Observation of a dynamic equilibrium between DNA hairpin and duplex forms of covalent adducts of a minor groove binding agent

Abstract

A dynamic equilibrium between covalent 1:1 hairpin and 2:1 duplex DNA adducts of a pyrrolobenzodiazepine (PBD) minor groove binding agent () has been observed for the first time. The equilibrium, which establishes over 1 hour and must require unfolding of both types of adducts, is surprising given that PBDs normally require DNA minor groove structure for binding and take 24 hours for complete reaction with duplex DNA. The equilibrium is interesting from an energetics perspective due to the well known DNA stabilizing effect of PBDs. This observation could have significance for the in vitro and in vivo biological activity of PBDs, as DNA hairpin and loop structures are known to be important in cellular processes such as transcription and replication.

From Anthramycin to Pyrrolobenzodiazepine (PBD)‐Containing Antibody–Drug Conjugates (ADCs)

“…In addition, a dynamic equilibrium has been observed between DNA hairpin and duplex forms of covalent PBD/DNA adducts. [79] Figure 12. Comparison of the reaction rates of SJG-136 with 12-mer duplex oligonucleotides containing Pu-GATC-Py, Pu-GATG-Py, Pu-GAATC-Py and Pu-GAATG-Py sequences.…”

DNA Sequence Preference and Adduct Orientation of Pyrrolo[2,1-c][1,4]benzodiazepine Antitumor Agents

“…It is known from previous studies that only covalent adducts provide MALDI TOF signals, as noncovalent adducts do not survive conditions within a mass spectrometer. 16 Annealed Seq-1 gave a single peak at RT 26.0 min, which was collected and identified by MALDI-TOF-MS ( Figure 3A). Preincubation of Seq-1 with 2 for 30 min at room temperature followed by immediate injection onto the HPLC column resulted in the rapid appearance of a new peak at RT 27.0 min ( Figure 3B) with near complete disappearance of Seq-1 by 60 min ( Figure 3C).…”

“…12,13 More specifically, 2 has been shown to inhibit binding of the NFΥ transcription factor to its cognate sequences (e.g., CCAAT) within the topoisomerase IIR promoter region, thus causing a decrease in topo IIR expression and blocking cell cycle progression, ultimately leading to apoptosis. A high-performance liquid chromatography/mass spectrometry (HPLC/MS) assay developed in our laboratory [14][15][16] has been used to study the reaction of 2 with a set of eight hairpin oligonucleotides ( Table 1) to establish both the rate of alkylation and the orientation of the PBD molecule in the adducts formed. Each oligonucleotide contained a single PBD-binding triplet at one of two different locations, with the triplets containing all possible combinations of X-G-X, where X was either A or T. The use of G or C (for X) was avoided to limit the number of possible sites of covalent interaction to one per oligonucleotide.…”

Entwicklung Pyrrolobenzodiazepin(PBD)‐haltiger Antikörper‐Wirkstoff‐Konjugate (ADCs) ausgehend von Anthramycin

“…Chemie Aufsätze 486 www.angewandte.de namisches Gleichgewicht zwischen den DNA-Haarnadelund DNA-Duplex-Formen von kovalenten PBD/DNA-Addukten [79] gefunden. Insgesamt zeigten diese HPLC-und Modellierungsstudien, dass SJG-136 ein breiteres Spektrum kovalenter DNAAddukte bilden kann, als ursprünglich angenommen.…”