Biology subjects

Arumugam, A.

Publications and source records attributed to Arumugam, A..

4 recordsLinked to original sources

bioRxiv2025

The Ski2 helicase ASCC3 unwinds DNA upon fork stalling to control replication stress responses

The activating signal co-integrator 1 complex subunit 3 (ASCC3), the largest subunit of ASCC, is one of two Ski2-like helicases with duplicated helicase cassettes encoded by the human genome. ASCC3 has been implicated in transcriptional regulation, alkylation damage repair, and ribosome quality control. In addition, published proteomics studies suggest that ASCC3 is associated with stalled forks. However, little is known about its role in replication stress. Here we report that ASCC3 is recruited to stalled forks by its binding partner ASCC2, whose recruitment to stalled forks is dependent upon both its ubiquitin binding activity and polyubiquitylation of PCNA at K164 that is catalyzed by SHPRH, HLTF, and RFWD3. In response to replication stress. ASCC3 unwinds DNA, generating both parental and nascent ssDNA. This unwinding activity is required to promote fork reversal. We demonstrate that ASCC3 also interacts with RPA and stimulates RPA accumulation on ssDNA upon replication stress, promoting ATR activation. Furthermore, ASCC3 functions to antagonize RAD51-mediated recombination and prevents accumulation of chromosome breaks/gaps and mis-segregation in response to replication stress. Our work underscores a previously uncharacterized but critical role of ASCC3 in controlling multiple replication stress responses to maintain genomic stability.

molecular biology↗

bioRxiv2021

Identification of potential carboxylic acid-containing drug candidate to design novel competitive NDM inhibitors: An in-silico approach comprising combined virtual screening and molecular dynamics simulation

Metallo-{beta}-lactamases (MBLs) producing bacteria especially the ones with New Delhi metallo-beta-lactamase-1 (NDM-1) and its variants can potentially hydrolyse all the major {beta}-lactam antibiotics, ultimately escalating anti-microbial resistance world-wide. There is a dearth of approved inhibitors to combat NDM and other MBLs producing bacteria. Hence we focussed to find novel inhibitor(s) in-silico which can potentially suppress the activity of NDM/ MBLs. 2400 compounds were virtually screened to identify a promising carboxylic acid-containing compound (CID-53986787) analogous to NDM antagonist Captopril. Our lead compound can bind adjacent to the active site zinc ions (Zn1 and Zn2) in all highly resistant NDM variants. CID-53986787 possesses ~5-8% higher binding affinity than Captopril, exhibiting molecular interactions with crucial residues that can destabilize the hydrolytic activity of NDM. CID-53986787 was virtually evaluated to ascertain its safe pharmacological/ toxicity profile. Molecular dynamics simulation studies elucidated its stable interaction with the target protein (NDM-1).

bioinformatics↗

bioRxiv2020

A Rapid COVID-19 RT-PCR Detection Assay for Low Resource Settings

Quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is the gold standard recommended to test for acute SARS-CoV-2 infection. It has been used by the Centers for Disease Control and Prevention (CDC) and several other companies in their Emergency Use Authorization (EUA) assays. RT-qPCR requires expensive equipment such as RNA isolation instruments and real-time PCR thermal cyclers, which are not available in many low resource settings and developing countries. As a pandemic, COVID-19 has quickly spread to the rest of the world. Many underdeveloped and developing counties do not have the means for fast and accurate COVID-19 detection to control this outbreak. Using COVID-19 positive clinical specimens, we demonstrated that RT-PCR assays can be performed in as little as 12 minutes using untreated samples, heat-inactivated samples, or extracted RNA templates. Rapid RT-PCR was achieved using thin-walled PCR tubes and a setup including sous vide immersion heaters/circulators. Our data suggest that rapid RT-PCR can be implemented for sensitive and specific molecular diagnosis of COVID-19 in situations where sophisticated laboratory instruments are not available.

molecular biology↗

bioRxiv2020

The Potential Use of Unprocessed Sample for RT-qPCR Detection of COVID-19 without an RNA Extraction Step

Quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is the gold standard recommended to test for acute SARS-CoV-2 infection.1-4 It has been used by the Centers for Disease Control and Prevention (CDC) and several other companies in their Emergency Use Authorization (EUA) assays. With many PCR-based molecular assays, an extraction step is routinely used as part of the protocol. This step can take up a significant amount of time and labor, especially if the extraction is performed manually. Long assay time, partly caused by slow sample preparation steps, has created a large backlog when testing patient samples suspected of COVID-19. Using flu and RSV clinical specimens, we have collected evidence that the RT-qPCR assay can be performed directly on patient sample material from a nasal swab immersed in virus transport medium (VTM) without an RNA extraction step. We have also used this approach to test for the direct detection of SARS-CoV-2 reference materials spiked in VTM. Our data, while preliminary, suggest that using a few microliters of these untreated samples still can lead to sensitive test results. If RNA extraction steps can be omitted without significantly affecting clinical sensitivity, the turn-around time of COVID-19 tests and the backlog we currently experience can be reduced drastically. Next, we will confirm our findings using patient samples.

molecular biology↗