binding site, a property which has facilitated studies of site-specific DNA recognition. 3 Recently, phi complexes of rhodium have also been utilized to initiate oxidative reactions on DNA.…”

“…2 Additional interest in intercalating phi complexes of Rh(III) arises from their role as electron acceptors in charge transfer mediated by the DNA base-pair stack. [5][6][7] Irradiation of Rh(phen) 2 (phi) 3+ and Rh(phi) 2 (bpy) 3+ (phen ) 1,10-phenanthroline, bpy ) 2,2′-bipyridine) in the ultraviolet region (λ irr ) 313 nm) in the absence of DNA leads to irreversible loss of phi ligand in basic media possibly via a ligand-to-metal charge transfer (LMCT) excited state. 8 It has been shown that irradiation of Rh(phen) 2 (phi) 3+ and Rh(phi) 2 -(bpy) 3+ intercalated in DNA leads to direct DNA strand scission with products consistent with 3′-hydrogen abstraction from the deoxyribose backbone of DNA.…”

Charge transfer and transport in DNA

“…The interpretation of the early experiments of Barton, Turro, and their colleagues (9-13) on charge separation between donor and acceptor complexes attached to DNA was fraught with some difficulties because of the possibility of aggregation effects (24). The recent data of Dandliker, Holmlin, and Barton (17)(18)(19) on hole migration between the electronically excited metal intercalator Rh(phi) 2 DMB ϩ3 and the thymine dimer, both of which are specifically incorporated in a 16-bp DNA duplex, provide evidence for long-range hole separation (over a distance scale of r ϭ 19-26 Å) with the yield being independent of donor-acceptor distance (R).…”

Role of quantum chemical calculations in molecular biophysics with a historical perspective

“…Thus, for the δ-function chain this procedure gave an energy gap of 2.057 eV, and for the harmonic oscillator case the energy gap is 2.056 eV. However, when considering the possibility of charge transport in DNA there are many contradictions within standard electron-transfer (ET) theory [127,128,129].…”