Computational approaches screening DNA aptamers against conserved outer membrane protein W of Vibrio cholerae O1- an investigation expanding the potential for point-of-care detection with aptasensors

Abstract

Foodborne outbreaks urge public health domain to upgrade diagnosis by means of simpler, quicker, and more affordable pathogen detection methods. A molecular recognition probe against an analyte of interest makes up a biosensor, along with a method for turning the recognition event into a quantifiable signal. Single-stranded DNA or RNA aptamers are promising bio-recognition molecules for a range of targets, including a wide range of non-nucleic acid targets with which they are highly specific and affine. In the proposed study, 40 DNA aptamers were screened and analyzed interactions using in-silico SELEX procedures, which can selectively interact with active sites at the extracellular region of the Outer membrane Protein W (OmpW) of Vibrio Cholerae. Multiple modeling techniques, like protein structural prediction with I-TASSER, aptamer structural modeling using M-fold, RNA composer, protein-DNA docking using HADDOCK, and large-scale (500 ns) molecular dynamics simulations through GROMACS have been employed. Out of 40, six aptamers having lowest free energy were docked against the predicted active site at the extracellular region of OmpW. VBAPT4-OmpW and VBAPT17-OmpW, the two highest-scoring Aptamer-Protein complexes, were chosen for molecular dynamics simulations. VBAPT4-OmpW is quite unable to attain its structural local minima after 500 ns. But VBAPT17-OmpW is showing great stability and is not destructive even after 500 ns. RMSF, DSSP, PCA, and Essential Dynamics all provided additional confirmation. Current findings, combined with the fabrication of biosensor devices, could pave the way for an innovative pathogen detection platform with high sensitivity, along with an effective and low-impact curative strategy for corresponding diseases.

Communicated by Ramaswamy H. Sarma

Keywords:

• DNA-aptamers
• Vibrio cholerae
• outer membrane protein W (OmpW)
• detection
• molecular docking
• molecular simulation

Acknowledgements

Author Lipi Poojara would like to extend gratitude for student support fellowship provided by ScHeme of Developing High quality research (SHODH), Education department, Government of Gujarat, India. Also, I really appreciate guidance and constant support received from Dr. Dweipayan Goswami, Jignesh Prajapati, Khushali thaker and Jaimini Patoliya.

Disclosure statement

The author has no conflict of interest to declare.

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.