Fluorescence and circular dichroism studies on binding and conformational aspects of an anti-leukemic drug with DNA

Hegde, Ashwini; Seetharamappa, J.

doi:10.1007/s11033-013-2838-2

Cited by 21 publications

(10 citation statements)

References 22 publications

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“…We also detected a much smaller increase in the ellipticity at~240 nm, which refers to the slight decrease in helicity for both poly AU and poly GC. Both of these results are key indicators of intercalation [48,49]. Therefore, our circular dichroism analysis further supports that synthetic dsRNAs adopted A-form helix and that MC can intercalate between RNA base pairs to cause increased stacking.…”

Section: Only the Open MC Form Interacts With Dsrnassupporting

confidence: 78%

Spiropyran as a potential molecular diagnostic tool for double-stranded RNA detection

et al. 2019

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Background: Long double-stranded RNAs (dsRNAs) are duplex RNAs that can induce immune response when present in mammalian cells. These RNAs are historically associated with viral replication, but recent evidence suggests that human cells naturally encode endogenous dsRNAs that can regulate antiviral machineries in cellular contexts beyond immune response.Results: In this study, we use photochromic organic compound spiropyran to profile and quantitate dsRNA expression. We show that the open form of spiropyran, merocyanine, can intercalate between RNA base pairs, which leads to protonation and alteration in the spectral property of the compound. By quantifying the spectral change, we can detect and quantify dsRNA expression level, both synthetic and cellular. We further demonstrate that spiropyrans can be used as a molecular diagnostic tool to profile endogenously expressed dsRNAs. Particularly, we show that spiropyrans can robustly detect elevated dsRNA levels when colorectal cancer cells are treated with 5-aza-2′-deoxycytidine, an FDAapproved DNA-demethylating agent used for chemotherapy, thus demonstrating the use of spiropyran for predicting responsiveness to the drug treatment. Conclusion:As dsRNAs are signature of virus and accumulation of dsRNAs is implicated in various degenerative disease, our work establishes potential application of spiropyrans as a simple spectral tool to diagnose human disease based on dsRNA expression.

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Section: Only the Open MC Form Interacts With Dsrnassupporting

confidence: 78%

Spiropyran as a potential molecular diagnostic tool for double-stranded RNA detection

et al. 2019

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“…For the static quenching process, the binding constant (K) and the number of BHA bound per ctDNA (n) of the system can be determined based on the following equation [37]:…”

Section: Quenching Mechanism and Binding Constantsmentioning

confidence: 99%

Intercalation binding of food antioxidant butylated hydroxyanisole to calf thymus DNA

Wang

Zhang

Pan

et al. 2014

Journal of Photochemistry and Photobiology B: Biology

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“…The binding constant between BPO and ctDNA could be determined through the modified Stern–Volmer equation:

\frac{F_{0}}{F_{0} - F} = \frac{1}{f_{a} K_{a}} \frac{1}{[Q]} + \frac{1}{f_{a}}

where K a and ƒ a mean the modified Stern–Volmer association constant for the accessible fluorophores and the fraction of accessible fluorescence. The K a values at different temperatures obtained by a linear regression of F 0 /( F 0 – F ) versus 1/[Q] (Table ) showed a conformity with those of the intercalators, such as AO (2.69 × 10 4 L mol –1 ), ethidium bromide (6.58 × 10 4 L mol –1 ), and methylene blue (2.13 × 10 4 L mol –1 ) .…”

Section: Resultsmentioning

confidence: 99%

Deciphering the intercalative binding modes of benzoyl peroxide with calf thymus DNA

2017

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The binding of benzoyl peroxide (BPO), a flour brightener, with calf thymus DNA (ctDNA) was predicted by molecular simulation, and this were confirmed using multi-spectroscopic techniques and a chemometrics algorithm. The molecular docking result showed that BPO could insert into the base pairs of ctDNA, and the adenine bases were the preferential binding sites which were validated by the analysis of Fourier transform infrared spectra. The mode of binding of BPO with ctDNA was an intercalation as supported by the results from ctDNA melting and viscosity measurements, iodide quenching effects and competitive binding investigations. The circular dichroism and DNA cleavage assays indicated that BPO induced a conformational change from B-like DNA structure towards to A-like form, but did not lead to significant damage in the DNA. The complexation was driven mainly by hydrogen bonds and hydrophobic interactions. Moreover, the ultraviolet-visible (UV-vis) spectroscopic data matrix was resolved by a multivariate curve resolution-alternating least-squares algorithm. The equilibrium concentration profiles for the components (BPO, ctDNA and BPO-ctDNA complex) were extracted from the highly overlapping composite response to quantitatively monitor the BPO-ctDNA interaction. This study has provided insights into the mechanism of the interaction of BPO with ctDNA and potential hazards of the food additive.

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Fluorescence and circular dichroism studies on binding and conformational aspects of an anti-leukemic drug with DNA

Cited by 21 publications

References 22 publications

Spiropyran as a potential molecular diagnostic tool for double-stranded RNA detection

Spiropyran as a potential molecular diagnostic tool for double-stranded RNA detection

Intercalation binding of food antioxidant butylated hydroxyanisole to calf thymus DNA

Deciphering the intercalative binding modes of benzoyl peroxide with calf thymus DNA

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