Short Target Sequences
Short Target Sequences - Related Videos
08:38
Targeted DNA Methylation Analysis by Next-generation Sequencing
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Cited by 83 •
2015
Bisulfite amplicon sequencing (BSAS) is a method for quantifying cytosine methylation in targeted genomic regions of interest. This method uses bisulfite conversion paired with PCR amplification of target regions prior to next-generation sequencing to produce absolute quantitation of DNA methylation at a base-specific level.
08:16
Comparative Lesions Analysis Through a Targeted Sequencing Approach
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2019
This article describes a method to identify clonal and subclonal alterations among different specimens from a given patient. Although the experiments described here focus on a specific tumor type, the approach is broadly applicable to other solid tumors.
08:48
Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers
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Cited by 5 •
2011
We illustrate the use of a constant force axial optical tweezers to explore the mechanical properties of short DNA molecules. By stretching DNA axially, we minimize steric hindrances and artifacts arising in conventional lateral manipulation, allowing us to study DNA molecules as short as ~100 nm.
05:17
Detection of Targetable Alterations in Non-small Cell Lung Cancer using Next-generation Sequencing
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2025
This protocol describes an automated, ISO15189-accredited next-generation sequencing workflow for detecting targetable genomic alterations in non-small cell lung cancer (NSCLC) formalin-fixed paraffin-embedded tissues.
11:52
Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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Cited by 15 •
2016
We describe a targeted RNA sequencing-based method that includes preparation of indexed cDNA libraries, hybridization and capture with custom probes and data analysis to interrogate selected transcripts for gene expression, mutations, and gene fusions. Targeted RNAseq permits cost-effective, rapid evaluation of selected transcripts on a desktop sequencer.
FAQs
Sequence complementarity determines whether a short target sequence forms a stable match with its intended DNA or RNA region. When recognition occurs under suitable conditions, the bound primer, probe, guide, or regulatory protein can mark, copy, measure, or alter that region. This molecular matching enables assays to distinguish closely related sequences rather than relying only on their presence in a sample.
Length, base composition, and experimental conditions jointly influence whether a short target sequence binds efficiently and selectively. A sequence must match the intended region while avoiding recognition patterns that also occur in closely related sequences. These variables therefore affect amplification, hybridization, sequencing, guide activity, or detection, making them central to accuracy and reproducibility.
These components use sequence recognition for different biological or analytical purposes. Primers provide matching sites that support amplification, probes identify targets through hybridization, nucleic acid guides direct recognition for gene editing, and regulatory proteins bind specific motifs to influence genetic activity. The shared principle is complementarity or motif recognition, but the resulting outcome ranges from measurement to manipulation.
Small sequence differences can change whether a primer, probe, guide, or other binding component recognizes a region. Designing the target around a distinguishing sequence allows researchers to separate closely related genomic regions or genetic variants. This capability supports tracking genetic variation and improves the interpretive value of amplification, hybridization, sequencing, or detection results.
Design begins by identifying the genomic region that must be recognized, amplified, measured, sequenced, edited, or detected. Researchers then consider sequence complementarity, target length, composition, and the conditions under which binding will occur. The selected sequence should distinguish the intended region from related sequences and match the requirements of the chosen molecular method.
The selected sequence is paired with a method suited to the research goal. Primers can support PCR amplification, probes can enable hybridization assays, and matching sequences can guide DNA sequencing, gene editing, or pathogen detection. In each workflow, the target provides a defined molecular reference, allowing researchers to analyze, identify, quantify, or manipulate a selected nucleic acid region.
Short target sequences can indicate whether a particular nucleic acid region is present, distinguish related targets, and support measurement of nucleic acid abundance. In broader biological studies, they help track genetic variation, examine genomic regions through sequencing, detect pathogens, and direct gene-editing activities. Their value comes from linking precise molecular recognition to a measurable or functional outcome.