DNA-Destabilizing Agents as an Alternative Approach for Targeting DNA: Mechanisms of Action and Cellular Consequences

Abstract

DNA targeting drugs represent a large proportion of the actual anticancer drug pharmacopeia, both in terms of drug brands and prescription volumes. Small DNA-interacting molecules share the ability of certain proteins to change the DNA helix's overall organization and geometrical orientation via tilt, roll, twist, slip, and flip effects. In this ocean of DNA-interacting compounds, most stabilize both DNA strands and very few display helix-destabilizing properties. These types of DNA-destabilizing effect are observed with certain mono- or bis-intercalators and DNA alkylating agents (some of which have been or are being developed as cancer drugs). The formation of locally destabilized DNA portions could interfere with protein/DNA recognition and potentially affect several crucial cellular processes, such as DNA repair, replication, and transcription. The present paper describes the molecular basis of DNA destabilization, the cellular impact on protein recognition, and DNA repair processes and the latter's relationships with antitumour efficacy.

Figure 1

Schematic representation of DNA structure. (a) Base pair orientation with x, y, and z axes result in different kind of rotation (tilt, roll, twist) or slipping of the bases (slide, flip) regarding to the helix central axis. (b) Native B-DNA with nearly 11 base pairs within one helix turn. (c) Mono- or bis-intercalation between adjacent base pairs result in an unwinding of the DNA helix (orange arrow on the top) and a lengthening of the DNA helix (ΔLength) depending on the x° and y Å values that are specific for a defined DNA intercalating compound. (d) Representation of the DNA bending, base flipping, or double strand opening induced by some DNA destabilizing alkylating agents (adduct). Adapted from Calladine and Drew's schematic boxes representation [13].

Figure 2

Mono- and bis-intercalating compounds inducing local destabilization of the DNA helix. (a) Structure of the compounds. (b) Three-dimensional organisation of morpholino doxorubicin bound to d(CGTACG) (left panel) and of ellipticine (right panel) intercalated between adjacent base pairs (from crystallographic data [mmdbId:52942] and [mmdbId:52189], respectively, [73, 74]).

Figure 3

Platinium derivatives. (a) Examples of platinated agents inducing local destabilization of the DNA helix. (b) The three-dimensional organization of cisplatin bound to DNA are drawn from crystallographic data [mmdbId:47796] [92] and evidenced strong DNA bending induced by cisplatin on a duplex DNA decamer oligonucleotide that fits with the L-shape angle of HMG-box DNA-binding domain.

Figure 4

Ruthenium derivatives. Ru-CYM, Ru-BIP, Ru-DHA, and Ru-THA are examples of ruthenium-containing agents inducing local destabilization of the DNA helix.

Figure 5

Other DNA alkylating agents inducing local destabilization of the DNA helix. (a) Structures of some DNA alkylating molecules that destabilize the DNA helix. (b) Three-dimensional organization of the psoralen derivative HMT (a) and (+)-anti-BPDE (b) bound to DNA (crystallographic data [mmdbId:52343] [118] and [mmdbId:52106], respectively, [119]).

Figure 6

DNA destabilization propensities of the benzo-acronycine dicarbamate derivative S29385-1. (a) CT-DNA was incubated with increasing concentrations of S29385-1 prior to the incubation with a mixture of ethidium bromide (BET) and Picogreen (PG from Molecular Probes, Invitrogen) to quantify only double-strand DNA or both double-strand and single-stranded DNA, respectively. Results are expressed as the percentage of the peak of emission for BET versus PG. (b) Variation of the melting temperature studies of a short 24-bp double-strand oligonucleotide incubated for 24 hours alone or with increasing concentrations of S29385-1 prior to ethanol precipitation of the sample and melting temperature measurement. The results are expressed as the melting temperature for the [DNA+drug] complex minus melting temperature for DNA alone. (Details for the corresponding experimental protocols are described in [91].)

Figure 7

Nuclease S1 mapping of locally opened DNA structure. Increasing concentrations of the benzo-b-acronycine derivatives presented in Figure 5 were incubated with a radio-labelled 117-bp DNA fragment prior to subjection to nuclease S1 mapping of the induced locally single-stranded DNA portions generated upon DNA alkylation. DNA samples were separated on a 10% native polyacrylamide gel. Concentrations are expressed in μM. The detailed experimental protocol is described in [91].