DisCoVer: Aptamer biosensors for the detection of SARS-CoV-2 on surfaces
Lead Research Organisation:
King's College London
Department Name: Analytical & Environmental Sciences
Abstract
The high survivability of SARS-CoV-2 on surfaces, such as metal, plastic, glass and some fabrics, means that fomite transmission is likely to play a key role in the spread of nosocomial COVID-19 infections. With effective vaccines or counteractive drugs against the virus yet to be fully realised, effective monitoring of surfaces potentially contaminated with SARS-CoV-2 is vital to managing infection rates and protecting healthcare workers.
However, such environmental monitoring efforts are limited by the length of current viral testing processes (i.e. through swabbing, genomic extraction and RT-PCR), which prevents the identification of viral contamination in real-time. Biosensors, a group of molecules able to produce measurable signals in response to biological interactions, may overcome these challenges by allowing the rapid, specific and sensitive detection of SARS-CoV-2 in situ, without the need for extensive processing or specialised equipment. This work will therefore involve the development of an optical biosensor towards SARS-CoV-2 based on aptamer recognition. Through delivery to surfaces as part of an aerosolised spray reagent, this sensor will allow the 'stand-off' visualisation of viral deposits through the production of discrete areas of fluorescence thereby allowing healthcare workers to quickly triage objects in need of decontamination. Biosensor construction will be based on a 'molecular beacon' design, in which an initially quenched dual-labelled probe is restored to a fluorescent state upon SARS-CoV-2 binding. Fluorescence emission signals will be provided by bright and highly stable conjugated polymer nanoparticles, whilst molecular dynamics simulation and modelling studies will be
used to ensure high biosensor specificity/sensitivity.
However, such environmental monitoring efforts are limited by the length of current viral testing processes (i.e. through swabbing, genomic extraction and RT-PCR), which prevents the identification of viral contamination in real-time. Biosensors, a group of molecules able to produce measurable signals in response to biological interactions, may overcome these challenges by allowing the rapid, specific and sensitive detection of SARS-CoV-2 in situ, without the need for extensive processing or specialised equipment. This work will therefore involve the development of an optical biosensor towards SARS-CoV-2 based on aptamer recognition. Through delivery to surfaces as part of an aerosolised spray reagent, this sensor will allow the 'stand-off' visualisation of viral deposits through the production of discrete areas of fluorescence thereby allowing healthcare workers to quickly triage objects in need of decontamination. Biosensor construction will be based on a 'molecular beacon' design, in which an initially quenched dual-labelled probe is restored to a fluorescent state upon SARS-CoV-2 binding. Fluorescence emission signals will be provided by bright and highly stable conjugated polymer nanoparticles, whilst molecular dynamics simulation and modelling studies will be
used to ensure high biosensor specificity/sensitivity.
Organisations
Publications
Ishkhanyan H
(2022)
NSAID solubilisation promotes morphological transitions in Triton X-114 surfactant micelles
in Journal of Molecular Liquids
López-Ríos De Castro R
(2023)
Topology-controlled self-assembly of amphiphilic block copolymers.
in Nanoscale
Santana-Bonilla A
(2023)
Modular Software for Generating and Modelling Diverse Polymer Databases
Santana-Bonilla A
(2023)
Modular Software for Generating and Modeling Diverse Polymer Databases.
in Journal of chemical information and modeling
Ziolek RM
(2022)
Conformational Heterogeneity and Interchain Percolation Revealed in an Amorphous Conjugated Polymer.
in ACS nano
| Description | This project aims to develop an optical aptamer-based biosensor for SARS-CoV-2 detection on surfaces using DNA aptamer as target binding component and fluorescent nanometerials as signalling moiety. Two DNA aptamers were identified from a published literature with strong binding to RBD protein of SARS-CoV-2 virus. Upon further investigation using various biophyscial techniques, these DNA aptamers demonstrated high RBD binding regardless of the 5'-end modification and immobilisation. This suggested good application of functionalising aptamers onto nanomaterial surface and aptasensor design. Further evaluation of the aptamer sequennce revealed the significance of aptamer's tertairy strucutre for RBD protein binding interaction. This information is essential for construction of the aptasensor and the detection of SARS-CoV-2 virus on surfaces. Various fluorescene turn-on assays from published literatures were evaluated to determine the best approach for our aptasensor design. An extensive work on in silico modelling has been performed to establish a suitable computational tool to study the tertiary structure of DNA aptamers and in silico interaction of the binding partners. This complements binding studies of DNA aptamer to the target protein(s) on SARs-CoV-2 virus. |
| Exploitation Route | For the first time, the in silico modelling allows reliable simulation of DNA aptamers' tertiary structures and their binding interactions with target partners. This can be used to any DNA aptamers development with any target molecules of interest. While the design and application of this novel aptamer-based biosensor will be directly important to SARS-CoV-2 virus detection, this biosensing system can also be applicable to virtually any types of target ligands. |
| Sectors | Education Environment Healthcare Other |
| Title | PySoftK |
| Description | Python Soft-matter King's College London (PySoftK) is a set of tools and Python modules for setting up, manipulating, and running atomistic simulations of polymers. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | By simply inputting the SMILES code(s) for the desired monomer(s), the code allows the user to build polymers with different compositions (homopolymers, block heterpolymers, sequenced heteropolymers and random heteropolymers) and topologies (linear and ring). In the end the code generates an equilibrated structure of the polymer that can be used as an input for building the desired initial configuration for a molecular dynamics simulation. |
| URL | https://alejandrosantanabonilla.github.io/pysoftk/ |
| Title | pySoftWhere |
| Description | pySoftWhere is a Python library for analyzing interfaces of soft matter nanostructures, such as micelles, nanoparticles, monolayers, and polymer films. N.B.: This project is still in development! |
| Type Of Technology | Webtool/Application |
| Year Produced | 2022 |
| Impact | pySoftWhere is a Python library for analyzing interfaces of soft matter nanostructures, such as micelles, nanoparticles, monolayers, and polymer films. |
| URL | https://pysoftwhere.readthedocs.io/en/latest/usage.html |
| Description | AEFS seminar |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | A departmenal seminar to inform and showcase the project and technical advances behind it. The seminar reaches out to researchers and academics within the department which allows a better understanding of the aptamer work and how it is appicable to COVID area. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Aptamer 2023 Oxford conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | A poster presentation at an international Aptamer conference to a group of experts on aptamers development and aptamer-based biosensor design. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Aptamer conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Poster presentation at Aptamer conference to a group of experts on aptamers development and aptamer-based biosensor design. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Research group meetings |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | With the nature of this project involving the multi-disciplinary of researchers from different fields, monthly meetings have been utilised as the means for group members to present their work progress and exchange knowledge and key findings. |
| Year(s) Of Engagement Activity | 2021,2022 |
| Description | Rob's CANES seminar |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Rob Ziolek, who is a PDRA funded by the grant, was invited to give a seminar on his work during the project at the CANES Centre for Doctoral Training's seminar series. The talk was attended by approximate 15 people and raised questions and interest from a couple of people in attendance. We are currently planning to discuss with them about further collaboration building on the work that has been done to day. |
| Year(s) Of Engagement Activity | 2022 |
| Description | School of Cancer and Pharmaceutical Sciences Research day 2022 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | School Wide Research Day at King's College London School of Cancer and Pharmaceutical Sciences. Attendances include staffs and students from the School estimating at about 50-100 participants both in person and virtually. Questions and discussions were prompted by several lecturers and staffs on the subject sparking potential future collaborations. |
| Year(s) Of Engagement Activity | 2022 |