Branching out with bDNA

Sep 18 2017

The bDNA assay is a molecular assay for the detection of nucleic acid sequences (DNA or RNA). It is a sandwich nucleic acid hybridization method that uses bDNA molecules to amplify signal from the sequence of interest, which is captured using target-specific oligonucleotides.

Similar in purpose to polymerase chain reaction (PCR) assays also intended to detect specific DNA or RNA nucleotide sequences, the bDNA assay differs in that it relies on amplification of the signal rather than amplification of the sequence itself. Signal amplification is achieved through the binding of an amplification scaffold (schematized as a tree/branch-like structure) to sequence-specific probes, to which the label producing a signal will also bind. This results in a many-fold signal amplification for every captured molecule of the target sequence. The readout can be either luminescence or fluorescence.

Several advantages of using the bDNA method include:

  • Lower occurrence of amplicon carryover or over-amplification due to excessive amplicon
  • Good reproducibility, accuracy, and precision
  • No requirement for RNA/DNA purification, although using purified materials also works
  • Supports a wide variety of sample types including blood, tissues, cells, etc.
  • Easy to automate and scale for high throughput
  • Not as labor-intensive as PCR
  • Sensitivities in the low pg/mL range
  • Assays can be multiplexed to look at several sequences/genes simultaneously

Some of the first applications of the bDNA assay were for diagnosing bacterial or viral infections and monitoring viral load (HIV, HCV) in patients during specific therapies. Many newer applications have emerged for use in preclinical drug discovery and toxicology, such as gene expression studies, biodistribution, and bioanalysis (for RNA-based therapeutics), as well as various biomarkers.

At Charles River, we have used the bDNA assay for the measurement of mRNA compounds in biodistribution studies and for the purpose of bioanalysis in blood and various tissues. Several biomarkers are also assessed in the context of disease or disease models such as cytokine transcripts in the liver and monitoring of Huntington’s disease-related genes in the brain. The bDNA technology is very versatile and can be used in a wide variety of studies, for many purposes, and can be multiplexed to look at patterns of gene expression in various tissues. Are you interested in bDNA? Do you need to look at gene up/down regulation? Is your compound an mRNA construct that requires bioanalysis and/or biodistribution studies? Feel free to contact us for more information.

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