Harmonic dynamics of a DNA hexamer in the absence and presence of the intercalator ethidium

Ethidium bromide interactions with DNA: an exploration of a classic DNA-ligand complex with unbiased molecular dynamics simulations

Visualization of double stranded DNA in gels with the binding of the fluorescent dye ethidium bromide has been a basic experimental technique in any molecular biology laboratory for >40 years. The interaction between ethidium and double stranded DNA has been observed to be an intercalation between base pairs with strong experimental evidence. This presents a unique opportunity for computational chemistry and biomolecular simulation techniques to benchmark and assess their models in order to see if the theory can reproduce experiments and ultimately provide new insights. We present molecular dynamics simulations of the interaction of ethidium with two different double stranded DNA models. The first model system is the classic sequence d(CGCGAATTCGCG)₂ also known as the Drew–Dickerson dodecamer. We found that the ethidium ligand binds mainly stacked on, or intercalated between, the terminal base pairs of the DNA with little to no interaction with the inner base pairs. As the intercalation at the terminal CpG steps is relatively rapid, the resultant DNA unwinding, rigidification, and increased stability of the internal base pair steps inhibits further intercalation. In order to reduce these interactions and to provide a larger groove space, a second 18-mer DNA duplex system with the sequence d(GCATGAACGAACGAACGC) was tested. We computed molecular dynamics simulations for 20 independent replicas with this sequence, each with ∼27 μs of sampling time. Results show several spontaneous intercalation and base-pair eversion events that are consistent with experimental observations. The present work suggests that extended MD simulations with modern DNA force fields and optimized simulation codes are allowing the ability to reproduce unbiased intercalation events that we were not able to previously reach due to limits in computing power and the lack of extensively tested force fields and analysis tools.

Local dynamics of DNA probed with optical absorption spectroscopy of bound ethidium bromide

We have studied the local dynamics of calf thymus double-helical DNA by means of an "optical labeling" technique. The study has been performed by measuring the visible absorption band of the cationic dye ethidium bromide, both free in solution and bound to DNA, in the temperature interval 360-30 K and in two different solvent conditions. The temperature dependence of the absorption line shape has been analyzed within the framework of the vibronic coupling theory, to extract information on the dynamic properties of the system; comparison of the thermal behavior of the absorption band of free and DNA-bound ethidium bromide gave information on the local dynamics of the double helix in the proximity of the chromophore. For the dye free in solution, large spectral heterogeneity and coupling to a "bath" of low-frequency (soft) modes is observed; moreover, anharmonic motions become evident at suitably high temperatures. The average frequency of the soft modes and the amplitude of anharmonic motions depend upon solvent composition. For the DNA-bound dye, at low temperatures, heterogeneity is decreased, the average frequency of the soft modes is increased, and anharmonic motions are hindered. However, a new dynamic regime characterized by a large increase in anharmonic motions is observed at temperatures higher than approximately 280 K. The DNA double helix therefore appears to provide, at low temperatures, a rather rigid environment for the bound chromophore, in which conformational heterogeneity is reduced and low-frequency motions (both harmonic vibrations and anharmonic contributions) are hindered. The system becomes anharmonic at approximately 180 K; however, above approximately 280 K, anharmonicity starts to increase much more rapidly than for the dye free in solution; this can be attributed to the onset of wobbling of the dye in its intercalation site, which is likely connected with the onset of (functionally relevant) DNA motions, involving local opening/unwinding of the double helix. As shown by parallel measurements of the melting curves, these motions precede the melting of the double helix and depend upon solvent composition much more than does the melting itself.

Ethidium bromide binding to unstructured and structured 2' GMP

For disordered 2' GMP and 5' GMP the ethidium cation (Etd) was found to form 1:1 and 2:1 Eth:nucleotide complex. For alkali metal solution self-structured 2'GMP and 5'GMP Etd was found to form 1:1 and 2:1 Etd: order nucleotide complex. The best computer fit was obtained for a structured nucleotide stoichiometry of Na4(2'GMP)8. Binding constants for the Etd:disordered 2'GMP complexes were determined to be (1.6 +/- 0.1) x 10(4)M(-1) and 6.3 +/- 0.5 M(-1) at O degrees C and (1.1 +/- 0.2) x 10(4) M(-1) and 18 +/- 11M(-1) for 5'GMP at 5 degrees C for the 1:1 and 1:2 complex, respectively. For the 1:1 and 1:2 2'GMP:Etd species the enthalpies were determined to be -19.8 +/- 1.0 kcal/mole and 0.1 +/- 0.3 kcal/mole, respectively, and the entropies were -53.3 +/- 6.6 eu and 3.9 +/- 1.6 eu, respectively. Binding constants for the Etd: structured 2'GMP complex, assuming a complex with stoichoimetry (Na+)4 (2'GMP)8 for the structured unit, were determined to be (1.9 +/- 0.1) x 10(4)M(-1) and 5.8 +/- 0.6) x 10(2)M(-1), respectively at 0 degrees C.

Binding site for ethidium cation in the major groove of B-form DNA

Molecular modeling of the system composed of ethidium cation initially intercalated through the major and minor grooves of the B-DNA form of 5'GCATGC3' into the central AT pairs, with the phenyl group oriented either toward or away from the helical axis, led upon energy minimization to intercalation complexes only when the phenyl group was initially oriented away from the helical axis. For the other two cases, energy minimization led to extrusion of the ethidium from the helix to form unanticipated outside-bound complexes stabilized by specific hydrogen bonds. It is suggested that outside-bound major groove complexes involving the GXXXG sequence may play important roles in the reaction mechanism of ethidium intercalation and in its action as a drug.

The contribution of cross-links to protein stability: a normal mode analysis of the configurational entropy of the native state

The vibrational entropy of native BPTI, with three disulfide bonds, was determined by use of normal mode calculations and compared with that of folded variants having either one less disulfide bond or lacking a peptide bond at the trypsin-reactive site. Favorable contributions to the free energy of 2.5-5.1 kcal/mol at 300 K were calculated for the reduction of disulfide bonds in the folded state, whereas no favorable contribution was found for the hydrolysis of the peptide bond cleaved by trypsin. This is on the order of the effect of disulfides in the unfolded state. The implications of these results for the stabilization of a folded protein by the introduction of cross-links are discussed.

Cellular harmonic information transfer through a tissue tensegrity-matrix system

Cells and intracellular elements are capable of vibrating in a dynamic manner with complex harmonics, the frequency of which can now be measured and analyzed in a quantitative manner by Fourier analysis. Cellular events such as changes in shape, membrane ruffling, motility, and signal transduction occur within spatial and temporal harmonics that have potential regulatory importance. These vibrations can be altered by growth factors and the process of carcinogenesis. It is important to understand the mechanism by which this vibrational information is transferred directly throughout the cell. From these observations we propose that vibrational information is transferred through a tissue tensegrity-matrix which acts as a coupled harmonic oscillator operating as a signal transucing system from the cell periphery to the nucleus and ultimately to the DNA. The vibrational interactions occur through a tissue matrix system consisting of the nuclear matrix, the cytoskeleton, and the extracellular matrix that is poised to couple the biologic oscillations of the cell from the peripheral membrane to the DNA through a tensegrity-matrix structure. Tensegrity has been defined as a structural system composed of discontinuous compression elements connected by continuous tension cables, which interact in a dynamic fashion. A tensegrity tissue matrix system allows for specific transfer of information through the cell by direct transmission of vibrational chemomechanical energy through harmonic wave motion.

Langevin modes of macromolecules: applications to crambin and DNA hexamers

Langevin modes describe the behavior of atoms moving on a harmonic potential surface subject to viscous damping described by a classical Langevin equation. We present applications to the protein crambin and to the DNA duplex d(CpGpCpGpCpG)2 and its complex with ethidium. Our friction matrix is weighted according to surface area exposed to solvent, and results are reported for various values of the solvent viscosity and models for hydrodynamic interactions. Even for relatively small solvent friction (eta = 0.3 cp) a substantial number of modes are overdamped, and time correlation functions decay smoothly without the oscillations characteristic of gas-phase calculations. Perturbation theory starting from the gas-phase modes is accurate for many low-frequency modes (which are overdamped in the presence of solvent), but fails badly for higher modes. For correlation functions of interest to fluorescence depolarization or nmr relaxation, the plateau values are insensitive to solvent viscosity, but the relaxation times are not. The advantages and limitations of this analysis of macromolecular motions are discussed.