Oligonucleotide Duplex
Oligonucleotide Duplex - Related Videos
11:42
Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes
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2012
Crystal structure of protein–DNA complexes can provide insight into protein function, mechanism, as well as, the nature of the specific interaction. Here, we report how to optimize the length, sequence and ends of duplex DNA for co-crystallization with Escherichia coli SeqA, a negative regulator of replication initiation.
08:45
Duplex Digital PCR for Simultaneous Quantification of Dual Genetic Markers
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2025
In this video, we demonstrate the duplex digital PCR (ddPCR) technique — a modification of the traditional PCR technique that is useful in detecting two different genetic markers simultaneously. A single PCR reaction is partitioned into nanoliter-sized emulsified droplets that are independently amplified, and the detection of differently colored fluorescence amplification signals from the fraction of droplets is used to compute the initial concentration of the target sequences.
04:10
Helicase Activity Measurement of a Target Protein Using Biotin-Labeled RNA Duplexes
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2025
In this video, we demonstrate the procedure to determine the helicase activity of a target protein to unwind the biotin-labeled dsRNA substrate. The activity of the enzyme was identified by analyzing the electrophoretic mobility shift, followed by a chemiluminescence assay using chemiluminescent enzyme-conjugated streptavidin.
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.
FAQs
Hydrogen bonds between complementary bases provide sequence-specific recognition, while stacking interactions between neighboring bases help stabilize the helical structure. These contributions work together rather than independently: base pairing determines which strands associate, and stacking strengthens the resulting arrangement. Their combined effect allows researchers to examine how sequence-guided molecular recognition produces a stable nucleic acid structure.
Temperature, salt concentration, and pH are central variables in duplex formation. Strands anneal under conditions that support complementary base pairing, whereas changes in these variables can alter duplex stability and melting behavior. Controlling them is therefore essential when comparing sequences, preparing a defined duplex, or interpreting whether an observed association reflects the intended molecular interaction.
Melting behavior provides a way to evaluate duplex stability under defined environmental conditions. As conditions change, the paired strands can become less associated, and the resulting transition reflects contributions from the sequence and the surrounding temperature, salt concentration, and pH. This measurement helps characterize hybridization and supports decisions about conditions for nucleic acid experiments.
A basic workflow begins with complementary DNA or RNA strands, brings them together under suitable temperature, salt, and pH conditions, and allows annealing to occur. The resulting structure can then be examined through its melting behavior or used in a biochemical experiment. Maintaining controlled conditions helps produce a reproducible duplex and makes comparisons between samples more meaningful.
Researchers use duplexes when they need a controllable model of nucleic acid structure, hybridization, or molecular recognition. They can also apply them in probe design, gene regulation studies, polymerase reactions, and nucleic acid-based diagnostics. The paired structure provides sequence-defined interactions that are useful for testing how nucleic acids associate or function under selected biochemical conditions.
In biochemistry, these structures provide defined systems for investigating sequence-specific hybridization and molecular recognition. In practical applications, complementary pairing supports probe design and nucleic acid-based diagnostics, while duplexes also contribute to studies of gene regulation and polymerase reactions. Their stability can be monitored through melting behavior, helping researchers evaluate whether experimental conditions support the intended interaction.