In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses
September 7th, 2022
We provide a protocol that can be generally applied to select aptamers that bind to infectious viruses only and not to viruses that have been rendered non-infectious by a disinfection method or to any other similar viruses. This opens the possibility of determining infectivity status in portable and rapid tests.
Overview
This protocol describes a method for selecting DNA aptamers that can distinguish between infectious and non-infectious viruses. This advancement enables the development of sensors for clinical diagnostics and environmental monitoring.
Key Study Components
Area of Science
- Biotechnology
- Virology
- Diagnostic Methods
Background
- Aptamers are short, single-stranded DNA or RNA molecules that can bind to specific targets.
- Current methods for detecting infectious viruses often lack specificity.
- This protocol aims to improve the detection of infectious viruses in various samples.
- It does not require prior knowledge of the virus's structure or sequence.
Purpose of Study
- To develop a protocol for selecting aptamers that specifically bind to infectious viruses.
- To enable rapid and portable testing for infectivity status.
- To facilitate the monitoring of environmental disinfection methods.
Methods Used
- Selection of DNA aptamers through a systematic process.
- Optimization of PCR conditions for aptamer amplification.
- Monitoring selection progress using qPCR.
- Demonstration of the procedure by a graduate student.
Main Results
- The protocol successfully identifies aptamers that bind selectively to infectious viruses.
- It provides a framework for developing sensors for various viruses.
- The method shows potential for both clinical and environmental applications.
- Results indicate improved specificity compared to existing detection methods.
Conclusions
- This protocol offers a reliable approach to detect infectious viruses.
- It can be adapted for use with emerging viruses.
- The technique enhances the ability to monitor public health and safety.
Frequently Asked Questions
Executive Industry Relevance
Distinguishing infectious from non-infectious viruses is a critical unmet need in both clinical diagnostics and environmental monitoring, directly impacting outbreak response and infection control. The SELEX-based aptamer selection protocol enables the development of molecular sensors that report on viral infectivity, supporting rapid decision-making and risk mitigation across the discovery and translational pipeline. This capability enhances predictive confidence at key inflection points, reducing ambiguity in pathogen detection and supporting portfolio-wide surveillance strategies.
Strategic Applications in Biopharma R&D
Early Discovery & Target Validation
- Enables functional interrogation of viral surface features without prior structural knowledge.
- Supports biological de-risking by isolating aptamers that differentiate infectious states.
- Facilitates target validation for pathogen-specific diagnostic and surveillance tools.
Screening & Assay Development
- Provides validated aptamer pools for integration into quantitative binding assays.
- Enables reproducible selection and monitoring via qPCR and high-throughput sequencing.
- Supports assay standardization for downstream sensor development and screening platforms.
Translational & Preclinical Research
- Aligns with translational biomarker strategies by enabling detection of functionally relevant viral states.
- Supports continuity from discovery to preclinical validation of diagnostic agents.
- Reduces risk in advancing candidate sensors for clinical and environmental deployment.
Pipeline & Workflow Integration
This SELEX protocol fits at the interface of early discovery and assay development, providing a bridge to translational research and preclinical validation for infectious disease diagnostics.
- Discovery Biology: Supports hypothesis testing on viral infectivity and surface state recognition.
- Screening: Delivers reproducible, quantitative outputs for aptamer enrichment and specificity.
- Analytics: Integrates qPCR and sequencing-based readouts for robust comparison of selection rounds.
- Translational Research: Enables alignment with functional biomarkers of infectivity for downstream validation.
- Enterprise Reuse: Provides a modular platform adaptable to emerging viral threats and new targets.
Operational & Enterprise Impact
- Scientific Value: Increases predictive confidence in distinguishing infectious agents, reducing mechanistic ambiguity.
- Operational Value: Standardizes aptamer selection and monitoring, supporting reproducibility and scalability.
- Strategic Value: Improves go/no-go decisions for diagnostic development and environmental monitoring tools.
- Portfolio Impact: Enables risk-adjusted prioritization of diagnostic and surveillance candidates.
Implementation Considerations
- Requires expertise in molecular biology, qPCR, and sequence analysis.
- Needs access to infectious and non-infectious viral stocks and appropriate biosafety infrastructure.
- Demands cross-team standardization of selection and analytical protocols.
- Adaptable to various viral systems without prior structural information.
- Dependent on optimization of PCR and sequencing workflows for robust output.
Biopharma FAQs
Chapters in this video
0:04
Introduction
1:05
Design and Synthesis of DNA Library and Primers and Infectious and Non‐Infectious Virus Samples
1:46
In Vitro Selection or SELEX Process: Initial Round
6:38
Subsequent Selection Rounds
7:55
Monitoring the SELEX Process
8:46
High‐Throughput Sequencing, Sequencing Analysis, and Aptamer Binding Validation and Assays
10:38
Results: SELEX Process of Aptamers for Distinguishing Infectious from Non‐Infectious Viruses
11:42
Conclusion
