Homogeneous assay for detection of active Epstein-Barr nuclear antigen 1 by thrombin activity modulation

Structural and Biophysical Investigation of the Key Hotspots on the Surface of Epstein-Barr Nuclear Antigen 1 Essential for DNA Recognition and Pathogenesis

Epstein-Barr Virus (EBV) is considered the most important human pathogen due to its role in infections and cellular malignancies. It has been reported that this Oncolytic virus infects 90% world’s population. EBNA1 is required for DNA binding and survival of the virus and is considered an essential drug target. The biochemical and structural properties of this protein are known, but it is still unclear which residues impart a critical role in the recognition of dsDNA. Intending to disclose only the essential residues in recognition of dsDNA, this study used a computational pipeline to generate an alanine mutant of each interacting residue and determine the impact on the binding. Our analysis revealed that R469A, K514A, Y518A, R521A and R522A are the key hotspots for the recognition of dsDNA by the EBNA1. The dynamics properties, i.e. stability, flexibility, structural compactness, hydrogen bonding frequency, binding affinity, are altered by disrupting the protein-DNA contacts, thereby decreases the binding affinity. In particular, the two arginine substitution, R521A and R522A, significantly affected the total binding energy. Thus, we hypothesize that these residues impart a critical role in the dsDNA recognition and pathogenesis. This study would help to design structure-based drugs against the EBV infections.

Aptamer-based turn-on detection of thrombin in biological fluids based on efficient phosphorescence energy transfer from Mn-doped ZnS quantum dots to carbon nanodots

This paper presents the first example of a sensitive, selective, and stable phosphorescent sensor based on phosphorescence energy transfer (PET) for thrombin that functions through thrombin-aptamer recognition events. In this work, an efficient PET donor-acceptor pair using Mn-doped ZnS quantum dots labeled with thrombin-binding aptamers (TBA QDs) as donors, and carbon nanodots (CNDs) as acceptors has been constructed. Due to the π-π stacking interaction between aptamer and CNDs, the energy donor and acceptor are taken into close proximity, leading to the phosphorescence quenching of donors, TBA QDs. A maximum phosphorescence quenching efficiency as high as 95.9% is acquired. With the introduction of thrombin to the "off state" of the TBA-QDs-CNDs system, the phosphorescence is "turned on" due to the formation of quadruplex-thrombin complexes, which releases the energy acceptor CNDs from the energy donors. Based on the restored phosphorescence, an aptamer-based turn-on thrombin biosensor has been demonstrated by using the phosphorescence as a signal transduction method. The sensor displays a linear range of 0-40 nM for thrombin, with a detection limit as low as 0.013 nM in pure buffers. The proposed aptasensor has also been used to monitor thrombin in complex biological fluids, including serum and plasma, with satisfactory recovery ranging from 96.8 to 104.3%. This is the first time that Mn-doped ZnS quantum dots and CNDs have been employed as a donor-acceptor pair to construct PET-based biosensors, which combines both the photophysical merits of phosphorescence QDs and the superquenching ability of CNDs and thus affords excellent analytical performance. We believe this proposed method could pave the way to a new design of biosensors using PET systems.