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J K Barton

Publications and source records attributed to J K Barton.

At least 73 records · Page 4Linked to original sources
PubMed1994

Correlations of crystal structures of DNA oligonucleotides with enantioselective recognition by Rh(phen)2phi3+: probes of DNA propeller twisting in solution.

Rh(phen)2phi3+ (phen = 1,10-phenanthroline; phi = 9,10-phenanthrenequinone diimine) avidly binds to DNA via intercalation from the major groove and upon photoactivation produces strand scission with single base 5' asymmetry. Enantiomers of Rh(phen)2phi3+, which lack hydrogen-bonding substituents in ancillary positions, distinguish a DNA site through shape-selection; site recognition depends upon the local variations in structure at a binding site. Here, we examine the application of delta-Rh(phen)2phi3+ as a sequence-dependent structural probe and, in particular, as a probe of DNA propeller twisting in solution, by comparing directly cleavage results using delta- and lambda-Rh(phen)2phi3+ on crystallographically characterized oligonucleotides with several sequence-dependent crystallographic parameters. The three oligonucleotides examined in this study are the Dickerson-Drew dodecamer, 5'-CGCGAATTCGCG-3', the NarI dodecamer, 5'-ACCGGCGCCACA-3', and the CG decamer, 5'-CCAACGTTGG-3', all of which have been crystallized in the B-form. Enantioselective cleavage and reaction favored by the delta-isomer is found to be governed locally by the opening of the site in the major groove. A correlation is demonstrated between cleavage by delta-Rh(phen)2phi3+ and the opening in the major groove that results from the change in propeller twist (differential propeller twist) at a base step. When the major groove is closed as a result of a change in propeller twist, there is little cleavage evident by either enantiomer; at sites which are indicated crystallographically to be open in the major groove, a direct correlation is observed between enantioselective cleavage and the degree of opening. A trend of higher enantioselectivity at sites possessing higher twist angles is also observed.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed1993

Long-range photoinduced electron transfer through a DNA helix.

Rapid photoinduced electron transfer is demonstrated over a distance of greater than 40 angstroms between metallointercalators that are tethered to the 5' termini of a 15-base pair DNA duplex. An oligomeric assembly was synthesized in which the donor is Ru(phen)2dppz2+ (phen, phenanthroline, and dppz, dipyridophenazine) and the acceptor is Rh(phi)2phen3+ (phi, phenanthrenequinone diimine). These metal complexes are intercalated either one or two base steps in from the helix termini. Although the ruthenium-modified oligonucleotide hybridized to an unmodified complement luminesces intensely, the ruthenium-modified oligomer hybridized to the rhodium-modified oligomer shows no detectable luminescence. Time-resolved studies point to a lower limit of 10(9) per second for the quenching rate. No quenching was observed upon metallation of two complementary octamers by Ru(phen)3(2+) and Rh(phen)3(3+) under conditions where the phen complexes do not intercalate. The stacked aromatic heterocycles of the DNA duplex therefore serve as an efficient medium for coupling electron donors and acceptors over very long distances.

Base Sequence↗
PubMed1993

Chemical probing of tDNAPhe with transition metal complexes: a structural comparison of RNA and DNA.

The three-dimensional folding of tDNAPhe has been examined and compared to native tRNAPhe using a series of shape-selective transition metal complexes as chemical probes of nucleic acid structure. Rh(phen)2 phi 3+ (phen = phenanthroline, phi = 9,10-phenanthrenequinonediimine), which targets sites of tertiary interaction in tRNAPhe, cleaves specifically at similar sites on tDNAPhe. However, this rhodium complex also targets 5'-pyr-pyr-pur-3' sites within the acceptor and anticodon stems of tDNA;Rh(phen)2 phi 3+ generally targets 5'-pyr-pyr-pur-3' sites in B-form duplex DNA. On tRNAPhe, Rh(DIP)3(3+) (DIP = 4,7-diphenyl-1,10-phenanthroline) specifically cleaves C70, which neighbors a GU mismatch, and targets psi 55 as well, within the hydrophobic region of tRNAPhe. On tDNAPhe no specific cleavage by Rh(DIP)3(3+) is observed. The cleavage studies, taken together, indicate that globally the tertiary folding of tDNAPhe resembles that of tRNAPhe. However, the double helical regions of the DNA analog differ from tRNAPhe, likely in adopting a more B-like conformation. As a consequence, the GT mismatch within the acceptor stem of tDNA does not present the same recognition elements as in tRNA, and the GT mismatch is no longer recognized by the shape-selective rhodium complex. The present work underscores the utility of applying DNA analogs to studies of RNA structure and function, since the general folding characteristics of the two polymers are likely to be similar. However, structural probing with transition metal complexes offers a valuable companion to such experiments, since the shape-selective probes, with sensitivity, may be used to delineate locally on the polymer those regions which may differ in structure.

DNA↗
PubMed1993

A distinct intron-DNA structure in simian virus 40 T-antigen and adenovirus 2 E1A genes.

Distinct structures delineating the introns of simian virus 40 T-antigen and adenovirus 2 E1A genes have been discovered. The structures, which are centered around the branch points of the genes inserted in supercoiled double-stranded plasmids, are specifically targeted through photoactivated strand cleavage by the metal complex tris(4,7-diphenyl-1,10-phenanthroline)rhodium(III). The DNA sites that are recognized lack sequence homology but are similar in demarcating functionally important sites on the RNA level. The single-stranded DNA fragment corresponding to the coding strand of the E1A gene was also found to fold into a structure apparently identical to that in the supercoiled E1A gene based on the recognition by the metal complex. Further investigation of different single-stranded DNA fragments showed that the structure requires the sequences at both ends of the intron plus the flanking sequences but not the middle of the intron. These results provide direct evidence that the positions of these introns are structurally encoded on the DNA level.

Adenovirus E1A Proteins↗
PubMed1992

Characterization of dipyridophenazine complexes of ruthenium(II): the light switch effect as a function of nucleic acid sequence and conformation.

Spectroscopic parameters for two novel ruthenium complexes on binding to nucleic acids of varying sequences and conformations have been determined. These complexes, Ru(bpy)2dppz2+ and Ru(phen)2dppz2+ (bpy = 2,2'-bipyridine; phen = 1,10-phenanthroline; dppz = dipyrido[3,2:a-2',3':c]-phenazine) serve as "molecular light switches" for DNA, displaying no photoluminescence in aqueous solution but luminescing intensely in the presence of DNA. The luminescent enhancement observed upon binding is attributed to the sensitivity of the excited state to quenching by water; in DNA, the metal complex, upon intercalation into the helix, is protected from the aqueous solvent, thereby preserving the luminescence. Correlations between the extent of protection (depending upon the DNA conformation) and the luminescence parameters are observed. Indeed, the strongest luminescent enhancement is observed for intercalation into DNA conformations which afford the greatest amount of overlap with access from the major groove, such as in triple helices. Differences are observed in the luminescent parameters between the two complexes which also correlate with the level of water protection. In the presence of nucleic acids, both complexes exhibit biexponential decays in emission. Quenching studies are consistent with two intercalative binding modes for the dppz ligand from the major groove: one in which the metal-phenazine axis lies along the DNA dyad axis and another where the metal-phenazine axis lies almost perpendicular to the DNA dyad axis. Ru(bpy)2dppz2+ and Ru(phen)2dppz2+ are shown here to be unique reporters of nucleic acid structures and may become valuable in the design of new diagnostics for DNA.

Anions↗
PubMed1992

Recognition of G-U mismatches by tris(4,7-diphenyl-1,10-phenanthroline)rhodium(III).

The coordination complex tris(4,7-diphenyl-1,10-phenanthroline)rhodium(III) [Rh(DIP)3(3+)], which promotes RNA cleavage upon photoactivation, has been shown to target specifically guanine-uracil (G-U) mismatches in double-helical regions of folded RNAs. Photoactivated cleavage by Rh(DIP)3(3+) has been examined on a series of RNAs that contain G-U mismatches, yeast tRNA(Phe) and yeast tRNA(Asp), as well as on 5S rRNAs from Xenopus oocytes and Escherichia coli. In addition, a "microhelix" was synthesized, which consists of seven base pairs of the acceptor stem of yeast tRNA(Phe) connected by a six-nucleotide loop and contains a mismatch involving residues G4 and U69. A U4.G69 variant of this sequence was also constructed, and cleavage by Rh(DIP)3(3+) was examined. In each of these cases, specific cleavage is observed at the residue which lies to the 3'-side of the wobble-paired U; some cleavage by the rhodium complex is also evident in several structured RNA loops. The remarkable site selectivity for G-U mismatches within double-helical regions is attributed to shape-selective binding by the rhodium complex. This binding furthermore depends upon the orientation of the G-U mismatch, which produces different stacking interactions between the G-U base pair with the Watson-Crick base pair following it on the 5'-side of U compared to the Watson-Crick pair preceding it on the 3'-side of U. Rh(DIP)3(3+) therefore serves as a unique probe of G-U mismatches and may be useful both as a model and in probing RNA-protein interactions as well as in identifying G-U mismatches within double-helical regions of folded RNAs.

Guanine Nucleotides↗
PubMed1992

Delineation of structural domains in eukaryotic 5S rRNA with a rhodium probe.

The three-dimensional folding of Xenopus oocyte 5S rRNA has been examined using the coordination complex Rh(phen)2phi3+ (phen = phenanthroline; phi = phenanthrenequinone diimine) as a structural probe. Rh(phen)2phi3+ binds neither double-helical RNA nor unstructured single-stranded regions of RNA. Instead, the complex targets through photoactivated cleavage sites of tertiary interaction which are open in the major groove and accessible to stacking. The sites targeted by the rhodium complex have been mapped on the wild-type Xenopus oocyte RNA, on a truncated RNA representing the arm of the molecule comprised of helix IV-loop E-helix V, and on several single-nucleotide mutants of the 5S rRNA. On the wild-type 5S rRNA, strong cleavage is found at residues U73, A74, A101, and U102 in the E loop and U80 and G81 in helix IV; additional sites are evident at A22 and A56 in the B loop, C29 and A32 in helix III, and C34, C39, A42, and C44 in the C loop. Given the similarity observed in cleavage between the full 5S RNA and the truncated fragment as well as the absence of any long-range effects on cleavage in mutant RNAs, the results do not support models which involve long-range tertiary interactions. Cleavage results with Rh(phen)2phi3+ do, however, indicate that the apposition of several noncanonical bases as well as stem--loop junctions may result in intimately stacked structures with opened major grooves. In particular, on the basis of cleavage results on mutant RNAs, both loops C and E represent structures where the strands constituting each loop are not independent of one another but are intrinsically structured.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1992

Recognition of tertiary structure in tRNAs by Rh(phen)2phi3+, a new reagent for RNA structure-function mapping.

With photoactivation Rh(phen)2phi3+ promotes strand cleavage at sites of tertiary interaction in tRNA. The rhodium complex, which binds double-helical DNA by intercalation in the major groove, yields no cleavage in double-helical regions of the RNA or in unstructured single-stranded regions. Instead, Rh(phen)2phi3+ appears to target regions which are structured so that the major groove is open and accessible for stacking with the complex, as occurs where bases are triply bonded. So as to examine the specificity of this novel reagent and to evaluate its use in probing structural changes in RNAs, cleavage studies have been conducted on two structurally characterized tRNAs, tRNA(Phe) and tRNA(Asp) from yeast, the unmodified yeast tRNA(Phe) transcript, and a chemically modified tRNA(Phe), as well as on a series of tRNA(Phe) mutants. On tRNA(Phe) strong cleavage is observed at residues G22, G45, U47, psi 55, and U59; weaker cleavage is observed at A44, m7G46, and C48. On tRNA(Asp) cleavage is found at residues A21 through G26, psi 32, and U48, with minor cleavage apparent at A44, G45, A46, psi 55, U59, and U60. There is a striking similarity in cleavage observed on these tRNAs, and the sites of cleavage mark regions of tertiary folding. Cleavage on the unmodified tRNA(Phe) transcript resembles closely that found on native yeast tRNA(Phe), but additional sites, primarily in the anticodon loop and stem, are evident. The results indicate that globally the structures containing or lacking the modified bases appear to be the same; the differences in cleavage observed may reflect a loosening or alteration in the structure due to the absence of the modified bases. Cleavage results on mutants of tRNA(Phe) illustrate Rh(phen)2phi3+ as a sensitive probe in characterizing tRNA tertiary structure. Results are consistent with other assays for structural or functional changes. Uniquely, Rh(phen)2phi3+ appears to target directly sites of tertiary interaction. Cleavage results on mutants which involve base changes within the triply bounded region of the molecule indicate that it is the structure of the triply bonded array rather than the individual nucleotides which are being targeted. Chemical modification to promote selective depurination of the third base (m7G46) involved in the triple in the folded, native tRNA leads to the reduction of cleavage by the metal complex; this result shows directly the importance of the stacked triple base structure for recognition by the metal complex.(ABSTRACT TRUNCATED AT 400 WORDS)

2,2'-Dipyridyl↗
PubMed1991

Structural polymorphism in the major groove of a 5S RNA gene complements the zinc finger domains of transcription factor IIIA.

Metal complexes that bind to DNA on the basis of shape-selection have been used to map the conformational features of the DNA binding site for transcription factor IIIA. Conformationally distinct segments are detected on the 5S rRNA gene that correspond closely to the binding sites identified for the individual zinc finger domains of the protein. The local conformations are characterized by a major groove opened because of a change in base pair inclination and/or displacement at a central 5'-pyrimidine-purine-3' step, flanked by a widened minor groove, as would arise at the junctions between alternating B- and A-like DNA segments. Docking experiments with a consensus structure of a zinc finger reveal that the mixed A-B binding site accommodates the peptide domain better than either canonical B- or A-DNA helices. The close structural matching of the conformational variations in the 5S rDNA both to the proposed sites of zinc finger binding and to the shape of an individual zinc finger domain points to DNA structural polymorphism as providing an important determinant in recognition. In particular, shape selection in the 5' half of the internal control region may orient the multiple finger domains.

Animals↗
PubMed1991

Luminescence of ruthenium(II) polypyridyls: evidence for intercalative binding to Z-DNA.

Photophysical studies have been undertaken to characterize the binding interactions of enantiomers of Ru(phen)3(2+), Ru(DIP)3(2+), and racemic Ru(bpy)2dppz2+ (where phen = 1,10-phenanthroline, DIP = 4,7-diphenylphenanthroline, and dppz = dipyridophenazine) with Z-form poly d(GC). Parallel enhancements in steady state luminescent intensity and a lengthening of luminescent lifetimes are seen for ruthenium enantiomers with Z-DNA as for B-DNA but with enantioselectivities reversed. Greater enhancements are seen for delta-isomers with the right-handed helix but for lambda-isomers with the left-handed helix. Ru(bpy)2dppz2+, an avid intercalator in B-DNA, displays no luminescence free in aqueous solution, but luminesces brightly bound to either B- or Z-poly d(GC). Stern-Volmer quenching studies also support the enantioselective preference in binding to B-DNA by delta-isomers and a reversal with binding to Z-DNA preferentially by the lambda-isomers. Steady state polarization studies indicate a rigid association of the complexes with both B- and Z-DNA on the time-scale of their emission and again with symmetrical enantioselectivities for the left and right-handed helices. Given the well characterized intercalative association of the complexes with B-DNA, the parallel results seen here with Z-DNA point strongly to a comparable intercalative association with the Z-form helix. That molecules may interact with Z-DNA through intercalation has not been demonstrated previously and now requires consideration in describing the range of interactions of small molecules and proteins with Z-DNA.

DNA↗
PubMed1991

Photoinduced electron transfer quenching of excited Ru(II) polypyridyls bound to DNA: the role of the nucleic acid double helix.

In the presence of double helical polynucleotides (sodium poly(dA-dT).poly(dA-dT) or calf thymus DNA), the efficiency of oxidative or reductive electron transfer between photoexcited ruthenium(II) chelates Ru(tap)2(hat)2+ or Ru(phen)2+(3) (where tap = 1,4,5,8-tetraazaphenanthrene, hat = 1,4,5,8,9,12-hexaazatriphenylene, and phen = 1,10-phenanthroline) and appropriate cationic quenchers (ethidium, Ru(NH3)3+(6), methyl viologen, or M(phen)3+(3), where M = Co, Rh, Cr) increases 1-2 orders of magnitude compared to the efficiency of the same quenching in microhomogeneous aqueous medium (kq = 0.3-1.8 x 10(9) M-1 s-1). The enhancement is more pronounced when the binding constant of the quencher (10(3) less than Kb less than 10(6) M-1) is large. Similar trends are found when the biopolymers are replaced by sodium poly(styrenesulfonate) (PSS). The accelerated electron transfer process is proposed to be due mainly to the effect of accumulation of the reagents in the electrostatic field of the polymer; if corrections for this effect are introduced (e.g. ratioing [quencher]/[polynucleotide]), the reaction rate becomes essentially independent of the polymer concentration. Based upon a model for electron transfer reaction of the complexes within a small cylindrical interface around the DNA helix, calculations of the bimolecular electron transfer rate constants are computed to be 10(3) times smaller when the reactants are bound to the double-stranded polynucleotides and decreased mobility of the cationic species is apparent. The effect is less pronounced if a simpler polyelectrolyte (PSS) is employed. Emission lifetimes of the Ru(II) polypyridyls bound to the DNA (0.32-2 microseconds, double exponential decays) are discussed as well.

Aza Compounds↗
PubMed1990

1H NMR studies of tris(phenanthroline) metal complexes bound to oligonucleotides: characterization of binding modes.

The binding of Ru(phen)3(2+), Rh(phen)3(3+), and Co(phen)3(3+) to the oligonucleotides d(GTGCAC)2 and 5'-pd(CGCGCG)2 has been examined by 1H NMR spectroscopy as a function of temperature, concentration, and chirality of the metal complex. The duplex oligonucleotides act as chiral shift reagents for the metal complexes; phenanthroline protons associated with each enantiomer are resolved upon binding to the oligomer. The spectral titrations, consistent with photophysical studies, indicate that the complexes bind to the oligomer through two modes: one assigned as intercalation favoring the delta-isomer, and the other assigned as the surface-bound interaction favoring the lambda-isomer. The ligand protons are perturbed in a manner that implies sensitivity of particular protons to binding mode; specifically, the H4,7 protons appear to be altered most for the lambda-enantiomer while the H5,6 protons are perturbed more for the delta-enantiomer. The NMR chemical shift variations appear particularly sensitive to this surface-bound interaction, which, on the basis of a comparison of binding and photophysical parameters for Ru(phen)3(2+), appears more prominant in binding to oligonucleotides than that to polynucleotides. With respect to oligonucleotide proton shifts, the adenine H2 proton, positioned in the minor groove of the helix, shows the largest upfield shifts with metal binding, and more dramatically with lambda-isomers. The major groove thymine methyl protons (TMe) shift downfield to a lesser extent, and more so for delta-isomers. The different binding modes also differ with respect to their dynamics of association; the longitudinal relaxation rates of delta- and lambda-4,7 phenanthroline protons of Rh(phen)3(3+) are 0.88 and 1.14 s, respectively, in the presence of d(GTGCAC)2.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed1990

1H NMR studies of tris(phenanthroline) metal complexes bound to oligonucleotides: structural characterizations via selective paramagnetic relaxation.

The selective paramagnetic relaxation of oligonucleotide protons of d(GTGCAC)2 by delta- and lambda-Ni(phen)3(3+) and delta- and lambda-Cr(phen)3(3+) has been examined to obtain some structural insight into the noncovalent binding of tris(phenanthroline) metal complexes to DNA. The experiments demonstrate that the relative rate of relaxation of different oligonucleotide protons by the paramagnetic metal complex varies with the chirality of the metal complex and, to a lesser extent, the metal charge. The proton most efficiently relaxed in all cases is the adenosine AH2, which is situated in the minor groove of the oligonucleotide helix. For both lambda-Ni(phen)3(2+) and lambda-Cr(phen)3(3+), the order of relaxation rates varies as AH2 much greater than AH8 greater than G3H8 = TMe = C4H5. For delta-Ni(phen)3(2+) it varies as AH2 greater than G3H8 greater than AH8 greater than TMe = C4H5 and for delta-Cr(phen)3(3+) as AH2 greater than TMe = G3H8 = AH8 greater than C4H5. Distances between the metal center and oligonucleotide protons were calculated on the basis of the relaxation data, and these distances were used to generate a set of models to describe the interactions of the rigid metal complex with the helix. For lambda-isomers, the data are consistent with a predominant surface-bound association in the minor groove of the DNA helix. The results of delta-isomers correlate better with models that incorporate also a major groove intercalative mode. Despite the absence of hydrogen-bonding groups in the metal complex, the surface-bound model of the phenanthroline complex in the minor groove of DNA resembles the noncovalent association seen with other DNA groove binding molecules.

Base Sequence↗
PubMed1990

Ligand-dependent interaction of ruthenium(II) polypyridyl complexes with DNA probed by emission spectroscopy.

The nature of the interaction in buffered aqueous solution of several homo and heteroleptic ruthenium(II) polypyridyl complexes containing 2,2'-bipyridine (bpy), 2,2'-bipyrazine (bpz), 1,10-phenanthroline (phen), 4,7-diphenyl-1,10-phenanthroline (dip), 3,4,7,8-tetramethyl-1,10-phenanthroline (tmp), 1,4,5,8-tetraazaphenanthrene (tap), and 1,4,5,8,9,12-hexaazatriphenylene (hat) with calf thymus DNA and poly(dA-dT).poly(dA-dT) (pdAT) has been investigated by steady-state spectroscopy and emission lifetime measurements. Those complexes containing two or more tap/hat ligands photo-oxidize the guanine base upon binding to DNA with efficiencies that parallel their excited state redox potentials, but display "normal" behavior (increase of both the emission intensity and lifetime) when bound to pdAT. However Ru(tap)(hat)2+2 and Ru(hat)2+3 even photooxidize the adenine base of pdAT, so that their excited states are also quenched in the presence of either polynucleotide. The electron transfer quenching mechanism has been confirmed previously by detection of the monoreduced complex in laser flash photolysis experiments in the presence of mononucleotides. Most of the complexes investigated appear to bind to DNA, at least in part via intercalation, with affinities being dependent on the nature of the largest ligand (hat shows the highest ability in heteroleptic complexes). From lifetime quenching experiments, in the presence of moderate amounts of NaCl, surface binding does not appear to be a general mode for the complexes investigated, and it has been demonstrated unequivocally only for Ru(phen)2+3. In addition, the intercalation of complexes into DNA increases as the ionic strength of the medium decreases, the DNA/Ru ratio increases, or when water is partially replaced by glycerol.

2,2'-Dipyridyl↗
PubMed1989

High resolution footprinting of EcoRI and distamycin with Rh(phi)2(bpy)3+, a new photofootprinting reagent.

The complex bis(phenanthrenequinone diimine)(bipyridyl)rhodium(III), Rh(phi)2(bpy)3+, cleaves DNA efficiently in a sequence-neutral fashion upon photoactivation so as to provide a novel, high resolution, chemical photofootpring reagent. Photofootprinting of two crystallographically characterized DNA-binding agents, distamycin, a small natural product which binds to DNA in the minor groove, and the endonuclease EcoRI, which binds in the major groove, gave respectively a 5-7 base pair footprint for the drug at its A6 binding site and a 10-12 base pair footprint for the enzyme centered at its recognition site (5'-GAATTC-3'). Both footprints agree closely with the crystallographic results. The photocleavage reaction can be performed using either a high intensity lamp or, conveniently, a simple transilluminator box, and the photoreaction is not inhibited by moderate concentrations of reagents which are sometimes required for examining interactions of molecules with DNA. When compared with other popular footprinting agents, the rhodium complex shows a number of distinct advantages: sequence-neutrality, high resolution, ability to footprint major as well as minor groove-binding ligands, applicability in the presence of additives such as Mg2+ or glycerol, ease of handling, and a sharply footprinted pattern. Light activated footprinting reactions furthermore offer the possibility of examining DNA-binding interactions with time resolution and within the cell.

2,2'-Dipyridyl↗