| 1. |
- Andersson, Johanna, 1983, et al.
(author)
-
Lifetime Heterogeneity of DNA-Bound dppz Complexes Originates from Distinct Intercalation Geometries Determined by Complex-Complex Interactions
- 2013
-
In: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 52:2, s. 1151-1159
-
Journal article (peer-reviewed)abstract
- Despite the extensive interest in structurally explaining the photophysics of DNA-bound [Ru(phen)(2)dppz](2+) and [Ru(bpy)(2)dppz](2+), the origin of the two distinct emission lifetimes of the pure enantiomers when intercalated into DNA has remained elusive. In this report, we have combined a photophysical characterization with a detailed isothermal titration calorimetry study to investigate the binding of the pure Delta and Lambda enantiomers of both complexes with [poly(dAdT)](2). We find that a binding model with two different binding geometries, proposed to be symmetric and canted intercalation from the minor groove, as recently reported in high-resolution X-ray structures, is required to appropriately explain the data. By assigning the long emission lifetime to the canted binding geometry, we can simultaneously fit both calorimetric data and the binding-density-dependent changes in the relative abundance of the two emission lifetimes using the same binding model. We find that all complex complex interactions are slightly unfavorable for Delta-[Ru(bpy)(2)dppz](2+), whereas interactions involving a complex canted away from a neighbor are favorable for the other three complexes. We also conclude that Delta-[Ru(bpy)(2)dppz](2+) preferably binds isolated, Delta-[Ru(phen)(2)dppz](2+) preferably binds as duplets of canted complexes, and that all complexes are reluctant to form longer consecutive sequences than triplets. We propose that this is due to an interplay of repulsive complex complex and attractive complex-DNA interactions modulated by allosteric DNA conformation changes that are largely affected by the nature of the ancillary ligands.
|
|
| 2. |
- Choi, S. D., et al.
(author)
-
Binding Mode of [Ruthenium(II) (1,10-Phenanthroline)2L]2+ with Poly(dT*dA-dT) Triplex. Ligand Size Effect on Third-Strand Stabilization
- 1997
-
In: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 36:1, s. 214-223
-
Journal article (peer-reviewed)abstract
- The binding of homochiral [Ru(II)(1,10-phenanthroline)(2)L](2+) complexes {where L = 1,10-phenanthroline (phen), dipyrido[3,2-a:2',3'-c]phenazine (DPPZ) or benzodipyrido[3,2-a:2',3'-c]phenazine (BDPPZ)} to poly(dT*dA-dT) triplex has been investigated by linear and circular dichroism and thermal denaturation. Analysis of the linear dichroism spectra indicates that the extended DPPZ and BDPPZ ligands lie approximately parallel to the base-pair and base-tripler planes consistent with intercalation which is also supported by strong hypochromism in the interligand absorption bands with either duplex or tripler. The spectral properties of any of the metal complex enantiomers were similar for binding to either duplex or tripler DNA, indicating that the third strand, which occupies the major groove of the template duplex, has little effect on the binding geometries and hence supports the hypothesis that the metal complexes all bind from the minor groove with the DPPZ and BDPPZ ligands intercalated but without intercalation in the case of [Ru(phen)(3)](2+). Third-strand stabilization depended on the nature of the third substituted phenanthroline chelate ligand but was not directly related to its size, with stabilizing power increasing in the order phen
|
|
| 3. |
- Ellouze, C., et al.
(author)
-
Difference between active and inactive nucleotide cofactors in the effect of DNA binding and the helical structure of RecA filament
- 1999
-
In: European Journal of Biochemistry. - : Wiley. - 0014-2956 .- 1432-1033. ; 262:1, s. 88-94
-
Journal article (peer-reviewed)abstract
- The RecA protein requires ATP or dATP for its coprotease and strand exchange activities. Other natural nucleotides, such as ADP, CTP, GTP, UTP and TTP, have little or no activation effect on RecA for these activities. We have investigated the activation mechanism, and the selectivity for ATP, by studying the effect of various nucleotides on the DNA binding and the helical structure of the RecA filament. The interaction with DNA was investigated via fluorescence measurements with a fluorescent DNA analog and fluorescein-labeled oligonucleotides, assisted by linear dichroism. Filament structure was investigated via small-angle neutron scattering. There is no simple correlation between filament elongation, DNA binding affinity of RecA, and DNA structure in the RecA complex. There may be multiple conformations of RecA, Both coprotease and strand exchange activities require formation of a rigid and well organized complex. The triphosphate nucleotides which do not activate RecA, destabilize the RecA-DNA complex, indicating that the chemical nature of the nucleotide nucleobase is very important for the stability of RecA-DNA complex. Higher stability of the RecA-DNA complex in the presence of adenosine 5'-O-3-thiotriphosphate or guanosine 5'-O-3-thiotriphosphate than ATP or GTP indicates that contact between the protein and the chemical group at the gamma position of the nucleotide also affects the stability of the RecA-DNA complex. This contact appears also important for the rigid organization of DNA because ADP strongly decreases the rigidity of the complex.
|
|
| 4. |
- Ellouze, C., et al.
(author)
-
Nucleotide Cofactor-Dependent Structural Change of Xenopus laevis Rad51 Protein Filament Detected by Small-Angle Neutron Scattering Measurements in Solution
- 1997
-
In: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 36:44, s. 13524-13529
-
Journal article (peer-reviewed)abstract
- Rad51 protein, a eukaryotic homologue of RecA protein, forms a filamentous complex with DNA and catalyzes homologous recombination. We have analyzed the structure of Xenopus Rad51 protein (XRad51.1) in solution by small-angle neutron scattering (SANS). The measurements showed that XRad51.1 forms a helical filament independently of DNA. The sizes of the cross-sectional and helical pitch of the filament could be determined, respectively, from a Guinier plot and the position of the subsidiary maximum of SANS data. We observed that the helical structure is modified by nucleotide binding as in the case of RecA. Upon ATP binding under high-salt conditions (600 mM NaCl), the helical pitch of XRad51.1 filament was increased from 8 to 10 nm and the cross-sectional diameter decreased from 7 to 6 nm. The pitch sizes of XRad51.1 are similar to, though slightly larger than, those of RecA filament under corresponding conditions. A similar helical pitch size was observed by electron microscopy for budding yeast Rad51 [Ogawa, T., et al. (1993) Science 259, 1896-1899]. In contrast to the RecA filament, the structure of XRad51.1 filament with ADP is not significantly different from that with ATP. Thus, the hydrolysis of ATP to ADP does not modify the helical filament of XRad51.1. Together with our recent observation that ADP does not weaken the XRad51.1/DNA interaction, the effect of ATP hydrolysis on XRad51.1 nucleofilament should be very different from that on RecA.
|
|
| 5. |
|
|
| 6. |
- Kim, Hye-Kyung, 1970, et al.
(author)
-
Co-Ion Dependence of DNA Nuclease Activity Suggests Hydrophobic Cavitation as a Potential Source of Activation Energy
- 2001
-
In: European Physical Journal E. - : Springer Science and Business Media LLC. - 1292-8941 .- 1292-895X. ; 4:4, s. 411-417
-
Journal article (peer-reviewed)abstract
- The source of the activation energy that allows cutting of DNA by restriction enzymes is unclear. A systematic study of the cutting efficiency of the type-II restriction endonuclease EcoRI, with varying background electrolyte ion pair and buffer reported here, shows only a modest dependence of efficiency on cation type. Surprisingly, efficiency does depend strongly on the presumed indifferent anion of the background salt. What emerges is that competition between the background salt anion and the buffer anion for the enzyme and DNA surfaces is crucial. The results are unexpected and counterintuitive from the point of view of conventional electrolyte theory. However, taken together with recent developments in surface chemistry, the results do fall into place and could also suggest a novel mechanism for enzyme activity as an alternative to metal-activated hydrolysis: microscopic cavitation in a hydrophobic pocket might be the source of activation energy.
|
|
| 7. |
|
|
| 8. |
- McKinley, A. W., et al.
(author)
-
DNA Sequence and Ancillary Ligand Modulate the Biexponential Emission Decay of Intercalated [Ru(L)2dppz]2+ Enantiomers
- 2012
-
In: Chemistry - A European Journal. - : Wiley. - 1521-3765 .- 0947-6539. ; 18:47, s. 15142-15150
-
Journal article (peer-reviewed)abstract
- The bi-exponential emission decay of [Ru(L)2dppz]2+ (L=N,N'-diimine ligand) bound to DNA has been studied as a function of polynucleotide sequence, enantiomer, and nature of L (phenanthroline vs. bipyridine). The lifetimes (ti) and pre-exponential factors (ai) depend on all three parameters. With [poly(dA-dT)]2, the variation of ai with [Nu]/[Ru] has little dependence on L for ?-[Ru(L)2dppz]2+ but a substantial dependence for ?-[Ru(L)2dppz]2+. With [poly(dG-dC)]2, by contrast, the ?-enantiomer ai values depend strongly on the nature of L, whereas those of the ?-enantiomer are relatively unaffected. DNA-bound linked dimers show similar photophysical behaviour. The lifetimes are identified with two geometries of minor-groove intercalated [Ru(L)2dppz]2+, resulting in differential water access to the phenazine nitrogen atoms. Interplay of cooperative and anti-cooperative binding resulting from complexcomplex and complexDNA interactions is responsible for the observed variations of ai with binding ratio. [Ru(phen)2dppz]2+ emission is quenched by guanosine in DMF, which may further rationalise the shorter lifetimes observed with guanine-rich DNA.
|
|
| 9. |
- McKinley, A. W., et al.
(author)
-
Environmental effects on the photophysics of transition metal complexes with dipyrido 2,3-a:3 ',2 '-c phenazine (dppz) and related ligands
- 2011
-
In: Coordination Chemistry Reviews. - : Elsevier BV. - 0010-8545. ; 255:21-22, s. 2676-2692
-
Journal article (peer-reviewed)abstract
- This review primarily covers studies of ruthenium(II) complexes with the dppz (dipyrido[2,3-a:3',2'-c]phenazine) ligand; in solution, in polymers and surfactant/lipid media, and when bound to DNA. Related studies with other transition metals, and with extended ligands that can form bimetallic as well as monometallic complexes are discussed. The review focuses on photophysics of these complexes with particular attention devoted to the nature of the excited states that give rise to emission, their dependence on solvent environment, and the behavior of the complexes as luminescent probes for DNA.
|
|
| 10. |
- McKinley, A. W., et al.
(author)
-
Sensitivity of Ru(phen)(2)dppz (2+) light switch emission to ionic strength, temperature, and DNA sequence and conformation
- 2013
-
In: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 42:11, s. 4081-4090
-
Journal article (peer-reviewed)abstract
- The luminescence of DNA-bound [Ru(phen)(2)dppz](2+) is shown to be highly sensitive to environmental conditions such as ionic strength, temperature, and the sequence and secondary structure of the nucleic acid, although not to bulky DNA substituents in the major groove. Each enantiomer has two characteristic lifetimes with any polynucleotide and their relative amplitudes vary as a function of binding ratio. For [poly(dA-dT)](2) as a model sequence, the longer lifetime for Delta-[Ru(phen)(2)dppz](2+) has been assigned to canted intercalation of the complex and the shorter lifetime is ascribed to symmetric intercalation. At a fixed binding ratio, the longer lifetime amplitude increases with increasing ionic strength, without significant change in lifetimes. Increasing temperature has a similar effect, but also affects lifetimes. In general, emission is strongest with AT-rich polynucleotides and with higher-order secondary structures, with intensity increasing as single-stranded
|
|
| 11. |
- Mårtensson, Anna, 1983, et al.
(author)
-
Diastereomeric Crowding Effects in the Competitive DNA Intercalation of Ru(phenanthroline)2dipyridophenazine2+ Enantiomers
- 2019
-
In: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 58:14, s. 9452-9459
-
Journal article (peer-reviewed)abstract
- The biexponential excited-state emission decay characteristic of DNA intercalated tris-bidentate dppz-based ruthenium complexes of the general form Ru(L)2dppz2+ has previously been explained by a binding model with two distinct geometry orientations of the bound ligands, with a distinct lifetime associated with each orientation. However, it has been found that upon DNA binding of Ru(phen)2dppz2+ the fractions of short and long lifetimes are strongly dependent on environmental factors such as salt concentration and, in particular, temperature. Analyzing isothermal titration calorimetry for competitive binding of Ru(phen)2dppz2+ enantiomers to poly(dAdT)2, we find that a consistent binding model must assume that the short and long lifetimes states of intercalated complexes are in equilibrium and that this equilibrium is altered when neighboring bound ligands affect each other. The degree of intercomplex binding is found to be a subtle manifestation of several attractive and repulsive factors that are highly likely to directly reflect the strong diastereomeric difference in the binding enthalpy and entropy values. In addition, as the titration progresses and the binding sites on the DNA lattice become increasingly occupied, a general resistance for the saturation of the binding sites is observed, suggesting diastereomeric crowding of the neighboring bound ligands.
|
|
| 12. |
|
|
| 13. |
- Ratilainen, Tommi, 1970, et al.
(author)
-
Hybridization of peptide nucleic acid
- 1998
-
In: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 37:35, s. 12331-12342
-
Journal article (peer-reviewed)abstract
- The thermodynamics of hybridization and the conformations of decameric mixed purine-pyrimidine sequence PNA/PNA, PNA/DNA, and DNA/DNA duplexes have been studied using fluorescence energy transfer (FET), absorption hypochromicity (ABS), isothermal titration calorimetry (ITC), and circular dichroism (CD) techniques. The interchromophoric distances determined in the FET experiments on fluorescein- and rhodamine-labeled duplexes indicate that the solution structures of the duplexes are extended helices in agreement with available NMR (PNA/DNA) and crystal X-ray data (PNA/PNA). The melting thermodynamics of the duplexes was studied with both FET and ABS. The thermodynamic parameters obtained with ABS are in good agreement with the parameters from calorimetric measurements while FET detection of duplex melting gives in most cases more favorable free energies of hybridization. This discrepancy between FET and ABS detection is ascribed to the conjugated dyes which affect the stability of the duplexes substantially. Especially, the dianionic fluorescein attached via a flexible linker either to PNA or to DNA seems to be involved in an attractive interaction with the opposite dicationic lysine when hybridized to a PNA strand. This interaction leads to an increased thermal stability as manifested as a 3-4 degrees C increase of the melting temperature. For the PNA/DNA duplex where fluorescein is attached to the PNA strand, a large destabilization (Delta T-m = -12 degrees C) occurs relative to the unlabeled duplex, probably originating from electrostatic repulsion between the fluorescein and the negatively charged DNA backbone. In the case of the PNA/PNA duplex, the sense of helicity of the duplex is reversed upon conjugation of fluorescein via a flexible linker arm, but not when the fluorescein is attached without a linker to the PNA.
|
|
| 14. |
- Ratilainen, Tommi, 1970, et al.
(author)
-
Thermodynamics of sequence-specific binding of PNA to DNA
- 2000
-
In: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 39:26, s. 7781-7791
-
Journal article (peer-reviewed)abstract
- For further characterization of the hybridization properties of peptide nucleic acids (PNAs), the thermodynamics of hybridization of mixed sequence PNA-DNA duplexes have been studied. We have characterized the binding of PNA to DNA in terms of binding affinity (perfectly matched duplexes) and sequence specificity of binding (singly mismatched duplexes) using mainly absorption hypochromicity melting curves and isothermal titration calorimetry. For perfectly sequence-matched duplexes of varying lengths (6-20 bp), the average free energy of binding (Delta G degrees) was determined to be -6.5 +/- 0.3 kT mol(-1) bp(-1), corresponding to a microscopic binding constant of about 14 M-1 bp(-1). A variety of single mismatches were introduced in 9- and 12-mer PNA-DNA duplexes. Melting temperatures (T-m) of 9- and 12-mer PNA-DNA duplexes with a single mismatch dropped typically 15-20 degrees C relative to that of the perfectly matched sequence with a corresponding free energy penalty of about 15 kT mol(-1) bp(-1). The average cost of a single mismatch is therefore estimated to be on the order of or larger than the gain of two matched base pairs, resulting in an apparent binding constant of only 0.02 M-1 per mismatch. The impact of a mismatch was found to be dependent on the neighboring base pairs. To a first approximation, increasing the stability of the surrounding region, i.e., the distribution of A.T and G.C base pairs, decreases the effect of the introduced mismatch.
|
|
| 15. |
- Tuite, Eimer, 1966, et al.
(author)
-
Effects of intercalators on complexation of RecA with duplex DNA
- 1995
-
In: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 34:50, s. 16365-16374
-
Journal article (peer-reviewed)abstract
- To elucidate the binding mode of recombination protein A (RecA) to double-stranded (ds) DNA, the effects on the RecA-DNA interaction of several mono- and bisintercalators of the acridine, phenanthridine, and cyanine classes have been investigated by linear dichroism spectroscopy. Simple monointercalators lacking side chains efficiently promoted the binding of RecA to dsDNA in the absence of nucleotide cofactor, which is otherwise required. Bisintercalators varied in their ability to induce RecA binding, while monointercalators with aminoalkyl side chains proved inefficient. Modification of DNA structure by the intercalator appears to be necessary for induction of RecA binding, but if the intercalator has a bulky minor-groove-binding side chain, it does not induce RecA binding. In detailed studies with acridines, neither the binding geometry of intercalators nor the structure of DNA was significantly modified upon binding of RecA without cofactor. Judged by circular dichroism, similar ReA conformational changes accompanied bis-9-aminoacridine- and ATPyS-induced RecA association with DNA. In the presence of ATPyS, the intercalators inhibited the rate of RecA binding to dsDNA and were extruded from DNA upon binding of RecA. This competitive aspect may suggest that intercalation of some amino acid residue(s) plays a role in nucleotide-induced RecA binding. The stoichiometry of the RecA-DNA-intercalator filament was determined; in the fully formed filament the base pair:intercalator ratio is 2, and the base pair:RecA ratio also 2. This contrasts with a base pair:RecA ratio of 3 in the ATPyS-induced filament, although in both cases the DNA experiences 50% extension.
|
|
| 16. |
- Tuite, Eimer, 1966, et al.
(author)
-
Effects of minor and major groove-binding drugs and intercalators on the DNA association of minor groove-binding proteins RecA and deoxyribonuclease I detected by flow linear dichroism
- 1997
-
In: European Journal of Biochemistry. - : Wiley. - 0014-2956 .- 1432-1033. ; 243:1-2, s. 482-492
-
Journal article (peer-reviewed)abstract
- Linear and circular dichroic spectroscopies have been employed to investigate the effects of small DNA ligands on the interactions of two proteins which bind to the minor groove of DNA, viz. RecA protein from Escherichia coli and deoxyribonuclease I (bovine pancreas). Ligands representing three specific non-covalent binding modes were investigated: 4',6-diamidino-2-phenylindole and distamycin A (minor groove binders), methyl green (major groove binder), and methylene blue, ethidium bromide and ethidium dimer (intercalators). Linear dichroism was demonstrated to be an excellent detector, in real time, of DNA double-strand cleavage by deoxyribonuclease I. Ligands bound in all three modes interfered with the deoxyribonuclease I digestion of dsDNA, although the level of interference varied in a manner which could be related to the ligand binding site, the ligand charge appearing to be less important. In particular, the retardation of deoxyribonuclease I cleavage by the major groove binder methyl green demonstrates that accessibility to the minor groove can be affected by occupancy of the opposite groove. Binding of all three types of ligand also had marked effects on the interaction of RecA with dsDNA in the presence of non-hydrolyzable cofactor adenosine 5'-O-3-thiotriphosphate, decreasing the association rate to varying extents but with the strongest effects from ligands having some minor groove occupancy. Finally, each ligand was displaced from its DNA binding site upon completion of RecA association, again demonstrating that modification of either groove can affect the properties and behaviour of the other. The conclusions are discussed against the background of previous work on the use of small DNA ligands to probe DNA-protein interactions.
|
|
| 17. |
|
|
| 18. |
- Tuite, Eimer, 1966, et al.
(author)
-
Intercalative interactions of ethidium dyes with triplex structures
- 1995
-
In: Bioorganic and Medicinal Chemistry. - 0968-0896 .- 1464-3391. ; 3:6, s. 701-711
-
Journal article (peer-reviewed)abstract
- The binding of phenanthridine dyes to tripler poly(dT)*poly(dA). poly(dT) and its precursor duplex poly(dA). poly(dT) is characterized using linear dichroism and circular dichroism spectroscopy, and thermal denaturation. The two monomeric dyes ethidium bromide and propidium iodide are shown to behave similarly to each other in intercalating into and stabilizing both the duplex and the tripler structures. However, contrary to expectations, the extra cationic side-chain of propidium iodide provides no significant extra stabilization of tripler compared with ethidium bromide, although propidium does stabilize the duplex more than ethidium. The monomeric dyes appear to have somewhat different binding geometries with the duplex and tripler polymers. The dimeric dye ethidium homodimer is found to bis-intercalate in the tripler as well as the duplex but, in contrast to the monomers, no variation in geometry between duplex and tripler is observed. However, although dimer stabilizes the duplex, it has no effect on the thermal stability of the tripler. This lack of binding preferentiality of the dimer for tripler compared with the monomeric dyes indicates greater constraints on the accommodation of a bis-intercalator in the tripler structure than in the duplex.
|
|
| 19. |
- Tuite, Eimer, 1966, et al.
(author)
-
Linear and circular dichroism characterization of thionine binding mode with DNA polynucleotides
- 2018
-
In: Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy. - : Elsevier BV. - 1386-1425. ; 189, s. 86-92
-
Journal article (peer-reviewed)abstract
- The binding mode of thionine (3,7-diamino-5-phenothiazinium) with alternating and non-alternating DNA poly nucleotides at low binding ratios was conclusively determined using linear and circular dichroism spectroscopies. The binding to [poly(dG-dC)](2) and poly(dG).poly(dC) was purely intercalative and was insensitive to ionic strength. Intercalative binding to [poly(dA-dT)](2) is observed at low ionic strength, but a shift of some dye to an non-intercalative mode is observed as the background salt concentration increases. With poly(dA).poly(dT), intercalative binding is unfavourable, although some dye molecules may intercalate at low ionic strength, and groove binding is strongly promoted with increasing concentration of background salt. However, stacking with bases is observed with single-stranded poly(dA) and with triplex poly(dT).poly(dA).poly(dT) which suggests that the unusual structure of poly(dA). poly(dT) precludes intercalation. Thionine behaves similarly to the related dye methylene blue, and small differences may be attributed either to the ability of thionine to form H-bonds that stabilize intercalation or to its improved stacking interactions in the basepair pocket on steric grounds.
|
|
| 20. |
- Tuite, Eimer, 1966, et al.
(author)
-
Methylene blue intercalates with triplex poly(dT)*poly(dA)·poly(dT) but not duplex poly(dA)·poly(dT)
- 1995
-
In: Journal of the Chemical Society - Series Chemical Communications. - : Royal Society of Chemistry (RSC). - 0022-4936. ; :1, s. 53-54
-
Journal article (peer-reviewed)abstract
- Methylene blue intercalates with tripler poly(dT*dA.dT) even though it binds to the precursor duplex poly(dA.dT) in the major groove; the switch may be related to conformational modifications of the polynucleotide structure upon binding of the third strand.
|
|
| 21. |
|
|
| 22. |
- Tuite, Eimer, 1966, et al.
(author)
-
SEQUENCE-SPECIFIC INTERACTIONS OF METHYLENE-BLUE WITH POLYNUCLEOTIDES AND DNA - A SPECTROSCOPIC STUDY
- 1994
-
In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 116:17, s. 7548-7556
-
Journal article (peer-reviewed)abstract
- The modes of binding of the phenothiazinium dye methylene blue (1) to alternating and nonalternating polynucleotides and to calf thymus (CT) DNA have been characterized using linear dichroism (LD) and circular dichroism (CD) spectroscopy. With the polynucleotide [poly(dG-dC)](2) the interaction at low binding ratios is shown to be purely intercalative and the binding mode is insensitive to changes in ionic strength. The observed CD spectrum is bisignate, which may be due to intercalation at the different base-pair steps (5'G-C3' and 5'C-G3'), giving rise to CD signals of different sign and shape, By contrast, a single intercalative binding mode with the alternating AT polynucleotide [poly(dA-dT)](2) is likely only at very low ionic strength; at high ionic strength (200 mM phosphate, pH 6.9), a second binding mode is also manifest which is attributed to groove binding of the dye. The absorption and linear dichroism spectroscopic features of the methylene blue/CT-DNA (42% GC) complex reflect those of complexes of the dye with both [poly(dA-dT)](2) and [poly(dG-dC)](2); the circular dichroism spectrum of the methylene blue/CT-DNA complex and its variation with ionic strength reflect the complexity of even this simple system where numerous possible binding sites exist. Comparative binding to the nonalternating polynucleotides poly(dA).poly(dT) and poly(da).poly(dC), which each possess only one base-pair step, was also examined. On the basis of the combined LD and CD evidence, it is proposed that the dye is loosely bound with poly(dA).poly(dT), probably in the major groove, and intercalated with poly(dG).poly(dC).
|
|
| 23. |
- Tuite, Eimer, 1966, et al.
(author)
-
Structural Heterogeneity in Polynucleotide-Facilitated Assembly of Phenothiazine Dyes
- 2018
-
In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 122:11, s. 2891-2899
-
Journal article (peer-reviewed)abstract
- The assembly of stacked dyes on DNA is of interest for electron transfer, light harvesting, sensing, and catalysis applications. A combination of UV/vis absorption, linear dichroism (LD), and circular dichroism (CD) was applied to characterize thoroughly the aggregation with DNA of the phenothiazine dyes methylene blue, azure B, and thionine. Aggregates of each dye with [poly(dG-dC)] 2 , [poly(dA-dT)] 2 , and calf thymus DNA were explored at high dye:DNA binding ratios, where excess dye groove-binds after all intercalation sites are filled. The organization of the aggregates (dimers, trimers, and multimers) with polydeoxynucleotides displays a structural diversity that depends on DNA sequence, extent of methylation of dye exocyclic amine groups, and ionic strength. The dyes typically form right-handed H-aggregates having negative LD, consistent with stepped stacking along the minor groove. However, aggregates in some dye:DNA aggregates show left-handed chirality or positive LD, indicating unusual modes of aggregation such as formation of adventitious dimers between intercalated and minor groove bound dye. In terms of sequence-dependence, methylene blue shows more extensive aggregation with [poly(dA-dT)] 2 , while thionine aggregates more with [poly(dG-dC)] 2 . Azure B has distinctive behavior that is unlike either other dyes. Thus, although these phenothiazine dyes possess a common tricyclic framework, the organization of their polynucleotide-facilitated aggregates depends sensitively on the extent of methylation of the exocyclic amines.
|
|
