The Best DNA Extraction Methods from Saliva or Buccal Swabs

Isolating nucleic acids from saliva and buccal swabs has become increasingly popular in recent years. Sample collection is easy, safe, and non-invasive, and collection kits can be mailed to donors for self-collection at home if required.

The method of DNA extraction is crucial to the yield and quality of the sample, with high purity DNA required for sensitive downstream analyses such as next generation sequencing, but cruder lysate preparations suitable for PCR.

Historically, the problem with isolating DNA from saliva and buccal swabs over other sample such as blood was low yields and microbial contamination, but improvements in sample collection protocols and devices have solved these issues. To accommodate different sampling protocols, equipment availability, downstream analyses, and storage requirements, Isohelix has developed a number of different extraction kits based on alternative chemistries. Users can select the most appropriate kit for their requirements, allowing them to achieve the best results with their particular application.

Isohelix offers four key technologies each offering user advantages for DNA extraction:

In the following article we discuss the different technologies and when to use them.

1. Precipitation-Based Chemistry: Effective & Fully Optimised

The simplest DNA extraction method offered by Isohelix, precipitation-based chemistry is included in the BuccalFix Plus (BFP), BuccalPrep Plus (BPP) and SalivaPrep-2 (GSPN) kits.

In the first DNA extraction step, buffers in the kits lyse cells in the samples, and then nucleic acids are purified via precipitation, leaving contaminants behind. Proteinase K is added during the protocol to increase purity by digesting contaminating proteins.

Precipitation methods enable the rapid and efficient extraction of high yields of high molecular weight DNA and can be easily scaled to accommodate different sample volumes. As these kits don’t require additional solvents, columns, or filtration, workflows are easy to automate, with fast handling times and reduced sample steps. The unique precipitation chemistry maximises recovery of high molecular weight DNA, while minimising co-precipitation of RNA and degraded low-weight DNA.

Benefits: User-friendly, fast protocol, easy to automate, high molecular weight DNA, scalable, no additional solvents needed.
Applications: PCR/qPCR, Microarray, Methylation Array, Sanger Sequencing, Next-Generation Sequencing (NGS).

2. Silica Spin-Columns: Familiar method, reliable results

Silica membrane-based spin columns, such as those included in the Xtreme (XME) and Xtreme-RNA (XMR) kits, are a tried and tested extraction method, allowing the purification of very high-purity, high molecular weight DNA or RNA that can be used in demanding downstream applications such as next generation sequencing or microarrays.

Cells are lysed to release nucleic acids, and then samples are centrifuged to filter them through a silica membrane inside the column. Under the right ionic conditions, nucleic acids selectively bind to the silica membrane, and unwanted proteins and inhibitors are then washed away. Finally, the ionic conditions are altered to elute nucleic acids from the column in an aqueous solution.

Using a silica column maintains the integrity of your nucleic acids while ensuring the removal of traces of PCR inhibitors. Isohelix spin column-based kits can be used to process large numbers of samples and are available in manual or high-throughput formats.

Benefits: Very high purity DNA or RNA
Applications: PCR/qPCR, Microarray, Methylation Array, Sanger Sequencing, NGS.

3. Magnetic Beads: High-Throughput Solutions

Magnetic-bead-based methods such as Buccal-Mag (BMG) and Saliva-Mag (GSM) can be used to produce high yields and purities, are fast and reliable for medium to high throughput applications, and extraction is performed in the original sample collection tube, reducing waste and cost. Buccal-Mag kits include magnetic beads with high nucleic acid binding capacities with a large surface area for fast attachment, enabling rapid extraction of intact genomic DNA using a bind/wash/elute workflow.

Magnetic separator racks are available for medium-throughput sample processing, (MR-24) or for high-throughput automated processing mag-bead-based kits can be used with most openly programmable automated DNA extraction and liquid handling systems fitted with magnetic racks and heat blocks.

Benefits: Designed for high throughput & automated applications.
Applications: PCR/qPCR, Microarray, Methylation Array, Sanger Sequencing, NGS.

4. Direct to PCR: Fast PCR-Ready DNA

Direct-to-PCR kits such as the Salivalyse (SEK) and Buccalyse (BEK) allow users to rapidly prepare DNA from saliva and buccal swabs ready for amplification-based analysis methods. This method bypasses the need for time-consuming DNA extraction and purification steps, thus reducing the overall time and effort required for DNA analysis. These kits are ideal for high throughput and automated workflows, and also reduce consumable waste.

Benefits: Rapid workflow, easy to automate, reduced waste
Applications: PCR, qPCR, Loop-Mediated Isothermal Amplification (LAMP)

Summary

Isohelix specialises in providing nucleic acid collection, stabilisation and extraction kits designed and optimised for saliva and buccal swab samples. DNA and RNA isolated using Isohelix products can be used for genotyping, diagnostics, paternity and heredity analysis, forensics, and population studies. Kits avoid the use of hazardous chemicals, and minimise plastic waste, reusing tubes where possible.

As well as providing products, Isohelix experts are always on hand to offer advice and technical support.

Any enquiries or questions can be emailed to us at info@isohelix.com.

	Precipitation			Spin Column		Magbeads		Direct to PCR
Kit Name	BuccalFix Plus	BuccalPrep Plus	Saliva-Prep 2	Xtreme	XtremeRNA	Buccal-Mag	Saliva-Mag	Buccalyse	Salivalyse
Sample Type	Buccal Swab	Buccal Swab	Stabilized Saliva	Buccal Swab & Saliva		Buccal Swab	Saliva	Buccal Swab	Saliva
Time	60 mins	60 mins	60 mins	90 mins	90 mins	60 mins		< 15 mins	< 20 mins
Automation Requirement	Heating block, Centrifuge					Magnetic Rack / Plate		Heating Block
Expected Purity	A260/280 > 1.7 A260/230 > 1.5	A260/280 > 1.7 A260/230 > 1.6	A260/280 > 1.75 A260/230 > 1.6	A260/280 > 1.8 A260/230 > 2.0	A260/280 > 1.9 A260/230 > 1.7	A260/280 > 1.8 A260/230 > 1.5		PCR-Ready DNA
Expected Yield	1 - 5μg DNA		>100μg DNA	1 - 5μg DNA	10 - 50μg Total RNA	1 - 5μg DNA	15 - 30μg DNA	100 - 1000ng	100 - 1000ng
Application	PCR, qPCR, NGS, Arrays						PCR and qPCR
Stabilization Reagent Compatible	BuccalFix	Dri-Capsules, RapiDri	GeneFix	Dri-Capsules, RapiDri, BuccalFix, GeneFix	BuccalFix and GeneFix	Dri-Capsules, RapiDri, BuccalFix	GeneFix	Dri-Capsules, RapiDri	GeneFix

The Best DNA Extraction Methods from Saliva or Buccal Swabs

1. Precipitation-Based Chemistry: Effective & Fully Optimised

2. Silica Spin-Columns: Familiar method, reliable results

3. Magnetic Beads: High-Throughput Solutions

4. Direct to PCR: Fast PCR-Ready DNA

Summary

If you want to find out more about how Isohelix can help with your buccal DNA and RNA collection, stabilization and isolation, then CONTACT US

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