Using Force Spectroscopy To Investigate the Binding of Complementary DNA in the Presence of Intercalating Agents

Abstract

Small molecules are known to bind to DNA via simple intercalation, which leads to the unwinding of the DNA helix. We have demonstrated using force spectroscopy a significant reduction in the unbinding forces measured in a 16-mer DNA duplex in the presence of sequence specific and nonspecific intercalating agents, 3,6-diaminoacridine and ethidium bromide. We also explore the effect of varying the intercalator strength on the unbinding forces measured from the DNA duplexes. At very dilute concentrations of the intercalating agents, the unbinding forces measured are similar to those measured in a hybridizing buffer.

Force measurements with the atomic force microscope: Technique, interpretation and applications

“…Several experiments also have been performed with DNA strands [1078,[1143][1144][1145][1146], DNA-ligands [1147][1148][1149][1150], RNA [1151], RNA-ligands [1152], peptides [1153], and other complementary molecules [389,1154,1155]. In particular, Schumakovitch et al [1156] have studied the temperature dependence of unbinding forces between complementary DNA strands.…”

AFM: a versatile tool in biophysics

“…In this work ten-base-pair resolution has been obtained in the force unzipping and it represents the best resolution to date. The unbinding force dependence on the presence of sequence-specific and unspecific intercalating agents such as 3,6-diaminoacridine and ethidium bromide has been explored [235]. The intercalating compounds lead to a reduction of the unbinding force, probably due to a conformational change of the DNA duplex to accommodate the molecules.…”

Novel stem-loop RNA and drug-bearing DNA hybrid nanostructures specific to LNCaP prostate carcinoma

“…Moreover, we showed that the 40-base long DNA fragments that we used can incorporate anti-cancer drugs such as doxorubicin, which possesses a phenyl ring that can interact with DNA. 35,36 The merger of tumor-specific RNA aptamers and DNA based anti-cancer storage structures yields RNA-DNA hybrid nanostructures that are novel, site-specific drug delivery systems.…”

“…35,36 The merger of tumor-specific RNA aptamers and DNA based anti-cancer storage structures yields RNA-DNA hybrid nanostructures that are novel, site-specific drug delivery systems. The RNAs that we used were able to interact specifically with PSMA markers on prostate cancer cell surfaces.…”

“…34 Dox can intercalate very well into double-stranded DNA and shows strong fluorescence at 585 nm. 35,36 In the past, Dox was selectively bound to prostate specific RNA aptamers with GC-rich regions. 37 Based on these characteristic features, we expected that A10-ds40 hybrids containing doxorubicin would have cancer-specific therapeutic effects in LNCaP cells.…”