Oligonucleotide Analysis
Oligonucleotide Analysis - Related Videos
13:14
Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform
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Cited by 3 •
2009
Gene microarrays are powerful tools in gene expression profiling at a genome-wide level. This technology has application in a variety of biological disciplines including developmental biology and toxicology. In this video, we detail a protocol for global gene expression analysis using a comprehensive oligonucleotide microarray platform for the zebrafish.
09:58
An Optimized Protocol for Electrophoretic Mobility Shift Assay Using Infrared Fluorescent Dye-labeled Oligonucleotides
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Cited by 15 •
2016
We describe here an optimized protocol of fluorescent Electrophoretic Mobility Shift Assays (fEMSA) using purified SOX-2 proteins together with infrared fluorescent dye-labeled DNA probes as a case study to tackle an important biological question.
11:33
Microinjection of mRNA and Morpholino Antisense Oligonucleotides in Zebrafish Embryos.
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Cited by 87 •
2009
Microinjection is a well-established and effective method for introducing foreign substances into fertilized zebrafish embryos. Here, we demonstrate a robust microinjection technique for performing mRNA overexpression, and morpholino oligonucleotide gene knockdown studies in zebrafish.
13:19
Chemical Triphosphorylation of Oligonucleotides
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Cited by 1 •
2022
Oligonucleotide 5′-triphosphates are ubiquitous components in essential biological pathways and have seen increasing use in biotechnology applications. Here, we describe techniques for the routine synthesis and purification of oligonucleotide 5′-triphosphates, starting from oligonucleotides prepared by standard automated synthesis techniques.
11:09
Multiplex Detection of Bacteria in Complex Clinical and Environmental Samples using Oligonucleotide-coupled Fluorescent Microspheres
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Cited by 5 •
2011
We describe a multiplex method for the detection of microorganisms within a sample using oligonucleotide-coupled fluorescent beads. Amplicon from all organisms within a sample is hybridized to a panel of probe-coupled beads. A Luminex or Bio-Plex instrument is used to query each bead for bead type and hybridization signal.
FAQs
Separation resolves molecules that differ in length, composition, or chemical state, while a subsequent detection method supplies additional characterization. Chromatographic or electrophoretic resolution can distinguish related products, and mass spectrometry or sequence-based measurements can then help assess identity and composition. Combining these approaches provides a more informative profile than relying on a single measurement.
The analysis examines differences in molecular properties that arise when synthesis or chemical integrity is incomplete. Separation can resolve full-length products from shorter species, while detection measurements help characterize composition and identify modified molecules. This distinction allows researchers to evaluate whether a preparation contains the intended product alongside truncated or chemically altered forms.
These detection approaches extend the information obtained from separation. Mass spectrometry contributes to characterization of molecular composition and chemical integrity, whereas sequence-based measurements help evaluate sequence identity. Used after resolution or alongside it, they help distinguish molecules that may appear related by size but differ in composition or sequence.
A typical workflow begins by applying a separation method, such as chromatography or electrophoresis, to resolve the sample into distinguishable molecular forms. Researchers then use mass spectrometry or sequence-based measurements to characterize the resolved material. The combined results support assessment of identity, length, composition, purity, and chemical integrity rather than treating the sample as a single uniform product.
Quality control applications include primers, probes, antisense oligonucleotides, and small interfering RNAs. Analysis can reveal whether these materials contain the intended full-length and chemically appropriate molecules, while identifying truncated or modified species that could affect interpretation or performance. This information is relevant to both biological research workflows and therapeutic development.
By characterizing the molecules present in a preparation, researchers can relate observed biological behavior to oligonucleotide identity, composition, purity, and chemical integrity. The same analytical information supports evaluation of nucleic acid interactions and stability, as well as assessment of activity. Consequently, analysis connects molecular quality measurements with functional studies in biology and development research.