Computational prediction of the melting temperature of a DNA biosensor to detect Mycobacterium tuberculosis

Alvarado-González, Mónica; Flores-Holgúın, Norma; Gallo, Marco; Orrantia‐Borunda, Erasmo; Glossman‐Mitnik, Daniel

doi:10.1016/j.theochem.2009.03.003

Cited by 3 publications

References 18 publications

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DFT study of the interaction between the conjugated fluorescein and dabcyl system, using fluorescene quenching method

et al. 2012

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Molecular beacon is a DNA probe containing a sequence complementary to the target that is flanked by self-complementary termini, and carries a fluorophore and a quencher at the ends. We used the fluorescein and dabcyl as fluorophore and quencher respectively, and studied with DFT calculations at the GGA/DNP level, and taking into account DFT dispersion corrections by the Grimme and Tkatchenko-Scheffler (TS) schemes, the distance, where the most favorable energetic interaction between the fluorophore and quencher in conjugated form occurs. This distance occurs at a separation distance of 29.451 Å between the centers of Dabcyl and fluorescein employing the TS DFT dispersion correction scheme, indicating FRET efficiency around 94.28 %. The calculated emission spectra of the conjugated pair in water indicated that the emission and absorption spectrum overlap completely and thus no fluorescence can be observed due to the fluorescence resonance energy transfer (FRET) effect. The DFT results confirmed the experimentally observing fluorescence quenching of the fluorescein-dabcyl conjugated system by FRET.

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DFT study of the interaction between the conjugated fluorescein and dabcyl system, using fluorescene quenching method

et al. 2012

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Zinc selenide based dual-channel SPR optical biosensor for HIV genome DNA hybridization detection

El-assar,

Taha,

El-Samie

et al. 2023

Opt Quant Electron

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Simultaneous measurement of human immunodeficiency virus (HIV) genome DNA hybridization and the DNA melting temperature in a prism-based surface plasmon resonance (SPR) biosensor is modeled theoretically using a simple dual-channel construction. The proposed sensor consists of a BK7 prism coated with silver as a plasmonic material. The metal surface is divided into two channels to detect medium refractive index (RI) and temperature. One half is covered with zinc selenide (ZnSe) semiconductor to enhance the hybridization detection sensitivity and to protect silver from oxidation. The other half is covered with polydimethylsiloxane (PDMS) polymer to detect the temperature variations. The proposed sensor is optimized numerically, and the optimum structure provides an excellent sensitivity of 208 deg/RIU, thanks to the use of the ZnSe layer, which is greater than double the reported dual-channel prism-based sensor in thickness. The polymer channel shows high sensitivity to the temperature variations of − 0.125 deg/°C, which is nearly 10 times the response of the RI channel to temperature variations. The data obtained from the polymer channel is used to compensate for the thermal perturbations of the sensing medium RI, and at the same time, to monitor the increments of the temperature in order to avoid reaching the DNA melting temperature. A mathematical expression is provided to consider the effect of the temperature variations on the RI of the sensing medium to get a better accurate detection process. The DNA hybridization detection of HIV is theoretically discussed in detail starting from the preparation of the sensing medium with the different ingredients until the hybridization between probe and complementary target DNA (ct-DNA) molecules.

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Exploring the Chemical Reactivity andBioactivity of Romidepsin: A CDFT-BasedComputational Peptidology Study

Flores-Holguín,

Frau,

Glossman-Mitnik

2023

Preprint

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Romidepsin is a cyclic peptide derived from a natural product that has shown remarkable therapeutic potential for the treatment of cancer and other diseases. In this study, we employ a CDFT-based Computational Peptidology methodology to investigate the chemical reactivity and bioactivity properties of Romidepsin. Our approach combines conceptual density functional theory descriptors with cheminformatics tools to estimate the bioactivity scores, and identify the drug-likeness of Romidepsin. Our results provide insights into the potential of Romidepsin as a useful drug candidate for various therapeutic applications beyond cancer treatment.

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Computational prediction of the melting temperature of a DNA biosensor to detect Mycobacterium tuberculosis

Cited by 3 publications

References 18 publications

DFT study of the interaction between the conjugated fluorescein and dabcyl system, using fluorescene quenching method

DFT study of the interaction between the conjugated fluorescein and dabcyl system, using fluorescene quenching method

Zinc selenide based dual-channel SPR optical biosensor for HIV genome DNA hybridization detection

Exploring the Chemical Reactivity andBioactivity of Romidepsin: A CDFT-BasedComputational Peptidology Study

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