Probing of DNA structure with osmium tetroxide. Effect of ligands

Fourteen OsO4 complexes with different ligands were tested as probes of DNA structure. Of these complexes, only OsO4-2,2'-bipyridine (Os-bipy), OsO4-bathophenanthrolinedisulfonic acid (Os-bpds) and OsO4-N,N,N',N'-tetramethylenediamine (Os-TMEN) site-specifically modified the ColE1 cruciform in a supercoiled plasmid pColIR215 at millimolar concentrations. Os-bipy, Os-bpds and Os-TMEN also displayed site-specific modification of the B-Z junctions in the supercoiled plasmid pRW751 containing (dC-dG)n inserts.     

Site-specific chemical modification of B-Z junctions in supercoiled DNA as detected by nuclease S1 digestion, inhibition of restriction cleavage and nucleotide sequencing

Structural distortions on the boundary between right-handed and left-handed segments in the superhelical plasmid pPK2 (a derivative of pUC19 containing (dC-dG)n segments cloned into polylinker) were studied by means of chemical probes. Strong osmium tetroxide, pyridine (Os,py) modification of DNA at native superhelical density (sigma) was found in four thymines surrounding the (dC-dG)13 segment. These results correlated with restriction cleavage inhibition (due to modification): BamHI cleavage was strongly inhibited, unlike the neighbouring XbaI and SalI (weak or no inhibition). In the (dC-dG)8 segment considerably weaker modification of the B-Z junctions was observed, accompanied by weak inhibition of BamHI cleavage, while the neighbouring SmaI and KpnI were not affected. Os,py modification of DNA at native sigma was not detected by nuclease S1 cleavage at and (dC-dG)n segment. However, this enzyme recognized and cleaved at the B-Z junction, osmium modified at more negative sigma. The results obtained with the glyoxal and diethyl pyrocarbonate modification support the idea of very narrow B-Z junctions at native sigma.     

Inhibition of restriction endonuclease cleavage due to site-specific chemical modification of the B-Z junction in supercoiled DNA

Structural distortions on the boundary between right-handed B and left-handed Z DNA segments in plasmid pRW751 (a derivative of pBR322 containing (dC-dG)13 and (dC-dG)16 segments) were studied by means of chemical probes. Samples of supercoiled DNA were treated with the respective chemical probe, linearized with EcoRI and inhibition of BamHI (whose recognition sequence GGATCC lies on the boundary between the (dC-dG)n segments and the pBR322 nucleotide sequence) cleavage was tested. Treatment with osmium tetroxide in the presence of pyridine or 2,2'-bipyridine, respectively, resulted in a strong inhibition of the BamHI cleavage at both restriction sites, provided the (dC-dG)n segments were in the left-handed form. In the presence of 2,2'-bipyridine submillimolar concentrations of OsO4 (at 26 degrees C) were sufficient to induce the inhibition of BamHI. Chloroacetaldehyde was used as a probe reacting selectively with atoms involved in the Watson-Crick hydrogen bonding. Similarly as in the case of osmium tetroxide treatment of pRW751 with this agent resulted in the inhibition of BamHI cleavage. It was concluded that the B-Z junction regions in pRW751 contain few solitary bases with disturbed hydrogen bonding or non-Watson-Crick base pairs.     

Osmium tetroxide recognized structural distortions at junctions between right- and left-handed DNA in a bacterial cell

It was shown for the first time that the structural distortions at the junctions between contiguous right-handed and left-handed Z-DNA segments can be recognized in bacterial cells. E. coli containing recombinant plasmid pPK1 (a derivative of pUC19 containing (dC-dG)13 and (dC-dG)16 blocks) were treated with osmium tetroxide, 2.2'-bipyridine (Os,bipy); after this treatment pPK1 DNA was isolated by the boiling method. pPK1 DNA was then cleaved with BglI, and inhibition of BamHI (with its recognition sequence GGATCC lying on the boundary between the (dC-dG)n segments and the pUC19 nucleotide sequence) cleavage was tested. Treatment of cells with 2 mmol/l Os,bipy resulted in a strong inhibition of BamHI cleavage at both restriction sites showing a site-specific osmium modification at the B--Z junction. About the same inhibition of BamHI cleavage was observed after treatment of isolated pPK1 DNA with 0.2 mmol/l Os,bipy.     

Site-specific OsO4 modification of the B-Z junctions formed at the (dA-dC)32 region in supercoiled DNA

OsO4 in the presence of pyridine specifically modifies the structural distortions of the primary helix of supercoiled pRW777 near the (dA-dC)32 sequence. Modification occurs at the same negative superhelix density value as required for formation of the Z-helix within the polymer block. Fine mapping of the distorted regions, which are probably the B-Z junctions, is presented. OsO4 reactions provide a powerful and sensitive chemical approach to study DNA polymorphism in solution.     

B-Z junctions in supercoiled pRW751 DNA contain unpaired bases or non-Watson-Crick base pairs

Structural distortions on the boundary between right-handed and left-handed DNA segments in negatively supercoiled plasmid pRW751 (a derivative of pBR322 containing (dC-dG)13 and (dC-dG)16 segments) were studied by means of osmium tetroxide, pyridine and glyoxal. These two probes react preferentially with single-stranded DNA, but only the latter requires non-paired bases for the reaction. Nuclease S1 and testing of the inhibition of BamHI cleavage (whose recognition sequences GGATCC lie on the "outer" boundaries between the (dC-dG)n and the pBR322 nucleotide sequence) were used to detect the site-specific chemical modification in pRW751. As a result of glyoxal treatment BamHI cleavage was strongly inhibited in topoisomeric samples whose superhelical density was sufficiently negative to stabilize the (dC-dG)n segments in the left-handed form. Osmium tetroxide, pyridine modification resulted in a similar inhibition of BamHI cleavage and in a formation of nuclease S1 sensitive sites. The results suggest that the "outer" B-Z junctions in pRW751 contain one or few non-paired bases or non-Watson-Crick base pairs.     

Monoclonal antibody against DNA adducts with osmium structural probes.

Osmium tetroxide complexes with nitrogen ligands (Os,L) have been widely used as probes of the DNA structure. A monoclonal antibody OsBP7H8 against DNA adducts with Os,L was produced in mice. OsBP7H8 does not bind to proteins or total yeast RNA modified with Os,2,2'-bipyridine (bipy) nor to the unmodified nucleic acids and proteins. The antibody recognizes DNA modified with Os,bipy (DNA-Os,bipy) or with OsO4,1,10-phenanthroline (DNA-Os,phen) but it does not cross-react with oxidized DNA and with DNA adducts of osmium tetroxide complexes with other ligands (such as pyridine, TEMED and bathophenanthroline disulfonic acid). The affinity of OsBP7H8 to DNA-Os,phen is about five-fold higher as compared to DNA-Os,bipy. The antibody can be thus applied either for recognition of single-stranded and distorted regions in DNA (after DNA modification with Os,bipy) or for detection of both single-stranded and double-stranded DNAs (after DNA modification with Os,phen). A new simplified procedure for the dot-blot analysis is proposed, not requiring the purification of DNA-osmium adduct prior to its application to the membrane.     

Probing of DNA structure with osmium tetroxide,2,2''-bipyridine. Adduct-specific antibodies.

Antibodies against DNA modified with a single-strand selective probe, OsO4 in complex with 2,2'-bipyridine (Os,bipy), were raised in rabbits. These antibodies were fractionated using affinity column chromatography and fractions S89-II and S89-III characterized as highly specific for DNA-Os,bipy adduct with no cross reactivity to at least 1000-fold excess of unmodified DNA, RNA and Os,bipy-modified and unmodified proteins. Cross-reactivity to Os,bipy-modified RNA was very small. S89-II showed no cross-reactivity to DNA modified with OsO4 complexed with tetramethylethylenediamine or with bathophenanthroline disulphonic acid and to DNA oxidized with KMnO4. It cross-reacted, however, with DNA modified with OsO4,1,10-phenanthroline complex. The limit of detection of immunodot-blot analysis of extensively Os,bipy-modified DNA was below 0.5 pg. Small extent of Os,bipy-modification of supercoiled and linearized plasmids can be detected by DNA gel retardation and immunoblotting techniques. E. coli cells contain DNA regions in which bases are accessible to the single-strand selective probe.     

B-Z Junctions in Supercoiled pRW751 DNA Contain Unpaired Bases or Non-Watson-Crick Base Pairs

Abstract

Structural distortions on the boundary between right-handed and left-handed DNA segments in negatively supercoiled plasmid pRW751 (a derivative of pBR322 containing (dC-dG)₁₃ and (dC-dG)₁₆ segments) were studied by means of osmium tetroxide, pyridine and glyoxal. These two probes react preferentially with single-stranded DNA but only the latter requires non-paired bases for the reaction. Nuclease SI and testing of the inhibition of BamHI cleavage (whose recognition sequences GGATCC lie on the “outer” boundaries between the (dC-dG)_n and the pBR322 nucleotide sequence) were used to detect the site-specific chemical modification in pRW751.

As a result of glyoxal treatment BamHI cleavage was strongly inhibited in topoisomeric samples whose superhelical density was sufficiently negative to stabilize the (dC-dG)_n segments in the left-handed form. Osmium tetroxide, pyridine modification resulted in a similar inhibition of BamHI cleavage and in a formation of nuclease SI sensitive sites. The results suggest that the “outer” B-Z junctions in pRW751 contain one or few non-paired bases or non-Watson- Crick base pairs.     

Methylation of cytosine in the 5-position alters the structural and energetic properties of the supercoil-induced Z-helix and of B-Z junctions

The structural and energetic consequences of cytosine methylation in the 5-position on the supercoil-dependent B-Z equilibrium in alternating dC-dG sequences cloned into recombinant plasmids were investigated. The helical parameters determined with the band shift method for right-handed [10.7 base pairs (bp)/turn] and left-handed (12.8 bp/turn) 5MedC-dG inserts were different from the helical repeat values for unmethylated dC-dG inserts (10.5 bp/turn in the right-handed and 11.5 bp/turn in the left-handed form). We analyzed the thermodynamic parameters delta GBZ (free energy difference per base pair between right-handed and left-handed helix structure), delta Gjx (free energy for formation of one B-Z junction), and b (helix unwinding at a junction region) for varying lengths of dC-dG inserts by two-dimensional gel electrophoresis and application of a statistical mechanics model. A comparison of plasmids fully methylated in vitro with HhaI methylase and their unmethylated counterparts revealed that delta Gjx is not significantly changed by cytosine methylation. However, this base modification results in an approximate 3-fold decrease of delta GBZ and an approximate 2-fold decrease of the unwinding b at B-Z junction regions. Analysis of a pair of related plasmids, each containing two dC-dG blocks, revealed qualitatively different transition behaviors. When the two dC-dG blocks were separated by 95 bp of a mixed sequence, they underwent independent B to Z transitions with separate nucleation events and junction formations. When the two blocks were separated by only a 4 bp GATC sequence, only one nucleation event was necessary, and the Z-helix spread across the nonalternating GATC region.(ABSTRACT TRUNCATED AT 250 WORDS)     

B-Z DNA junctions contain few, if any, nonpaired bases at physiological superhelical densities

The reactions of bromoacetaldehyde (BAA) with recombinant plasmids that contain sequences which can adopt left-handed Z structures or, at other locations, cruciforms were studied as a function of supercoil density. The sequence in pRW756 that undergoes a supercoil induced transition from a right to left-handed helix was (dC-dG)16 and regions near the replication origin of the pBR322 vector were converted from linearforms to cruciforms. The locations of the most nonpaired structural features were mapped by S1 nuclease cleavage of the "wedged open" duplexes after linearization of the DNAs. Three cruciforms in the pBR322 portions of the plasmids were specifically detected by BAA reaction at physiological supercoil densities (sigma = -0.067). However, the B-Z junctions did not react with BAA under these conditions although the junctions were present since the (dC-dG)16 was shown to be left-handed. Thus, the B-Z junctions have less single-stranded character than the pBR322 cruciforms (3-6 nonpaired bases) and may be fully paired. At much higher superhelical densities (sigma = -0.11-0.12), the B-Z junctions as well as the cruciforms react with BAA indicating a change in the nature of the junctions. Studies were also performed with pRW777 which harbors the mouse kappa immunoglobin sequence (dT-dG)32 . (dC-dA)32 that adopts a left-handed helix under appropriate conditions; the results were similar to those found with pRW756.     

Activation of DNA cleavage by dynemicin A in a B-Z conformational junction.

We report here that the DNA strand scission by dynemicin A is not only sequence-specific but also conformation-specific. The salt-induced B----Z conformational transition dramatically enhanced the cleavage by dynemicin A in a B-Z junction region. By contrast, the bleomycin-Fe(II) complex, the elsamicin A-Fe(II) complex, and esperamicin A1 did not induce any preferential DNA cutting in such a DNA structure. The characteristic hyperreactivity of dynemicin A is observed in (dC-dG)8- and (dC-dG)12-inserted DNAs, but not in (dC-dG)5-inserted DNA. These results suggest value in the use of dynemicin A as proof of the existence of a B-Z junction in vivo and also may aid in understanding the structure of B-Z junctions.     

Electrochemical characterization and DNA-binding property of dipyridophenazine complexes of osmium (II).

Novel dipyridophenazine (DPPZ) complexes of osmium (II), [Os(L)2(DPPZ)]2+ [L = 2,2'-bipyridyl (bpy)(1), 4,4'-diamino-2,2'-bipyridyl (DA-bpy)(2), 4,4'-dimethyl-2,2'-bipyridyl(DM-bpy)(3), and 4,4'-dicarboxyl-2,2'-bipyridyl (DC-bpy)(4)] have been synthesized and characterized. The DNA-binding properties of the complexes were studied by electrochemical methods. As the results, complex 2 shows higher affinity to DNA than other osmium complexes. The binding constant, K of complex 2 to calf thymus DNA has been determined to be 2.3 x 10(7) M-1 by normal pulse voltammetry (NPV).     

Effects of 5 cytosine methylation on the B-Z transition in DNA restriction fragments and recombinant plasmids

Alternating (dC-dG)n regions in DNA restriction fragments and recombinant plasmids were methylated at the 5 position of the cytosine residues by the HhaI methylase. Methylation lowers the concentration of NaCl or MgCl2 necessary to cause the B-Z conformational transition in these sequences. Ionic strengths higher than physiological conditions are required to form the Z conformation when the methylated (dC-dG)n tract is contiguous with regions that do not form Z structures, in contrast to the results with the DNA polymer poly(m5dC-dG) . poly(m5dC-dG). In supercoiled plasmids containing (dC-dG)n sequences, methylation reduces the number of negative supercoils necessary to stabilize the Z conformation. Calculations of the observed free energy contributions of the B-Z junction and cytosine methylation suggest that two junctions offset the favorable effect of methylation on the Z conformation in (dC-dG)n sequences (about 29 base-pairs in length). Studies with individual methylated topoisomers demonstrate that increasing Na+ concentration up to approximately 0.2 M inhibits the formation of the Z conformation in the (m5dC-dG)n region of supercoiled plasmids. The results suggest that methylation may serve as a triggering mechanism for Z DNA formation in supercoiled DNAs.     

Probing of DNA polymorphic structure in the cell with osmium tetroxide

It is shown that osmium tetroxide, 2,2'-bipyridine can be applied as a probe of DNA structure in a bacterial cell. Using this probe we demonstrate (a) presence of structural distortions at the junctions between the right-handed B and left-handed Z DNA in a recombinant plasmid pRW751 and (b) unusual structure of the d(A-T)16 insert in pAT32 plasmid in E. coli cells and in in vitro.     

Recognition of the structural distortions at the junctions between B and Z segments in negatively supercoiled DNA by osmium tetroxide

It has been shown for the first time that conformational junction between contiguous right-handed B and left-handed Z segments can be recognized by a chemical probe. Plasmid pRW751 containing (dC-dG)13 and (dC-dG)16 blocks was treated with osmium tetroxide, pyridine (a reagent known to be single-strand selective) at physiological ionic conditions (0.1 and 0.2 M NaCl) and neutral pH. Mapping of the osmium binding sites by restriction enzyme digestion followed by nuclease S1 cleavage has revealed selective binding of osmium at, or near to, the end of the (dC-dG)n segments proximal to the 95 bp lac sequence. The junction of the shorter (dC-dG)13 segment was modified to a substantially greater extent than that of the longer segment. Partial inhibition of DNA cleavage by BamHI was observed at the restriction sites neighbouring to the both (dC-dG)n segments as a result of DNA modification by osmium tetroxide. The site-selective modification occurred only in supercoiled and not in relaxed molecules. Differences in the sensitivity of the B/Z junctions in pRW751 to the osmium tetroxide were explained by different structural features of these junctions.     

Synthesis, complete characterization, and enantioselective electrokinetic separation of functionalized ruthenium complex enantiomers

Electrokinetic chromatography was employed to separate the enantiomers of two novel functionalized ruthenium(II) complexes with different polypyridyl coordination spheres. The use of anionic carboxymethyl-beta-cyclodextrin as chiral mobile phase additive resulted in maximum efficiency and resolution for the enantiomer separation of both transition metal complexes. The syntheses of the [4-(3-hydroxypropyl)-4'-methyl-2,2'-bipyridine]-bis(2,2'-bipyridine)rethenium(II)-bis(tetrafluoroborate) and [4-(3-hydroxypropyl)-4'-methyl-2,2'-bipyridine]-bis(4,4'-dimethyl-2,2'-bypyridine)ruthenium(II)-bis(tetrafluoroborate) complexes and their complete characterization by means of two-dimensional (1)H and (13)C[(1)H] NMR techniques ((1)H-(1)H COSY and (1)H-(13)C HMQC) as well as elemental analyses and MALDI-TOFMS are described in detail. The functionalized complexes can be used as building blocks for further reactions with polymers, biopolymers, surfaces and nanoparticles.     

Production and characterization of a polyclonal antibody for Os(II) and Ru(II) polypyridyl complexes

The characterization of a polyclonal antibody produced via immunization with an [Os(bpy)(2)dcbpy] hapten is described. Bpy is 2,2'-bipyridine and dcbpy is 2,2'-bipyridine-4,4'-dicarboxylic acid. The cross-reactivity of the antibody for the Ru(II) analogue of the hapten was also investigated. Large increases in the emission and luminescent lifetime of a series of Os and Ru complexes were observed on binding of the antibody. Association equilibrium constants were derived from luminescence titration data and were found to be 5.6 x 10(8) and 5.0 x 10(8)M(-1) for [Os(bpy)(2)dcbpy] and [Ru(bpy)(2)dcbpy], respectively. Spectroscopic changes were likely due to the exclusion of H(2)O from the complex/antibody binding cleft and blocking of vibrational relaxation pathways of the Os/Ru excited state. D(2)O/H(2)O experiments confirmed that the antibody protected approx. 82% of [Os(bpy)(2)dcbpy] and 80% of [Ru(bpy)(2)dcbpy] from excited state deactivation by the aqueous solvent.     

Photophysical behavior and intramolecular energy transfer in Os(II) diimine complexes covalently linked to anthracene.

The photophysical behavior of two Os(II) complexes having a bipyridine ligand with anthracene attached directly to the bipyridine (4-(9-anthryl)-2,2'-bipyridine, bpy-AN) is reported. The two complexes [(bpy)2Os(bpy-AN)]2+ and [(bpy-AN)2Os(CO)Br]+ have (3)MLCT excited states that differ in energy by less than 800 cm(-1). Despite this fact, the observed photophysical behavior of the two complexes is entirely different. The complex with the higher energy 3MCLT state, [(bpy-AN)2Os(CO)Br]+, is nonemissive at room temperature, but has a long lived excited state that is localized on the 3(pi-pi*) state of the anthracene substituent. The other complex, [(bpy)2Os(bpy-AN)]2+, exhibits emission at room temperature and has a transient absorption spectrum that is consistent with a localized 3MLCT state. The excited state decay behavior of the two complexes can be fit well assuming a model in which noninteracting 3MLCT and 3(pi-pi*) states are in equilibrium.     

Intercalation into the DNA double helix and in vivo biological activity of water-soluble planar [Pt(diimine)(N,N-dihydroxyethyl-N'-benzoylthioureato)]+Cl- complexes: a study of their thermal stability, their CD spectra and their gel mobility

The interaction of newly synthesised water-soluble planar complexes of general structure [Pt(diimine)(N,N-dihydroxyethyl-N'-benzoylthioureato)]+Cl- with DNA was investigated by means of DNA melting studies, CD spectroscopy, and DNA gel mobility studies. Addition of stoichometric amounts of [Pt(diimine)H2L-S,O]Cl complexes to polynucleotides caused a significant increase in the melting temperature of poly(dA-dT) and calf-thymus DNA, respectively, indicating that these complexes interacted with DNA and stabilised the double helical structure. The CD spectra confirmed the relatively strong binding of three related Pt(II) complexes ([Pt(2,2'-bipyridine)H2L-S,O]Cl, [Pt(4,4'-dimethyl-2,2'-bipyridine)H2L-S,O]Cl, and [Pt(1,10-phenanthroline)H2L-S,O]Cl), to DNA. Comparison with the published CD spectra of ethidium bromide/DNA complex suggests a similar intercalation mode of binding. cis-[(4,4'-di-tert-butyl-2,2'-bipyridyl)N,N-di(2-hydroxyethyl)-N'-benzoylthioureatoplatinum(II)] chloride, with its very bulky tert-butyl groups, did not intercalate into the polynucleotide double helix. In DNA mobility studies in the presence of the four [Pt(diimine)H2L-S,O]Cl complexes, only [Pt(2,2'-bipyridine)H2L-S,O]Cl affected the DNA mobility to any detectable extent. Finally, in vivo studies on the biological activity of the complexes, using an Escherichia coli DNA excision repair deficient uvrA mutant strain, indicated that only the [Pt(2,2'-bipyridine)H2L-S,O]Cl complex showed significant cellular toxicity and that this was, in part, linked to DNA damage.