Designing DNA probe from HPV 18 and 58 in the E6 region for sensing element in the development of genosensor‐based gold nanoparticles. (12th October 2021)

• Record Type: Journal Article
• Authors: Jaapar, F. Nadhirah; Parmin, N.A.; Halim, N. Hamidah A; Hashim, Uda; Gopinath, Subash C.B.; Halim, F. Syakirah; Ruslinda, A. Rahim; Voon, C.H.; Uda, M.N.A.; Uda, M.N.Afnan; Nadzirah, Sh.; Rejali, Zulida; Afzan, Amilia; Zakaria, Iffah Izzati
• Is Part Of: Biotechnology and applied biochemistry. Volume 69:Number 5(2022)
• Page Start: 1966
• Page End: 1983
• Publication Date: 2021-10-12
• Subjects: BLAST -- Clustal OMEGA -- DNA probe -- GenBank -- Human Papillomavirus biosensor -- human papillomavirus; Biotechnology -- Periodicals; Biochemical engineering -- Periodicals; Biochemistry -- Periodicals; Biochemistry -- Periodicals; Genetic Techniques -- Periodicals; Microbiological Techniques -- Periodicals; 660.6
• DOI: 10.1002/bab.2260
• Languages: English
• ISSNs: 0885-4513

Abstract

Abstract: The E6 region has higher protuberant probability annealing than consensus probe focusing on another region in the human papillomavirus (HPV) genome in terms of detection and screening method. Here, we designed the first multiple virus single‐stranded deoxyribonucleic acid (ssDNA) for multiple detections in an early phase of screening for cervical cancer in the E6 region and became a fundamental evolution of detection electrochemical HPV biosensor. Gene profiling of the virus ssDNA sequences has been carried by high‐end bioinformatics tools such as GenBank, Basic Local Alignment Searching Tools (BLAST), and Clustal OMEGA in a row. The output from bioinformatics tools resulted in 100% of similarities between our virus ssDNA probe and HPV complete genome in the databases. The cross‐validation between HPV genome and our designed virus ssDNA provided high specificity and selectivity during screening methods compared with Pap smear. The DNA probe for HPV 18, 5′ COOH‐GAT CCA GAA GGT ACA GAC GGG GAG GGC ACG 3′, while 5′COOH‐GGG CGC TGT GCA GTG TGT TGG AGA CCC CGA3′ as DNA probe for HPV 58 designed with 66.77% guanine (G) and cytosine (C) content for both. Our virus ssDNA probe for the HPV biosensor promises high sensitivity, specificity, selectivity, repeatability, low fluid consumption, and will be useful in mini‐size diagnostic devices for cervical cancer detection. Abstract : This study provides knowledge and process on designing virus ssDNA of HPV from E6 region as a probe for developing HPV biosensor. Virus ssDNA designed by facile bioinformatics tools which analyse, identify and finding the similarities with the nucleotides database. The self assemble monolayer of virus ssDNA for HPV 18 and 58 resulted high sensitivity, specificity, and selectivity probe when immobilized on the Interdigitated Electrodes (IDEs) with gold‐nanoparticles (AuNPs).