Nucleic acid sample preparation techniques for bead-based suspension arrays

• Published in: Methods (San Diego, Calif.) Calif.), 2023-11, Vol.219, p.22-29
• Main Author: Dunbar, Sherry A.
• Format: Article
• Language: English
• Subjects: Bead-based; Luminex; Multiplex; Nucleic acid; Suspension array; xMAP
• ISSN: 1046-2023; 1095-9130
• DOI: 10.1016/j.ymeth.2023.09.003

•Multiplexing technologies, such as bead-based suspension microarrays, have advanced the ability to perform high-throughput nucleic acid measurements.•These analysis systems require the nucleic acids to be extracted and purified from the specimens and sample types of interest.•The method used must be capable of providing purified nucleic acids sufficient for use with the up-front assay chemistry (e.g., PCR, primer extension, branched DNA, etc.).•For bead-based microarrays, the nucleic acid sample must be sufficiently pure to undergo hybridization, often with a heat denaturation step, without leading to agglutination of the beads. Multiplexing in biological assays allows the simultaneous detection of multiple analytes in a single reaction, which reduces time, labor, and cost as compared to single reaction-based detection methods. Microsphere- or bead-based suspension array technologies, such as the Luminex® xMAP® system, offer high-throughput detection of nucleic acids through a variety of different assay chemistries. Common with most nucleic acid chemistries, for bead-based or other microarray technologies, is the need for efficient extraction and purification of the nucleic acids from the specimen of interest. Often, the optimal method will be dictated by the requirements of the up-front enzymatic chemistry, such as PCR, primer extension, branched DNA (bDNA), etc. For bead-based microarray platforms, the user must also be cognizant of proteins and other contaminants present in reactions that require heat denaturation, as that can lead to bead aggregation or agglutination, preventing the reading of assay results. This review describes and highlights some of the nucleic acid extraction and purification methods that have been used successfully for bead-based nucleic acid analysis, for both prokaryotic and eucaryotic nucleic acids, from a variety of sample types.