What’s DNA size selection?
DNA size selection (or DNA sizing) is the targeted capture of DNA fragments of a specific size or a size range. It’s broadly used in sequencing. And it’s one sample preparation step that has the greatest impact on the quality of sequencing results. Ineffective sizing can waste sequencing capacity on low molecular weight material such as adapter-dimers or primer-dimers and imprecise sizing can hurt data quality. Precise DNA sizing can boost sequencing efficiency, save money, improve data, and even allow sequencing of low-input samples.
Why is DNA size selection important?
There are two types of sequencers: short-read sequencers (Illumina and Ion Torrent) and long-read sequencers (Pacific Biosciences and Oxford Nanopore Technologies). Both benefit from precise sizing, in a slightly different way.
Short-read sequencers operate best when fed DNA libraries that contain fragments of similar sizes, often in a very specific range recommended by the manufacturer. When libraries are not properly size-selected, these sequencers become significantly less efficient. It may take two lanes of sequencing, to accomplish what could be done in a single lane with a well-sized library.
Long-read sequencers tend to produce very-long reads by fully sequencing a long DNA fragment. When fragments are short, the read is limited. So it’s desired to remove smaller fragments using size selection, which allows the sequencers to focus on the DNA fragments most amenable to producing the longest reads.
How does DNA size selection work?
The size selection workflow is usually like below.
- Mix: Mix MagVigen™ nanoparticles with DNA/RNA sample.
- Bind: When mixed with a sample, MagVigen™ nanoparticles bind to the desired target (i.e. cells, pathogenic microorganisms, nucleic acids, peptides, proteins or protein complexes, etc). This interaction relies on the specific affinity of the ligand conjugated to the surface of the nanoparticles. NVIGEN engineers desired surface conjugations.
- Wash: The beads respond to a magnetic force (by use of a magnet), allowing bound material to be rapidly and efficiently separated from the rest of the sample. After unbound materials are removed by aspiration, the nanoparticle-bound targets are washed by using the magnet.
- Elute: The bound target is released from the nanoparticle and can be used for downstream applications.
Beads-based protocols among the best methods
Beads-based protocols don’t need column or centrifugation. They use magnetic force to aggregate, wash and elute targets. This makes the workflow simple and easy for automation, which leads to higher throughput.
While some tutorial source (e.g. BiteSizeBio‘s dna-sizing-tutorial) says beads-based protocols should not be used when more precise sizing is needed and they’re most useful in experiments where DNA is abundant, this knowledge is outdated.
The capability and capacity of any DNA size selection methods come from the functional groups assembled to beads, not directly from the beads themselves. Nanobeads, like MagVigen, manufactured with the state of the art nanotechnologies can be engineered at the molecular level to assemble a variety of functional groups. And nanobeads are in fractional (1/10) size of conventional beads, which creates 10x bigger surface area off the same amount of beads, and new advanced beads dynamics. These new properties have increased the capability and capacity of beads-based protocols to be among the best methods now.
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