Showing papers by "Jacqueline K. Barton published in 1999"
TL;DR: A more complete understanding of how to target DNA sites with specificity will lead not only to novel chemotherapeutics but also to a greatly expanded ability for chemists to probe DNA and to develop highly sensitive diagnostic agents.
Abstract: The design of small complexes that bind and react at specific sequences of DNA becomes important as we begin to delineate, on a molecular level, how genetic information is expressed. A more complete understanding of how to target DNA sites with specificity will lead not only to novel chemotherapeutics but also to a greatly expanded ability for chemists to probe DNA and to develop highly sensitive diagnostic agents.
1,769 citations
TL;DR: Fluorescent analogs of adenine that selectively oxidize guanine were used to investigate photoinduced electron transfer through the DNA pi-stack as a function of reactant stacking and energetics, and may resolve the range of disparate results previously reported.
Abstract: Fluorescent analogs of adenine that selectively oxidize guanine were used to investigate photoinduced electron transfer through the DNA π-stack as a function of reactant stacking and energetics Small variations in these factors led to profound changes in the kinetics and distance dependences of DNA-mediated electron-transfer reactions Values of β, a parameter reflecting the dependence of electron transfer on distance, ranged from 01 to 10 per angstrom Strong stacking interactions result in the fastest electron-transfer kinetics Electrons are thus transported preferentially through an intrastrand rather than interstrand pathway Reactant energetics also modulate the distance dependence of DNA-mediated charge transport These studies may resolve the range of disparate results previously reported, and paradigms must now be developed to describe these properties of the DNA π-stack, which can range from insulator- to “wire”-like
855 citations
TL;DR: Differential mismatch detection was accomplished irrespective of DNA sequence composition and mismatch identity, and single-base changes in sequences hybridized at the electrode surface are also detected accurately.
Abstract: High-throughput DNA sensors capable of detecting single-base mismatches are required for the routine screening of genetic mutations and disease. A new strategy for the electrochemical detection of single-base mismatches in DNA has been developed based upon charge transport through DNA films. Double-helical DNA films on gold surfaces have been prepared and used to detect DNA mismatches electrochemically. The signals obtained from redox-active intercalators bound to DNA-modified gold surfaces display a marked sensitivity to the presence of base mismatches within the immobilized duplexes. Differential mismatch detection was accomplished irrespective of DNA sequence composition and mismatch identity. Single-base changes in sequences hybridized at the electrode surface are also detected accurately. Coupling the redox reactions of intercalated species to electrocatalytic processes in solution considerably increases the sensitivity of this assay. Reporting on the electronic structure of DNA, as opposed to the hybridization energetics of single-stranded oligonucleotides, electrochemical sensors based on charge transport may offer fundamental advantages in both scope and sensitivity.
510 citations
TL;DR: The DNA double helix can facilitate long-range electron transfer, but only in the presence of a well-stacked pathway.
Abstract: Regardless of its position within the DNA film, cross-linked daunomycin (DM) is efficiently reduced electrochemically, indicating that the electron transfer exhibits a shallow distance dependence. Upon the introduction of an intervening cytosine-adenine (CA) mismatch, the electrochemical response is dramatically attenuated (shown schematically). Therefore, the DNA double helix can facilitate long-range electron transfer, but only in the presence of a well-stacked pathway.
399 citations
TL;DR: Guanines are oxidized as a result of DNA-mediated charge transport over significant distances (e.g. 200 A).
391 citations
TL;DR: The results reveal the nature of ultrafast ET and its mechanism: in DNA, ET cannot be described as in proteins simply by a phenomenological parameter, beta, Instead, the involvement of the base pairs controls the time scale and the degree of coherent transport.
Abstract: Diverse biophysical and biochemical studies have sought to understand electron transfer (ET) in DNA in part because of its importance to DNA damage and its repair. However, the dynamics and mechanisms of the elementary processes of ET in this medium are not fully understood and have been heavily debated. Two fundamental issues are the distance over which charge is transported and the time-scale on which the transport through the pi-stack of the DNA base pairs may occur. With femtosecond resolution, we report direct observation in DNA of ultrafast ET, initiated by excitation of tethered ethidium (E), the intercalated electron acceptor (A); the electron donor (D) is 7-deazaguanine (Z), a modified base, placed at different, fixed distances from A. The ultrafast ET between these reactants in DNA has been observed with time constants of 5 ps and 75 ps and was found to be essentially independent of the D-A separation (10-17 A). However, the ET efficiency does depend on the D-A distance. The 5-ps decay corresponds to direct ET observed from 7-deazaguanine but not guanine to E. From measurements of orientation anisotropies, we conclude that the slower 75-ps process requires the reorientation of E before ET, similar to E/nucleotide complexes in water. These results reveal the nature of ultrafast ET and its mechanism: in DNA, ET cannot be described as in proteins simply by a phenomenological parameter, beta. Instead, the involvement of the base pairs controls the time scale and the degree of coherent transport.
309 citations
TL;DR: In this article, a family of polypyridyl complexes of Os(II) bearing one dipyridophenazine (dppz) derivative and two ancillary ligands derived from bipyridine (bpy) or phenanthroline (phen) was prepared.
Abstract: Polypyridyl complexes of Os(II) bearing one dipyridophenazine (dppz) derivative and two ancillary ligands derived from bipyridine (bpy) or phenanthroline (phen) exhibit emission maxima at ∼740 nm and average excited-state lifetimes in the 10 ns range upon binding to DNA by preferential intercalation of the dppz ligand. A family of [Os(L^1)(L^2)(L^3)]^(2+) and [Os(L^1)_2(L^2)]^(2+) complexes with simple modifications in the ancillary phen or bpy ligands (L^1 and L^3) as well as the intercalating dppz ligand (L^2) was prepared. By cyclic voltammetry, electron-donating substituents on the ancillary ligands lowered the Os(3+/2+) reduction potential but did not affect the reduction potential of the dppz ligand. A methyl substituent at the 7-, 8-, or 6-position of the dppz ligand shifted the phenazine reduction toward the negative but did not affect the Os(3+/2+) potential. Absorption titrations indicated intercalative binding to DNA with high affinity (K_B ∼10^6 M^(-1)) for the family of complexes, although at high ratios (50:1) of base pairs to metal, complexes with ancillary 4,7-dimethylphenanthroline or 4,4‘-dimethylbipyridine ligands exhibit less hypochromism (26−27%) in the π−π* transition on the dppz ligand compared to complexes with 5,6-dimethylphenanthroline (30−37%) or the parent phen (31−35%). By steady-state and time-resolved emission spectroscopy, complexes bound to DNA by intercalation with substituents on the 4,7- or 4,4‘-positions of the ancillary phen or bpy displayed lower quantum yields for emission (Φ_(em)) compared to complexes with the parent phen, while complexes with methyl substituents on the dppz ligand had the greatest Φ_(em). Studies with poly d(AT), poly d(GC), and mixed-sequence DNA revealed that the emission yields are also sequence-dependent. Comparative luminescence studies in CH_2Cl_2 demonstrated that these effects arise from a combination of (i) the inherent sensitivity of the excited state to ligand structure and (ii) perturbations in DNA binding geometry introduced by substituents on the ancillary and intercalating ligands. Our results clarify the relationships between ligand architecture and emission yield and lifetime in the presence and absence of DNA and illustrate the utility of dppz complexes of Os(II) as luminescent probes for DNA.
141 citations
TL;DR: [Rh(bpy)2(chrysi)]3+ is a novel, sterically bulky DNA intercalator that has been designed to bind specifically in the destabilized regions near DNA base mismatches and, upon photoactivation, to cleave the DNA backbone.
Abstract: [Rh(bpy)2(chrysi)]3+ is a novel, sterically bulky DNA intercalator that has been designed to bind specifically in the destabilized regions near DNA base mismatches and, upon photoactivation, to cleave the DNA backbone. Here the molecule is shown to be both a general and remarkably specific mismatch recognition agent. Specific DNA cleavage is observed at over 80% of mismatch sites in all the possible single base pair sequence contexts around the mispaired bases. Moreover, the complex is highly site-specific; it is shown to recognize and photocleave at a single base mismatch in a 2725 base pair linearized plasmid heteroduplex. Sterically demanding intercalators such as [Rh(bpy)2(chrysi)]3+ may have application both in mutation detection systems and as mismatch-specific chemotherapeutic agents.
141 citations
106 citations
TL;DR: The results indicate that these complexes reorient before ET, and the impact of orientational and solvation effects on ET between E and mononucleotides must be considered in the application of E as a probe of DNA ET.
Abstract: Ethidium (E) is a powerful probe of DNA dynamics and DNA-mediated electron transfer (ET). Molecular dynamical processes, such as solvation and orientation, are important on the time scale of ET. Here, we report studies of the femtosecond and picosecond time-resolved dynamics of E, E with 2'deoxyguanosine triphosphate (GTP) in water, and E with 7-deaza-2'-deoxyguanosine triphosphate (ZTP) in water; E undergoes ET with ZTP but not GTP. These studies elucidate the critical role of relative orientational motions of the donor-acceptor complex on ET processes in solution. For ET from ZTP to E, such motions are in fact the rate-determining step. Our results indicate that these complexes reorient before ET. The time scale for the solvation of E in water is 1 ps, and the orientational relaxation time of E is 70 ps. The impact of orientational and solvation effects on ET between E and mononucleotides must be considered in the application of E as a probe of DNA ET.
75 citations
TL;DR: These strategies for preparing metallointercalator-DNA conjugates offer a useful approach to generate chemical assemblies to probe long-range DNA-mediated charge transfer where the redox initiator is confined to and intercalated in a well-defined binding site.
TL;DR: Thermodynamic dissociation constants were determined for these metallointercalator-peptide conjugates by photoactivated DNA cleavage assays with the rhodium intercalators, and single amino acid changes can lead to single or multiple base changes in the DNA site targeted.
Abstract: Metallointercalator−peptide conjugates that provide small molecular mimics to explore peptide−nucleic acid recognition have been prepared. Specifically, a family of peptide conjugates of [Rh(phi)_2(phen‘)]^(3+) [where phi = 9,10-phenanthrenequinone diimine and phen‘ = 5-(amidoglutaryl)-1,10-phenanthroline] has been synthesized and their DNA-binding characteristics examined. Single amino acid modifications were made from the parent metallointercalator−peptide conjugate [Rh(phi)_2(phen‘)]^(3+)-AANVAIAAWERAA-CONH_2, which targets 5‘-CCA-3‘ site-specifically. Moving the glutamate at position 10 in the sequence of the appended peptide to position 6 {[Rh(phi)_2(phen‘)]^(3+)-AANVAEAAWARAA-CONH_2} changed the sequence preference of the metallointercalator−peptide conjugate to 5‘-ACA-3‘. Subsequent mutation of the glutamate at position 6 to arginine {[Rh(phi)_2(phen‘)]^(3+)-AANVARAAWARAA-CONH_2} caused more complex changes in DNA recognition. Thermodynamic dissociation constants were determined for these metallointercalator−peptide conjugates by photoactivated DNA cleavage assays with the rhodium intercalators. At 55 °C in the presence of 5 mM MnCl_2, [Rh(phi)_2(phen‘)]^(3+)-AANVAIAAWERAA-CONH_2 binds to a 5‘-CCA-3‘ site with K_d = 5.7 × 10^(-8) M, whereas [Rh(phi)_2(phen‘)]^(3+)-AANVAEAAWARAA-CONH_2 binds to its target 5‘-ACA-3‘ site with K_d = 9.9 × 10^(-8) M. The dissociation constant for [Rh(phi)_2(phen‘)]^(3+) with random-sequence DNA is 7.0 × 10^(-7) M. Structural models have been developed and refined to account for the observed sequence specificities. As with much larger DNA-binding proteins, with these metal−peptide conjugate mimics, single amino acid changes can lead to single or multiple base changes in the DNA site targeted.
TL;DR: The metallointercalator Λ-1-Rh(MGP)_2phi^(5+) was used in this article to examine competitive interactions between this small metal complex and a DNA-binding transcription factor.
Abstract: The metallointercalator Λ-1-Rh(MGP)_2phi^(5+) binds tightly and specifically to the site 5‘-CATATG-3‘ in the major groove of double helical DNA by a combination of direct readout and shape selection. To examine competitive interactions between this small metal complex and a DNA-binding transcription factor, the preferred binding site for Λ-1-Rh(MGP)_2phi^(5+) was engineered into the AP-1 recognition element (ARE) of the major-groove binding bZIP transcription factor yAP-1, the yeast analogue of mammalian AP-1. Binding experiments confirmed that the modified ARE retained normal yAP-1 binding affinity. Photocleavage experiments demonstrated that the modified ARE contained a high-affinity binding site for Λ-1-Rh(MGP)_2phi^(5+), whereas the native ARE showed no interaction. Competition experiments using gel shift mobility assays demonstrated that Λ-1-Rh(MGP)_2phi^(5+) at 120 nM competes 50% of yAP-1 binding to the 5‘-CATATG-3‘ containing oligonucleotide. In contrast, competitive disruption of protein binding to the native ARE requires 3 μM Λ-1-Rh(MGP)_2phi^(5+). Metallointercalator derivatives, including geometric isomers of Λ-1-Rh(MGP)_2phi^(5+), show no specific binding to the target site and show no inhibition of yAP-1/DNA complexes at concentrations as high as 20 μM. Thus, metallointercalators can be tuned to show selectivity for major groove sites on DNA comparable to transcription factors and indeed can inhibit transcription factor binding site selectively.
TL;DR: In this paper, angeknupftes Daunomycin (DM) is reduziert, ein Hinweis auf eine nur geringe Abhangigkeit des Elektronentransfers von der Entfernung.
Abstract: Unabhangig von der Position im DNA-Film wird kovalent an die DNA angeknupftes Daunomycin (DM) elektrochemisch effizient reduziert – ein Hinweis auf eine nur geringe Abhangigkeit des Elektronentransfers von der Entfernung. Nach Einfuhrung einer C-A-Fehlpaarung geht das elektrochemische Ansprechen drastisch zuruck (schematisch dargestellt). Die DNA-Doppelhelix kann demnach weitreichenden Elektronentransfer erleichtern, aber nur bei Vorliegen eines Ubertragungsweges durch einen geordneten π-Basenstapel.
TL;DR: Questions concerning charge migration through DNA arise that can now be addressed through well-defined chemical experiments and need to be addressed in the context of delineating mechanisms of DNA damage and repair.
Abstract: The reaction of the DNA bases with radical species generated by radiation, carcinogens, or oxidative stress can lead to mutagenic damage [1]. The efficiency and dynamics of radical transport through the DNA helix therefore hold profound biological implications. Intriguing questions concerning charge migration through DNA arise that can now begin to be addressed through well-defined chemical experiments. Does radical migration through DNA occur over long molecular distances? How is it modulated by DNA sequence and the structural variations in DNA? Is it physiologically important? How general is this phenomenon? These are issues that need to be addressed in the context of delineating mechanisms of DNA damage and repair.
TL;DR: During the course of the ongoing research into artificial hydrolytic nucleases, an ethidium−peptide conjugate is prepared that displays metal-dependent ICD, which may represent a first example of metal- dependent intramolecular chiral induction.
Abstract: Ethidium bromide is an aromatic organic dye that for many years has been known to bind via intercalation to the minor groove of DNA. When the ethidium cation binds to DNA, the chirality of the right-handed double helix is imposed upon ethidium (Et), producing induced circular dichroism (ICD). Other examples of ICD have been observed in the heme group of hemoglobin and myoglobin as well as synthetic porphyrin assemblies, and in host−guest assemblies. In every case, an ICD spectrum is produced as a result of the close association of an achiral chromophore with a chiral moiety (e.g., a biopolymer). During the course of our ongoing research into artificial hydrolytic nucleases, we prepared an ethidium−peptide conjugate that displays metal-dependent ICD. Here we report the synthesis and spectroscopic characterization of a metal−peptide assembly which may represent a first example of metal-dependent intramolecular chiral induction.
TL;DR: Rhodium complexes of chrysenequinone diimine not only represent new DNA binding molecules targeted to mismatches but also provide an illustration of a pH "gated" ligand conformational switch.
Abstract: Rhodium(III) complexes containing 9,10-phenanthrenequinone diimine (phi) ligands have been broadly applied for the construction of DNA binding and recognition molecules, and more recently, derivatives containing the 5,6-chrysenequinone diimine (chrysi) ligand have been shown specifically to recognize base mismatches in DNA. Here the structural properties of [Rh(bpy)_2(chrysi)]Cl_3 and spectroscopic properties of derivatives are examined and compared to those of phi complexes of rhodium. Although similar in many respects, phi and chrysi complexes display distinctly different protonation behavior. The pK_a values of chrysi complexes are as much as 1 unit lower than analogous phi compounds, and visible spectra of the chrysi complexes differ markedly from the phi counterparts in acidic but not basic solution. This protonation behavior is traced to the presence of a steric clash between a proton on the aromatic ring of the chrysi ligand and the acidic immino proton of the metal complex. In avoidance of this steric clash, a significant disruption in the planarity of the chrysi ligand is evident crystallographically in the structure of [Rh(bpy)_2(chrysi)]Cl_3·3CH_3CN·2H_2O (triclinic crystal system, space group P1 (No. 2), Z = 2, a = 9.079(3) A, b = 10.970(3) A, c = 21.192(8) A, α = 86.71(3)°, β = 89.21(3)°, γ = 78.58(3)°, V = 2065.4(12) A^3). Phi complexes, lacking the additional aromatic ring, require no similar distortion from ligand planarity. NMR spectra support this pH-dependent structural distortion for the chrysi complex. Rhodium complexes of chrysenequinone diimine, therefore, not only represent new DNA binding molecules targeted to mismatches but also provide an illustration of a pH “gated” ligand conformational switch.
TL;DR: The design of small complexes that bind and react at specific sequences of DNA becomes important as we begin to delineate, on a molecular level, how genetic information is expressed.
Abstract: The design of small complexes that bind and react at specific sequences of DNA becomes important as we begin to delineate, on a molecular level, how genetic information is expressed. A more complete understanding of how to target DNA sites with specificity will lead not only to novel chemotherapeutics but also to a greatly expanded ability for chemists to probe DNA and to develop highly sensitive diagnostic agents.