Republication – GelApp: Mobile gel electrophoresis analyser

Sim, Jia-Zhi; Nguyen, Phi-Vu; Lee, Hwee-Kuan; Gan, Samuel Ken‐En

doi:10.30943/2019/23122019

Cited by 11 publications

(18 citation statements)

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“…These findings highlighted that compound 1, but not compound 2, inhibited the RT p66 subunits. with GelApp [20] and bands were found to be within the expected size of ~300bp.…”

Section: Experimental Inhibition On Separate Hiv-1 Rt P66 and P51 Submentioning

confidence: 89%

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An alternative HIV-1 non-nucleoside Reverse Transcriptase inhibition mechanism: Targeting the p51 subunit

Chan

Krah

et al. 2019

Preprint

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Since drug resistance mutations in HIV-1 have been increasingly reported to resist most of the current drug repertoire in the antiretroviral therapy, there is a demand for new drugs. In this study, we focused on the viral enzyme Reverse Transcriptase (RT) as it is a good drug target given its absence in non-viruses. Through a reverse transcription assay screen, we found two out of forty compounds from the NCI Diversity Set V to inhibit HIV-1 RT activity. The less potent compound also inhibited MMLV RT. Molecular docking, structural conservation and binding pocket analyses suggested similar binding mechanisms of the dual inhibitor to the targets, implying that the phenylbenzoic scaffold may be potentially used to design broad-spectrum inhibitors against multiple Reverse Transcriptase enzymes from multiple viruses.

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“…These findings highlighted that compound 1, but not compound 2, inhibited the RT p66 subunits. with GelApp [20] and bands were found to be within the expected size of ~300bp.…”

Section: Experimental Inhibition On Separate Hiv-1 Rt P66 and P51 Submentioning

confidence: 89%

“…carried out on the PCR products using 2% agar gels and GAPDH amplified products. Band sizes were confirmed using GelApp [20].…”

Section: Cdna Synthesis Reverse Transcription (Hiv-1)mentioning

confidence: 99%

An alternative HIV-1 non-nucleoside Reverse Transcriptase inhibition mechanism: Targeting the p51 subunit

Chan

Krah

et al. 2019

Preprint

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“…High-fidelity Q5 Polymerase PCR (New England Biolabs) was used to amplify cDNA templates using the following primers for the respective genes: HIV-1 Gag -forward (5 '-TAT TAG GAA TTC ATG GGT GCG AGA GCG-3') and reverse (5' -CTG GTA AAG CTT CTA GTG GTG GTG GTG -3'); for protease -forward (5' -GCG GCC GAA TTC ATG CCT CAA ATC AC -3') and reverse (5' -TAT AAT AAG CTT CTA GTG GTG GTG GTG -3'); for RT p66 -forward (5' -ATG GCC TTG ACC TTT GCT TTA CTG -3') and reverse (5'-CTT GTC GTC ATC GTC TTT GTA GTC -3'); for codon mutated p66 -forward (5'-GCG GTG ATG GAT GGA CCA AAA GTA AA -3') and reverse (5'-CTG CGC CTA ATG ATG ATG ATG AT -3') as per manufacturer's recommendations. PCR products were analysed by gel electrophoresis using GelApp (84) and purified using Gel extraction and PCR purification kits as previously described (85). Purified Q5 Polymerase PCR products were cloned using Zero Blunt TOPO PCR cloning kit (Invitrogen) as per manufacturer's protocol and transformed into in-house competent DH5α cells as previously described (80).…”

Section: Amplification Of Cdna and Topo Cloningmentioning

confidence: 99%

Spontaneous Mutations in HIV-1 Gag, protease, RT p66 in the first replication cycle and how they appear: Insights from anin vitroBSL2 assay on mutation rates and types

Yeo

Koh

Yap

et al. 2019

Preprint

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Drug resistant mutants of HIV-1 is largely credited to its error prone HIV-1 RT, making it an important aspect for investigation. Previous HIV-1 RT studies rely on reporter genes (LacZ) as template, leaving the effects on HIV genes still uncharacterized. To address this, we studied HIV-1 RT mutation rates and bias on the Gag, protease, and RT p66 in an in-vitro selection pressure free assay and found clinical mutations with a general avoidance of key sites and detrimental mutations in the backdrop of mutations rates: 4.71 x 10^-5, 6.03 x 10^-5, and 7.09 x 10^-5 mutations/bp for Gag, protease and RT p66 respectively. Gag and p66 had significant A to G hypermutations we attributed to cellular adenosine deaminases and from comparisons with silently mutated p66 sequences, we observed an increase in mutation rates (1.88 x 10^-4 mutations/bp) and A to G mutations in regions reminiscent of ADAR recognition motifs. Analysis of change in mutational free energies of the A to G mutations revealed a general tendency to avoid destabilizing effects with the natural p66 gene codon usage providing barriers to effects of ADAR. Our study demonstrates the importance of studying mutation emergence in HIV genes to understand how fast drug resistance can emerge, and in this, provide potential transferable understanding to other viruses to how new viral disease and drug resistance can emerge.

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“…Smartphones and tablet are increasingly popular for doing scientific analysis in recent years . Analysis of nucleic sequences is a common task in many fields of biological research, from genetic data analysis to understanding of human disease causations.…”

Section: Introductionmentioning

confidence: 99%

“…These applications are, in fact, researcher assistants that can conveniently analyze data, whenever there exist limitations to access assistant and computers. Recently, some mobile apps have been developed for biological and medical purposes : GelApp for detection and quantification of gel electrophoresis bands, DNA2app and DNAApp for sequence analysis, and YASARA View as an app for molecular modeling. OligoCOOL is an easy tool to use application designed for professionals and amateurs, capable of performing fast and useful nucleic sequence analyses through smartphones and tablets.…”

Section: Introductionmentioning

confidence: 99%

OligoCOOL: A mobile application for nucleotide sequence analysis

Khorsand

Khammari

Shirvanizadeh

et al. 2019

Biochem Molecular Bio Educ

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Today smartphones are inseparable parts of modern life and are capable of performing many desktop computers' tasks such as scientific analysis with greater convenience. Here, we present OligoCOOL, which is an Android application for analyzing nucleic sequences. This application enables users to perform several common biomedical analyses for a given nucleotide sequence. OligoCOOL is a freely accessible Android app at http://bioinf.modares.ac.ir/software/OligoCOOL, which can be a suitable tool for the experimental design in the laboratories. This application also can be used to learn the basics of nucleotide sequence analysis.

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Republication – GelApp: Mobile gel electrophoresis analyser

Cited by 11 publications

References 0 publications

An alternative HIV-1 non-nucleoside Reverse Transcriptase inhibition mechanism: Targeting the p51 subunit

An alternative HIV-1 non-nucleoside Reverse Transcriptase inhibition mechanism: Targeting the p51 subunit

Spontaneous Mutations in HIV-1 Gag, protease, RT p66 in the first replication cycle and how they appear: Insights from anin vitroBSL2 assay on mutation rates and types

OligoCOOL: A mobile application for nucleotide sequence analysis

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