Unwinding and hydrodynamic flow linear dichroism characteristics of supercoiled DNA covalently modified with two isomeric methylchrysene diol epoxides of different biological activities

Balasta, Luisa; Xu, Rong; Geacintov, Nicholas E.; Swenberg, Charles E.; Amin, Shantu; Hecht, Stephen S.

doi:10.1021/tx00035a005

Cited by 3 publications

(4 citation statements)

References 40 publications

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“…Finally, we note that structural distortions such as bends and flexible hinge joints induced by the covalent binding of drugs or bulky mutagenic and/or carcinogenic compounds are not uncommon. Examples of such ligands include 2-aminofluorene and its N-2-acetyl-derivative ( 27), (+)-CC1065 (43), cis-platin adducts (44), UV light-induced thymine dimers (45) and certain positional and configurational isomers of the polycyclic aromatic diol epoxide derivatives of 5-methylchrysene (34) and benz[a] anthracene (46).…”

Section: Discussionmentioning

confidence: 99%

“…The DNA was reacted with either (+)or (-)-anti-BPDE to generate BPDEmodified DNA molecules as described earlier (35). Aqueous DNA solutions were subjected to a hydrodynamic flow gradient in a Couette cell, and the absorbance was measured with linearly polarized light as described in detail elsewhere (34,35). The linear dichroism signal (LD) is defined as A// -A1, where A// and A I are the absorbances conrsponding to the light polarization being oriented parallel or perpendicular to the flow direction, respectively (+-trans rb (xl00)…”

Section: Bpde-modified Native Dna and Flow Linear Dichroism Measurementsmentioning

confidence: 99%

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Stereochemistry-dependent bending in oligonucleotide duplexes induced by site-specific covalent benzo[a]pyrene diol epoxide-guanine lesions

Mao

et al. 1995

Nucl Acids Res

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The apparent persistence length of enzymatically linearized pIBI30 plasmid DNA molecules approximately 2300 bp long, as measured by a hydrodynamic linear flow dichroism method, is markedly decreased after covalent binding of the highly tumorigenic benzo[a]pyrene metabolite 7R,8S-dihydroxy-9S,10R-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene [(+)-anti-BPDE]. In striking contrast, the binding of the non-tumorigenic, mirror-image 7S,8R,9R,10S enantiomer [(-)-anti-BPDE] to DNA has no measurable effect on its alignment in hydrodynamic flow gradients (< or = 2.2% of the DNA bases modified). In order to relate this effect to BPDE-nucleotide lesions of defined stereochemistry, the bending induced by site-specifically placed and stereochemically defined (+)- and (-)-anti-BPDE-N2-dG lesions in an 11mer deoxyoligonucleotide duplex was studied by ligation and gel electrophoresis methods. Out of the four stereochemically isomeric anti-BPDE-N2-deoxyguanosyl (dG) adducts with either (+)-trans, (-)-trans, (+)-cis, and (-)-cis adduct stereochemistry, only the (+)-trans adduct gives rise to prominent bends or flexible hinge joints in the modified oligonucleotide duplexes. Since both anti-BPDE enantiomers are known to bind preferentially to dG (> or = 85%), these observations can account for the differences in persistence lengths of DNA modified with either (+)-anti-BPDE or the chiral (-)-anti-BPDE isomer.

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Section: Discussionmentioning

confidence: 99%

Section: Bpde-modified Native Dna and Flow Linear Dichroism Measurementsmentioning

confidence: 99%

Stereochemistry-dependent bending in oligonucleotide duplexes induced by site-specific covalent benzo[a]pyrene diol epoxide-guanine lesions

Mao

et al. 1995

Nucl Acids Res

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“…Strong dependence of reduced FLD (ρ) on its superhelix density (σ) was first observed for circular DNA. Titration of the sc DNA pIBI30 [24] or φX174 phage [16,17] with intercalating dyes, which unwind DNA and change its topological state, revealed the bell‐shaped dependence of ρ on σ, with the maximum value of ρ corresponding to the nonsupercoiled (relaxed) DNA. Our measurements demonstrated close dependence; however these differed from data published in [12,25].…”

Section: Resultsmentioning

confidence: 99%

Catalytic transformations of supercoiled DNA as studied by flow linear dichroism technique

et al. 2005

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The dynamic of supercoiled DNA (scDNA) transformations is the key point for understanding the numerous processes taking place in the living cell [1]. DNA topology changes are vital in replication, transcription, recombination, chromosome condensation, and segregation. From the topological point of view DNA can be represented as a closed ribbon [2][3][4]. A study of the dynamic aspects of the DNA topology is closely associated with a design of an adequate mathematical description of the DNA polymeric molecule and methods for monitoring its properties [5][6][7][8]. The main topological changes of scDNA are catalyzed by DNA-topoisomerases I and II, which induce single and double nicks in DNA strains, respectively. These correspond to changes in the linking number (Lk) of the polymer substrate by 1 or 2. From the chemical point of view, the substrates and products of DNA topoisomerization are identical and catalytic events result in only slight topological changes. The product of the previous turnover acts as a substrate at the next stage, so an ensemble of topoisomers exists at each step of the reaction. This fact stipulates a description of scDNA biocatalytic A catalytic turnover of supercoiled DNA (scDNA) transformation mediated by topoisomerases leads to changes in the linking number (Lk) of the polymeric substrate by 1 or 2 per cycle. As a substrate of the topoisomerization reaction it is chemically identical to its product; even a single catalytic event results in the quantum leap in the scDNA topology. Non-intrusive continuous assay to measure the kinetics of the scDNA topoisomerization was performed. The development of such a technique was hindered because of multiple DNA species of intermediate topology present in the reaction mixture. The interrelation of DNA topology, its hydrodynamics, and optical anisotropy enable us to use the flow linear dichroism technique (FLD) for continuous monitoring of the scDNA topoisomerization reaction. This approach permits us to study the kinetics of DNA transformation catalyzed by eukaryotic topoisomerases I and II, as well as mechanistic characteristics of these enzymes and their interactions with anticancer drugs. Moreover, FLD assay can be applied to any enzymatic reaction that involves scDNA as a substrate. It also provides a new way of screening drugs dynamically and is likely to be potent in various biomedical applications.

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“…The slower electrophoretic mobilities of the (+)-enantiomermodified duplexes appear to be related to either greater extents of static bending, higher flexibilities at the sites of the lesions, or to differences in the hydration of the non-polar pyrenyl residues (42). Interestingly, these conclusions are supported by changes in persistence lengths (measured by linear dichroism techniques) caused by the binding of these two BPDE (23,(43)(44)(45) and 5-MeCDE enantiomers (32,46) to native DNA, or to synthetic polynucleotides. The persistence lengths of the (+)enantiomer-modified DNA are significantly reduced relative to unmodified DNA, while those of adducts derived from the (-)-enantiomers are not changed to any significant extent.…”

Section: Stereoselective Resistance To Svpd Enzyme Digestionmentioning

confidence: 96%

Site-specific adducts derived from the binding of anti-5-methylchrysene diol epoxide enantiomers to DNA: Synthesis and characteristics

Xu¹,

Dwarakanath²,

Cosman³

et al. 1996

Carcinogenesis

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The direct synthesis and characterization of site-specific adducts derived from the binding of (+)-1R,2S-dihydroxy-3S,4R-epoxide-1,2,3,4-tetrahydro-5-methylchrysene and the (-)-1S,2R,3R,4S-enantiomer [(+)- and (-)-5-MeCDE, respectively], to the N2-guanine residues in the oligonucleotide d(CCATCGCTACC) are described. The spectroscopic characteristics of the 5-MeCDE-modified oligonucleotides are discussed, and it is shown that their CD characteristics can be used to distinguish between the trans-addition products of the binding of the (+)- and (-)-enantiomers of 5-MeCDE (C4 position). The 11-mer duplexes with the normal complementary strands are destabilized by the site-specific, covalently bound 5-MeCDE residues: the melting points, Tm, are 5-10 degrees lower than in the case of the unmodified duplex. Stereoselective exonuclease enzyme digestion patterns of the single-stranded (+)- and (-)-trans-5-MeCDE-modified oligonucleotides (Mao et al, 1993, Biochemistry, 32, 11785-11793) were used to probe the orientations of the covalently bound 5-MeCDE residues relative to the modified guanine and the 5'-3' strand polarity; the aromatic residues are positioned either on the 5'-side [(+)-5-MeCDE], or the 3'-side [(-)-5-MeCDE adduct] of the modified guanine residues. The electrophoretic mobilities of the (+)-5-MeCDE-modified 11-mer duplexes in native polyacrylamide gels are slower than those of unmodified and modified duplexes containing the stereoisomeric (-)-5-MeCDE-N2-dG lesions. This indicates that the lesions derived from the tumorigenic (+)-5-MeCDE induce greater degrees of bending or local flexibility than the non-tumorigenic (-)-5- MeCDE enantiomer. These differences in the orientational and structural characteristics are similar to those observed with analogous DNA adducts derived from the tumorigenic (+)-7R,8S-dihydroxy-9S,10R-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene and the non-tumorigenic 7S,8R,9R,10S-enantiomer, respectively. The adducts derived from BPDE and 5-MeCDE enantiomers thus display similar characteristics that depend primarily on the PAH diol epoxide enantiomer stereochemistry. This direct synthesis approach can be used to generate milligram quantities of site-specific 5-MeCDE-modified oligonucleotides that are suitable for NMR studies (Cosman, et al., 1995, Biochemistry, 34, 6247-6260).

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Unwinding and hydrodynamic flow linear dichroism characteristics of supercoiled DNA covalently modified with two isomeric methylchrysene diol epoxides of different biological activities

Cited by 3 publications

References 40 publications

Stereochemistry-dependent bending in oligonucleotide duplexes induced by site-specific covalent benzo[a]pyrene diol epoxide-guanine lesions

Stereochemistry-dependent bending in oligonucleotide duplexes induced by site-specific covalent benzo[a]pyrene diol epoxide-guanine lesions

Catalytic transformations of supercoiled DNA as studied by flow linear dichroism technique

Site-specific adducts derived from the binding of anti-5-methylchrysene diol epoxide enantiomers to DNA: Synthesis and characteristics

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