Base-sequence dependence of noncovalent complex formation and reactivity of benzo[a]pyrenediol epoxide with polynucleotides

Abstract

The base-sequence selectivity of the noncovalent binding of (+/-)-trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyr ene (BPDE) to a series of synthetic polynucleotides in aqueous solutions (5 mM sodium cacodylate buffer, 20 mM NaCl, pH 7.0, 22 degrees C) was investigated. The magnitude of a red-shifted absorbance at 353 nm, attributed to intercalative complex formation, was utilized to determine values of the association constant Kic. Intercalation in the alternating pyridine-purine polymers poly(dA-dT).(dA-dT) (Kic = 20,000 M-1), poly(dG-dC).(dG-dC) (4200 M-1), and poly(dA-dC).(dG-dT) (9600 M-1) is distinctly favored over intercalation in their nonalternating counterparts poly(dA).(dT) (780 M-1), poly(dG).(dC) (1800 M-1), and poly(dA-dG).(dT-dC) (5400 M-1). Methylation at the 5-position of cytosine gives rise to a significant enhancement of intercalative binding, and Kic is 22,000 M-1 in poly(dG-m5dG).(dG-m5dC). In a number of these polynucleotides, values of Kic for pyrene qualitatively follow those exhibited by BPDE, suggesting that the pyrenyl residue in BPDE is a primary factor in determining the extent of intercalation. Both BPDE and pyrene exhibit a distinct preference for intercalating within dA-dT and dG-m5dC sequences. The catalysis of the chemical reactions of BPDE (hydrolysis to tetrols and covalent adduct formation) is enhanced significantly in the presence of each of the polynucleotides studied, particularly in the dG-containing polymers. A model in which catalysis is mediated by physical complex formation accounts well for the experimentally observed enhancement in reaction rates of BPDE in the alternating polynucleotides; however, in the nonalternating polymers a different or more complex catalysis mechanism may be operative.(ABSTRACT TRUNCATED AT 250 WORDS)

Cytosine Methylation in a CpG Sequence Leads to Enhanced Reactivity with Benzo[a]pyrene Diol Epoxide That Correlates with a Conformational Change

“…Most relevant to the present study, it has been shown through computational analyses (44) that cytosine methylation affords an increased helical stability resulting in increased hydrophobicity and molecular polarizability (51), and it may be these characteristics that lead to the increased reactivity of BPDE at these sites. In agreement with this prediction, the presence of multiple 5-methylcytosines in duplex DNA were shown to result in greater levels of noncovalent intercalation (52). Since BPDE is believed to first intercalate with DNA prior to forming a covalent adduct, an increase in intercalation or an altered structure may lead to the preferential modification seen in this study.…”

Methylation of Cytosine at C5 in a CpG Sequence Context Causes a Conformational Switch of a Benzo[a]pyrene diol epoxide-N2-guanine Adduct in DNA from a Minor Groove Alignment to Intercalation with Base Displacement

“…17,20,21,51,52 While this view has been challenged, 53,54 there is accumulating in vitro evidence that the methylation of cytosine in CpG dinucleotide steps indeed enhances the reactivity of B[a]PDE with the guanine residue in meCpG sequence contexts. 23,24,26,55,56 This effect is most likely associated with the hydrophobicity of the methyl group that enhances both the non-covalent intercalative binding of B[a]PDE to double-stranded poly(dG-me dC)·poly(dG-me dC) and the subsequent yield of covalent [BP]G adduct formation 55,57 as observed in p53 oligonucleotide sequence 17,20,21,23,24,26 and other sequence contexts. 25 …”

Cytosine methylation determines hot spots of DNA damage in the human P 53 gene

“…BPDE forms noncovalent intercalative complexes with double-stranded DNA that are thought to precede covalent binding of BPDE to DNA (51). It has previously been reported that methylation of the 5 position of cytosine gives rise to an enhancement of intercalative BPDE binding to the synthetic polymer poly(dG-dC)⅐(dG-dC) (52). Hydrophobic effects (52) or increased molecular polarizability and base stacking (53) derived from the methyl group may facilitate the creation of an intercalation site for BPDE.…”