The fluorescence anisotropy decay due to energy transfers occuring in the ethidium bromide-DNA complex. Determination of the deformation angle of the DNA helix

It has been shown in a preceding work that the fluorescence anisotropy decay of ethidium bromide-DNA complex is accelerated by energy migration between dyes bound to the same DNA molecule. In the present work, this result is confirmed. A quantitative analysis has been performed in the following way. The spectroscopic term of the transfer rate constant has been accurately reevaluated by quantum yield and spectral measurements. One assumes that the dye intercalates between two adjacent base pairs and that its distribution is random along the DNA molecule. One introduces the deformation angle δ of the DNA helix induced by the ethidium bromide intercalation. For several values of δ, the energy migration contribution to the anisotropy decay is computed by a Monte Carlo method. In multiplying these computed functions by the measured brownian anisotropy, one obtains the anisotropy decay curve. Comparison with the experimental data leads to the conclusion that the ethidium bromide molecule unwinds the DNA helix by an angle δ = ?16°. This result is m agreement with the work of other authors. We think that the method used here may provide accurate information on the spatial distribution of an array of chromophores bound to a rigid structure.     

Diffusion-enhanced lanthanide energy-transfer study of DNA-bound cobalt(III) bleomycins: comparisons of accessibility and electrostatic potential with DNA complexes of ethidium and acridine orange

Energy transfer in the "rapid-diffusion" limit reflects the equilibrium properties of a donor-acceptor system. Rates of energy transfer from freely diffusing terbium chelates to DNA-binding chromophores change dramatically when DNA is added; energy transfer from an electrically neutral chelate is reduced because the energy acceptor becomes partially buried in DNA, while energy transfer from a positive chelate is increased because of electrostatic attraction. The rate constants for energy transfer to DNA-bound chromophores from a positively charged terbium chelate, relative to those from a neutral chelate, were used to estimate the following values for the electrostatic potential near the surface of each DNA-bound acceptor at 298 K in the presence of 1.0 mM added salt (in units of -e/kT): acridine orange, 4.54 +/- 0.11; ethidium, 4.66 +/- 0.07; green Co(III) bleomycin A2, 4.06 +/- 0.11; orange Co(III) bleomycin A2, 3.11 +/- 0.10. Smaller numbers indicate less negative potentials; these can be due to a combination of (1) positive charge on the chromophore, (2) location of the chromophore [particularly Co(III) bleomycin] away from the DNA phosphates, and/or (3) separation of DNA phosphate negative charges by an intercalator. The magnitudes of the individual rate constants indicate that all the DNA-bound chromophores can be directly encountered by the terbium probes. Energy-transfer rate constants from a neutral terbium chelate to DNA-bound and free acceptors can provide a measure of the accessibility of the terbium probe to each bound chromophore. The ratios of these rate constants were as follows: acridine orange, 0.17 +/- 0.01; ethidium, 0.27 +/- 0.02; green form of Co(III) bleomycin A2, 0.48 +/- 0.06; orange form of Co(III) bleomycin A2, 0.71 +/- 0.06. These results are consistent with the probable differences in binding mechanisms for the intercalating chromophores (ethidium and acridine orange) as compared to the Co(III) bleomycins (in which the relevant chromophores are nonintercalating metal centers). In addition, all the results imply that the green Co(III) bleomycin chromophore binds closer to DNA than the orange; this provides a first step toward understanding the structural basis for the different biological properties of these metallobleomycins. Control experiments and theoretical considerations necessary to establish the validity of the results are also presented.     

DNA Bifunctional intercalators. 2. Fluorescence properties and DNA binding interaction of an ethidium homodimer and an acridine ethidium heterodimer

An ethidium homodimer and acridine ethidium heterodimer have been synthesized (Gaugain, B., Barbet, J., Oberlin, R., Roques, B. P., & Le Pecq, J. B. (1978) Biochemistry 17 (preceding paper in this issue)). The binding of these molecules to DNA has been studied. We show that these dimers intercalate only one of their chromophores in DNA. At high salt concentration (Na+ greater than 1 M) only a single type of DNA-binding site exists. Binding affinity constants can then be measured directly using the Mc Ghee & Von Hippel treatment (Mc Ghee, J. D., & Von Hippel, P. H. (1974) J. Mol. Biol. 86, 469). In these conditions the dimers cover four base pairs when bound to DNA. Binding affinities have been deduced from competition experiments in 0.2 M Na+ and are in agreement with the extrapolated values determined from direct DNA-binding measurements at high ionic strength. As expected, the intrinsic binding constant of these dimers is considerably larger than the affinity of the monomer (ethidium dimer K = 2 X 10(8) M-1; ethidium bromide K = 1.5 X 10(5) M-1 in 0.2 M Na+). The fluorescence properties of these molecules have also been studied. The efficiency of the energy transfer from the acridine to the phenanthridinium chromophore, in the acridine ethidium heterodimer when bound to DNA, depends on the square of the AT base pair content. The large increase of fluorescence on binding to DNA combined with a high affinity constant for nucleic acid fluorescent probes. In particular, such molecules can be used in competition experiments to determine the DNA binding constant of ligands of high binding affinity such as bifunctional intercalators.     

DNA-ethidium reaction kinetics: demonstration of direct ligand transfer between DNA binding sites.

Study of the relaxation kinetics of the interaction of ethidium and DNA reveals a novel and potentially important general binding mechanism, namely direct transfer of the ligand between DNA binding sites without requiring dissociation to free ligand. The measurable relaxation spectrum shows three relaxation times, indicating that three bound dye species are present at equilibrium; about 80% of the dye is in the major intercalated form. For each relaxation the reciprocal relaxation time varies linearly with concentration up to very high DNA concentrations. The failure of the longer relaxation times to plateau at high concentration can be accounted for by including a bimolecular pathway for conversion from one complex form to another. This we envisage as direct transfer of an ethidium molecule, bound to one DNA molecule, to an empty binding site on another DNA molecule. Additional evidence for this direct transfer mechanism was obtained from an experiment showing that DNA (which binds ethidium relatively rapidly) accelerates the binding of ethidium to poly(rA) · poly(rU), presumably by first forming a DNA-ethidium complex and then transferring the ethidium to RNA. The bimolecular rate constant for transfer is found to be about four times larger than the constant for intercalating the free dye. The transfer pathway thus provides a highly efficient means for the ligand to equilibrate over its DNA binding sites, especially at high polymer concentration. The potential importance of direct transfer for DNA-binding regulatory proteins is emphasized.     

Interaction of chloroquine with linear and supercoiled DNAs. Effect on the torsional dynamics, rigidity, and twist energy parameter

The magnitude and uniformity of the torsion elastic constant (alpha) of linear pBR322 DNA and supercoiled pBR322 DNAs with high-twist (sigma = -0.083) and normal-twist (sigma = -0.48) are measured in 0.1 M NaCl as a function of added chloroquine/base-pair ratio (chl/bp) by studying the fluorescence polarization anisotrophy (FPA) of intercalated ethidium dye. The time-resolved FPA is measured by using a picosecond dye laser for excitation and time-correlated single-photon counting detection. A general theory is developed for the binding of ligands that unwind superhelical DNAs, and the simultaneous binding of two different intercalators is treated in detail. The equilibrium constant (K) for binding chloroquine to linear pBR322 DNA and the number (r) of bound chloroquines per base pair are determined from the relative amplitude ratio of the slow (normally intercalated) and fast (free) components in the decay of the (probe) ethidium fluorescence intensity as a function of chl/bp. For chloroquine binding to supercoiled pBR322 DNAs, the intrinsic binding constant is assumed to be the same as for the linear DNA, but the twist energy parameter ET (N times the free energy to change the linking number from 0 to 1 in units of kBT) is regarded as adjustable. Using the best-fit ET, the binding ratios r are calculated for each chl/bp ratio. Twist energy parameters are also determined for ethidium binding to these supercoiled DNAs by competitive dialysis. For chloroquine binding, we obtain ET = 360 and 460 respectively for the normal-twist and high-twist supercoiled DNAs. For ethidium binding the corresponding values are ET = 280 +/- 70 and 347 +/- 50. Like other dye-binding values, these are substantially lower than those obtained by ligation methods. In the absence of chloroquine, the torsion constants of all three DNAs are virtually identical, alpha = (5.0 +/- 0.4) x 10(-12) dyn.cm. For linear pBR322 DNA, the magnitude and uniformity of alpha remain unaltered by intercalated chloroquine up to r = 0.19. This finding argues that the FPA is not significantly relaxed by diffusion of any kinks or solitons. If alpha d denotes the torsion constant between a dye and a base pair and alpha 0 that between two base pairs, then our data imply that alpha d/alpha 0 lies in the range 0.65-1.64, with a most probable value of 1.0.(ABSTRACT TRUNCATED AT 400 WORDS)     

Fluorescence energy transfer as a probe for nucleic acid structures and sequences.

The primary or secondary structure of single-stranded nucleic acids has been investigated with fluorescent oligonucleotides, i.e., oligonucleotides covalently linked to a fluorescent dye. Five different chromophores were used: 2-methoxy-6-chloro-9-amino-acridine, coumarin 500, fluorescein, rhodamine and ethidium. The chemical synthesis of derivatized oligonucleotides is described. Hybridization of two fluorescent oligonucleotides to adjacent nucleic acid sequences led to fluorescence excitation energy transfer between the donor and the acceptor dyes. This phenomenon was used to probe primary and secondary structures of DNA fragments and the orientation of oligodeoxynucleotides synthesized with the alpha-anomers of nucleoside units. Fluorescence energy transfer can be used to reveal the formation of hairpin structures and the translocation of genes between two chromosomes.     

Effect of ethidium on the torsion constants of linear and supercoiled DNAs.

The torsion elastic constants (alpha) of linear pBR322 (4363 bp) and pUC8 (2717 bp) DNAs and supercoiled pBR322 and pJMSII (4375 bp) DNAs are measured in 0.1 M NaCl as a function of added ethidium/base-pair (EB/BP) ratio by studying the fluorescence polarization anisotropy (FPA) of the intercalated ethidium. The time-resolved FPA is measured by using a picosecond dye laser for excitation and time-correlated single photon counting detection. Previously developed theory for the emission anisotropy is generalized to incorporate rotations of the transition dipole due to excitation transfer. The excitation transfers are simulated by a Monte Carlo procedure (Genest et al., Biophys. Chem. 1 (1974) 266-278) and the consequent rotations of the transition dipole are superposed on the Brownian rotations. After accounting for excitation transfer, the torsion constants of the linear DNAs are found to be essentially independent of intercalated ethidium up to a binding ratio r = 0.10 dye/bp. Dynamic light scattering measurements on linear pUC8 DNA confirm that the torsion constant is independent of binding ratio up to r = 0.20 dye/bp. If alpha d denotes the torsion constant between ethidium and a base-pair, and alpha 0 that between two base-pairs, then our data imply that alpha d/alpha 0 lies in the range 0.65 to 1.64 with a most probable value of 1.0. The torsion constants of supercoiled DNAs decrease substantially with increasing binding ratio even after accounting for excitation transfer. At the binding ratio r* = 0.064, where the superhelix density vanishes and superhelical strain is completely relaxed, the torsion constant of the supercoiled pBR322 DNA/dye complex lies below that of the corresponding linear DNA/dye complex by about 30%. This contradicts the conventional view according to which linear, nicked circular, and supercoiled DNA/dye complexes with r = r* should coexist with the same concentration of free dye, display the same distribution of bound dye, and exhibit identical secondary structures, twisting and bending rigidities, and FPA dynamics. These and other observations imply the existence of metastable secondary structure in freshly relaxed supercoiled DNAs. A tentative explanation is presented for these and other unexpected observations on supercoiled DNAs.     

蓝藻(A.variabilis)藻胆体核结构与功能的研究II.变藻蓝蛋白六聚体内能量传递过程的物理机制

以变藻蓝蛋白的晶体结构和光谱性质为基础,利用密度矩阵理论对变藻蓝蛋白六聚体内的激发能传递物理机制进行分析,并利用时间分辨荧光光谱技术对其能量传递途径进行实时探测。结果表明：在变藻蓝蛋白六聚体内,色素对（毗邻单体上的色素αｉ８４βｊ８４,其中ｊ＝ｉ±１,和β＊ＬＣＭ４２）内的能量传递服从激子偶极－偶极相互作用机制;而色素对之间的能量传递机制则为Ｆｒｓｔｅｒ偶极－偶极相互作用机制,并且其能量传递途径分为两类：（１）．两个变藻蓝蛋白三聚体之间色素对的能量传递,其时间常数大约为１５ｐｓ左右;（２）．同一变藻蓝蛋白三聚体内色素对间的能量传递,在ＡＰＩＩ三聚体内,其能量传递时间大约为４５ｐｓ左右,而在ＡＰＩ三聚体内,其能量传递时间常数为４５ｐｓ和６５ｐｓ。     

蓝藻(A.variabilis)藻胆体核结构与功能的研究II.变藻蓝蛋白六聚体内能量传递过程的物理机制

以变藻蓝蛋白的晶体结构和光谱性质为基础,利用密度矩阵理论对变藻蓝蛋白六聚体内的激发能传递物理机制进行分析,并利用时间分辨荧光光谱技术对其能量传递途径进行实时探测。结果表明：在变藻蓝蛋白六聚体内,色素对（毗邻单体上的色素αｉ８４βｊ８４,其中ｊ＝ｉ±１,和β＊ＬＣＭ４２）内的能量传递服从激子偶极－偶极相互作用机制;而色素对之间的能量传递机制则为Ｆｒｓｔｅｒ偶极－偶极相互作用机制,并且其能量传递途径分为两类：（１）．两个变藻蓝蛋白三聚体之间色素对的能量传递,其时间常数大约为１５ｐｓ左右;（２）．同一变藻蓝蛋白三聚体内色素对间的能量传递,在ＡＰＩＩ三聚体内,其能量传递时间大约为４５ｐｓ左右,而在ＡＰＩ三聚体内,其能量传递时间常数为４５ｐｓ和６５ｐｓ。     

Theoretical Study of Ethidium Intercalation in Triple-Stranded DNA and at Triplex-Duplex Junctions

Abstract

The contribution of different factors in the interaction of ethidium intercalated into various sequences of a triple helix, or in the region of the junction between the double- and triple-stranded DNA has been studied by energy minimization. It is found that in the total energy of the ethidium - triple helix complexes, a particular electrostatic contribution emerges due to the presence of protonated cytosines in the triple helix. This parameter is determinant in the sequence-specificity of ethidium binding to the triple helix. The preferred intercalation sites of ethidium in the triple helix are proposed. The interaction of ethidium at the triplex-duplex junction, and its effects are also discussed. This study is aimed at searching for new drugs specific for the triple helix, or for the triplex-duplex junctions.     

Theoretical study of ethidium intercalation in triple-stranded DNA and at triplex-duplex junctions.

The contribution of different factors in the interaction of ethidium intercalated into various sequences of a triple helix, or in the region of the junction between the double- and triple-stranded DNA has been studied by energy minimization. It is found that in the total energy of the ethidium- triple helix complexes, a particular electrostatic contribution emerges due to the presence of protonated cytosines in the triple helix. This parameters is determinant in the sequence-specificity of ethidium binding to the triple helix. The preferred intercalation sites of ethidium in the triple helix are proposed. The interaction of ethidium at the triplex-duplex junction, and its effects are also discussed. This study is aimed at searching for new drugs specific for the triple helix, or for the triplex-duplex junctions.     

Analysis of fluorescence energy transfer in duplex and branched DNA molecules

Nonradiative fluorescence energy transfer (FET) is thought to be a highly sensitive measure of distance, occurring through a dipole coupling (Forster) mechanism in which the efficiency of FET depends on the inverse sixth power of the distance between fluorophores. The current work assesses the utility of FET for measuring distances in duplex and branched DNA molecules. The apparent efficiencies of FET between donor (fluorescein) and acceptor (eosin) fluorophores attached to opposite ends of oligonucleotide duplexes of varying length were determined; the results suggest that FET is a useful qualitative indicator of distance in DNA molecules. However, the apparent FET efficiency values cannot be fit to the Forster equation without the specification of highly extended DNA-to-fluorophore tethers and motionally restricted fluorophores, conditions that are unlikely to coexist. Three other lines of evidence further suggest that factors in addition to Forster transfer contribute to apparent FET in DNA: (1) The efficiency of FET appears to depend on the base sequence in some instances. (2) Donor fluorescence changes with the extent of thermally induced DNA melting in a sequence-dependent fashion, indicating dye-DNA interactions. (3) The distances between the ends of various pairwise combinations of arms of a DNA four-way junction do not vary as much as expected from previous work. Thus, the occurrence of any nondipolar effects on energy transfer in oligonucleotide systems must be defined before distances in DNA molecules can be quantified by using FET.     

Attempts to observe through-chain energy transfer and electron transfer on α-helical polypeptide chain

Singlet singlet energy transfer between the two terminal chromophores attached to an α-helical polypeptide chain has been studied. The transfer efficiency was satisfactorily explained by Förster's theory when the interchromophore distance was calculated from the α-helical structure. Therefore, it was concluded that no particular effect from the possible energy band structure of the α-helical conformation was detected in the end-to-end energy transfer. Similarly, end-to-end electron transfer was attempted between the electron donor acceptor pair attached to the ends of α-helcial polypeptide chain. However, no intramolecular interaction was found between the donor acceptor pair, indicating that the exciton structure of the α-helical polypeptides is not effective enough to realize through-chain electron transfer.     

Fluorescence anisotropy decay due to rotational brownian motion of ethidium intercalated in double strand DNA

The transient fluorescence of solutions of ethidium bromide . DNA complexes has been measured by pulse fluorimetry at different temperatures and in solvents containing various amounts of sucrose. The molar ratio of ethidium to nucleotides was low. Under these conditions the anisotropy decay was due to the Brownian motion of ethidium molecules intercalated in the double strand DNA molecules. This anisotropy decay could be described by a sum of 3 exponential terms, with correlation times 01, 02, 03 which were linear functions of the ratio of the solvent viscosity to the absolute temperature (n/T). The amplitude of the exponential term characterized by the shortest correlation time (01) has been found to depend on temperature while the ratio of the amplitude of the two other terms (characterized by 02 and 03) was independent of temperature. These results were interpreted as follows: 01 corresponds to a fast motion of the dye in its site. 02 and 03 describe a tortional motion of the ethidium bromide. DNA complex, involving several nucleotide pairs.     

Intercalation of ethidium bromide into a triple-stranded oligonucleotide.

We have examined the ability of a cationic planar chromophore, ethidium bromide, to intercalate into a short, defined triple helix. Using UV absorption, fluorescence spectroscopy and a gel retardation assay we demonstrate that ethidium bromide is able to bind to a triple helix with a lower affinity than to the corresponding duplex. Energy transfer from base triplets to ethidium shows that ethidium is intercalated into the triple helix. The spectroscopic characteristics of ethidium intercalated into a triplex are similar to those observed for intercalation into duplex DNA.     

Photodynamics of excitation energy transfer in self-assembled dyads. Evidence for back transfer.

Three self-assembled photonic dyads comprising a zinc porphyrin donor and a free base acceptor have been studied by time-resolved fluorescence spectroscopy. The driving force of the assembly is the site selective binding of an imidazole connected to a free base porphyrin. Three spacers have been incorporated between the imidazole connector and the free base porphyrin, providing three different distances separating the donor and the acceptor. The high efficiencies and the rates of energy transfer in the set of dyads is consistent with the Forster energy transfer mechanism. Evidence for Forster back transfer has been obtained, and its efficiency and rate have been quantitatively evaluated for the first time.     

Induced circular dichroism as an indicator of double intercalation

The circular dichroism bands induced by exciton interaction between chromophores intercalated into DNA is shown to be a simple test for double intercalation of bis-phenanthridinium ions. The same technique should be applicable to other chromophores as well. The number of base pairs occupied by a bound double intercalator can be inferred from the dependence of the intensity of the CD bands on saturation of DNA binding sites.     

Fluorescence anisotropy decay of ethidium bound to chromatin

The fluorescence anisotropy decays of the chromatin ethidium complexes have been measured in solutions in which the dye was bound to the high affinity sites of the nucleosome DNA. Energy transfers between chromatin-bound ethidium molecules cause an increase of the anisotropy decay rate for much smaller values of the concentration ratio of dye to nucleotide than in the case of nacked DNA-ethidium complexes. This result implies that the high affinity sites are clustered on a short nucleosomal DNA segment. Quantitative analysis of the experimental data by computer simulations of the energy transfer process, shows that these sites are gathered on a single nucleosomal DNA segment, 28 base pairs long. Such a segment probably belongs to the nucleosome “linker”, contributing about half of it.     

Electrostatic factors in DNA intercalation

The factors that determine the binding of a chromophore between the base pairs in DNA intercalation complexes are dissected. The electrostatic potential in the intercalation plane is calculated using an accurate ab initio based distributed multipole electrostatic model for a range of intercalation sites, involving different sequences of base pairs and relative twist angles. There will be a significant electrostatic contribution to the binding energy for chromophores with a predominantly positive electrostatic potential, but this varies significantly with sequence, and somewhat with twist angle. The usefulness of these potential maps for understanding the binding of intercalators is explored by calculating the electrostatic binding energy for 9-aminoacridine, ethidium, and daunomycin in a variety of model binding sites. The electrostatic forces play a major role in the positioning of an intercalating 9-aminoacridine and a significant stabilizing role in the binding of ethidium in its sterically constrained position, but the intercalation of daunomycin is determined by the side-chain binding. Sequence preferences are likely to be determined by a complex and subtle mixture of effects, with electrostatics being just one component. The electrostatic binding energy is also unlikely to be a major determinant of the twist angle, as its variation with angle is modest for most intercalation sites. Overall, the electrostatic potential maps give guidance on how positively charged chromophores can be chemically adapted by heteroatomic substitution to optimise their binding.     

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.