Intercalator-Induced DNA Superstructure Formation: Doxorubicin and a Synthetic Quinoxaline Derivative

Abstract

Small molecules that intercalate DNA have tremendous therapeutic potential. Typically, DNA intercalators do not alter the overall DNA double-helical structure, except locally at the intercalation sites. In a previous report, we showed that a quinoxaline-based intercalator with a mandatory benzyl substitution (1d) induced an unusually large circular dichroism signal upon DNA binding, suggesting the formation of intercalated DNA superstructures. However, no detailed structural studies have been reported. Using atomic force microscopy, we have probed the nature of the superstructure and report the formation of a plectonemically oversupercoiled structure of pBR322 plasmid DNA by 1d, where close association of distant DNA double-helical stretches is the predominant motif. Without the benzyl moiety (1a), no such DNA superstructure was observed. Similar superstructures were also observed with doxorubicin (dox), a therapeutically important DNA intercalator, suggesting that the superstructure is common to some intercalators. The superstructure formation, for both intercalators, was observed to be GC-specific. Interestingly, at higher concentrations (1d and dox), the DNA superstructure led to DNA condensation, a phenomenon typically associated with polyamines but not intercalators. The superstructure may have important biological relevance in connection to a recent study in which dox was shown to evict histone at micromolar concentrations.

DNA Structural Alteration Leading to Antibacterial Properties of 6-Nitroquinoxaline Derivatives

“…DNA structural change induced by small molecules can also be determined by change in the circular dichroism (CD) spectra of DNA . Appearance of an induced CD (ICD) has a direct relation to the structural change and superstructure formation, which is mediated by close association of DNA bound nitroquinoxaline scaffold. , Titrating calf thymus DNA (CT-DNA) with increasing concentrations of 3a , 3q , or 3u leads to decrease in the typical B-DNA CD peak at 265 nm (Figure A–C). A negative ICD also appeared at 320–325 nm wavelength indicating DNA intercalation induced structural change.…”

“…CD spectra were recorded from 230 to 500 nm at 100 nm/min scan speed. For genomic DNA CD experiment, S. aureus and A. chlorophenolicus genomic DNA was isolated from an overnight grown culture using GenElute bacterial genomic DNA isolation kit from Sigma-Aldrich, genomic DNA concentrations was measured using a Cary 50 Bio UV–vis spectrophotometer, and further experiments were performed following previously described experimental conditions. , …”

“…Considering the importance of the structural integrity of bacterial genome in its survival, we have synthesized a series of monoquinoxaline based derivatives by substitutional tuning of 3g that possesses the distinct ability to induce change in the native DNA structure. These small molecules can cause intercalation induced structural change, which ultimately leads to an over-supercoiled form in a dose dependent manner . The DNA structure-changing property is dependent on the substitution at C-2 and C-3 positions of the 6-nitroquinoxaline scaffold (Figure C), which correlate with the antibacterial properties of these derivatives against Gram-positive bacteria.…”

Cleavage of Abasic Sites in DNA by an Aminoquinoxaline Compound: Augmented Cytotoxicity and DNA Damage in Combination with an Anticancer Drug Chlorambucil in Human Colorectal Carcinoma Cells

“…This binding event leads to histone eviction from in vitro assembled nucleosomes similar to the anticancer drug Doxorubicin. 35 , 36 Moreover, the derivatives of 1d (nitroquinoxaline) were also able to kill certain Gram-positive and Gram-negative bacterial cells causing bacterial DNA damage and morphological alteration of bacterial cells. 37 Besides, quinoxaline derivatives of 1d also bind to HCV RNA at the internal ribosome entry site and inhibit HCV-mediated translation and replication.…”

A Pyrimido‐Quinoxaline Fused Heterocycle Lights Up Transfer RNA upon Binding at the Mg2+ Binding Site

“…Here, we report the design and synthesis of water soluble, fluorescent scaffold which contain quinoxaline and piperazine moieties to achieve a better tRNA binder. Design of compound 1 (Scheme 1) was inspired by the transformation of a DNA intercalator N 2 -benzyl-N 3 -(3-(dimethylamino)propyl)-6-nitroquinoxaline-2,3-diamine [11,12] into a pyrimido-quinoxaline fused ring system. This transformation was needed to avoid the DNA intercalation by the flat quinoxaline ring system in between base pairs of DNA.…”