Chemistry of the Bleomycin-Induced Alkali-Labile DNA Lesion

Abstract

Treatment of B-form DNA with the antitumor antibiotic bleomycin in the presence of Fe2+ and O2 affords both DNA strand scission and the formation of alkali-labile lesions, the proportion of which is quite sensitive to the concentration of O2 present. The alkali-labile lesions can undergo fragmentation cleanly in the presence of n-butylamine to afford DNA fragments containing 5‘- and 3‘-phosphate termini at the site of the alkali-labile lesion. The mechanism of decomposition of the alkali-labile lesion was studied, leading to identification of a putative intermediate that is converted readily to an (oligo)nucleotide 3‘-phosphate in the presence of n-BuNH2, as well as the identification of the byproduct of the fragmentation reaction containing the carbon atoms originally present within the alkali-labile lesion.

Thermodynamics and kinetics of the cleavage of DNA catalyzed by bleomycin A5

“…The v 2 value of Eqn (18) used to perform a nonlinear least-squares analysis for the binding of BLM-A 5 to DNA is 0.0268, indicating a good appropriateness of the model proposed. The remaining standard thermodynamic parameters for the binding, D b G 0 m and D b S 0 m , are calculated by Eqns (19) and (20), respectively.…”

“…It has been found that BLM-induced autoxidation of ferrous iron follows the Michaelis-Menten kinetics [9,10]. Although a significant number of experimental approaches have been used to elucidate the mechanism of DNA cleavage by BLM in the past two decades [2][3][4][5][6][11][12][13][14][15][16][17][18][19][20], thermodynamic information for the scission, which is necessary for a thorough understanding of the mechanism, is eagerly awaited. The purpose of this investigation is to provide detailed thermodynamic and kinetic data for BLMmediated DNA degradation to furnish insights into the anticancer mechanism of BLM.Microcalorimetry is an important tool for the study of both thermodynamic and kinetic properties of biological macromolecules by virtue of its general applicability, high accuracy and precision [21][22][23][24].…”

Identification and Characterization of an Intermediate in the Alkali Degradation of (6-4) Photoproduct-containing DNA

“…This alkali lability has also been applied for footprinting experiments to analyze protein-DNA interactions in vivo (13,14). While the reactions of other alkali-labile DNA damages such as the apurinic/apyrimidinic (AP) site (15) and the bleomycin-induced lesion (16) have been analyzed in detail, the mechanism of the strand break caused at the (6-4) photoproduct by the alkali treatment has not been elucidated so far. Franklin et al (8) suggested the hydrolysis of the glycosyl bond of the 3Ј component of this photoproduct, but there have been no subsequent reports.…”

Bioconjugation of Oligodeoxynucleotides Carrying 1,4-Dicarbonyl Groups via Reductive Amination with Lysine Residues

“…15 We found that OAS reacted efficiently with a primary amine under mild conditions to yield lactam 4 and ODN fragments; this did not require additional reagents. [16][17][18] The ability of the 1,4-dicarbonyl system in 3 to form kinetically and thermodynamically favored 5-membered-ring aminal 5 19 results in facile lactam formation. We envisaged that bioconjugation of an ODN containing an OAS with lysine residues in close proximity to the C1-aldehyde and/or the C-4 ketone in the Scheme 1.…”