Comparison of DNA Extraction Methods: Phenol-Chloroform Extraction, Silica Column Method, Magnetic Bead Method, CTAB Method, and Rapid Lysis Method

The core goal of DNA extraction is to obtain intact, pure DNA suitable for downstream experiments from cells, tissues, blood, plants, microorganisms, or environmental samples. Method selection should consider sample type, DNA fragment integrity, inhibitor removal capacity, throughput requirements, and downstream application needs.

Keywords: DNA extraction; genomic DNA; phenol-chloroform extraction; silica column method; magnetic bead method; CTAB method; DNA purification; nucleic acid quality assessment

1 Goals and Quality Requirements of DNA Extraction

1.1 DNA Extraction Is Not Merely Obtaining Nucleic Acids

DNA extraction must simultaneously accomplish cell lysis, nucleic acid release, removal of proteins and lipids, RNA degradation, inhibitor clearance, DNA enrichment, and buffer exchange. Different methods vary in DNA integrity, purity, recovery rate, and operational efficiency; therefore, method performance should not be judged only by whether DNA can be extracted.

(1) Yield

DNA yield is related to sample amount, cell number, lysis efficiency, and recovery method. High-yield methods are suitable for genome library preparation, Southern blot, large-scale PCR template preparation, and metagenomic analysis, but high yield does not necessarily indicate high purity.

(2) Purity

DNA purity is mainly affected by contaminants such as proteins, phenol, salts, ethanol, polysaccharides, polyphenols, heme, and humic acids. PCR, qPCR, restriction digestion, ligation, sequencing, and library construction are sensitive to residual inhibitors.

(3) Integrity

High-molecular-weight DNA extraction requires reduced mechanical shearing, repeated freeze-thaw cycles, and vigorous vortexing. Long-read sequencing, optical mapping, and large-insert library construction require higher DNA integrity than ordinary PCR.

(4) Compatibility

Different downstream experiments have different DNA quality requirements. Ordinary PCR can tolerate some degree of DNA fragmentation; qPCR places greater emphasis on inhibitor removal; NGS library preparation requires stable fragment distribution and low contamination; long-read sequencing places greater emphasis on preserving high-molecular-weight DNA.

Table 1 Main evaluation indicators for DNA extraction results

Evaluation Dimension	Common Indicators	Result Meaning	Applicable Scenarios
Yield	DNA concentration, total amount	Evaluates extraction recovery efficiency	PCR, sequencing, library construction
Purity	A260/A280, A260/A230	Evaluates residual protein, salts, organic compounds, or inhibitors	qPCR, restriction digestion, sequencing
Integrity	Agarose gel bands, DIN value, fragment distribution	Evaluates DNA degradation or shearing	Long-fragment PCR, long-read sequencing
Inhibitors	PCR amplification efficiency, spike-in amplification result	Evaluates whether sample matrix affects enzymatic reactions	Soil, feces, plants, blood
Stability	Concentration and integrity after freeze-thaw	Evaluates suitability of storage conditions	Sample banks, long-term storage

1.2 Extraction Challenges of Different Samples

(1) Animal tissues and cells

Animal cell membranes are relatively easy to lyse. The main challenges are removal of proteins, lipids, and RNA. Tissue samples also require sufficient homogenization to avoid incomplete local lysis.

(2) Blood and body fluids

Heme, anticoagulants, and proteins in blood samples may inhibit PCR. Extraction of genomic DNA from leukocytes requires control of red blood cell removal, protein digestion, and salt clearance.

(3) Plant samples

Plant samples contain cell walls, polysaccharides, polyphenols, and secondary metabolites. The CTAB method is commonly used for plant DNA extraction, with a focus on removing polysaccharides and polyphenols to avoid DNA browning, gelatinous precipitation, or PCR inhibition.

(4) Bacteria and fungi

Bacterial and fungal cell walls are structurally robust. Gram-positive bacteria, yeast, and filamentous fungi usually require lysozyme, proteinase K, mechanical disruption, or freeze-thaw-assisted lysis.

(5) Soil, feces, and environmental samples

Environmental samples contain PCR inhibitors such as humic acids, polyphenols, bile salts, complex polysaccharides, and metal ions. For these samples, inhibitor removal is more critical than simply maximizing DNA yield.

2 Basic Workflow of DNA Extraction

2.1 Sample Lysis and Nucleic Acid Release

The first step of DNA extraction is to disrupt cell membranes, cell walls, or nuclear membranes so that DNA is released into solution. Lysis systems are usually composed of detergents, salts, chelating agents, and proteases.

(1) Detergent lysis

SDS, Triton X-100, and other detergents can disrupt cell membranes and nuclear membranes and denature proteins. SDS has strong lysis capacity and is suitable for most animal tissues, cells, and some microbial samples.

(2) Proteinase K digestion

Proteinase K can degrade histones, nucleases, and structural proteins, improving DNA release efficiency and reducing DNA degradation. Proteinase K digestion is commonly required for tissue, blood, cell, and swab samples.

(3) Mechanical disruption

Grinding, homogenization, bead beating, and liquid nitrogen grinding can enhance lysis of plants, fungi, and bacteria. Excessive mechanical treatment can shear DNA, so shear intensity should be reduced when extracting long-fragment DNA.

(4) Chelator protection

EDTA can chelate divalent ions such as Mg²⁺ and inhibit metal-dependent nuclease activity. EDTA is commonly included in DNA extraction buffers to reduce the risk of DNA degradation.

2.2 Removal of Proteins, RNA, and Inhibitors

After lysis, samples contain proteins, lipids, RNA, salts, and sample-specific inhibitors. Removing these contaminants is a key step affecting the success of downstream experiments.

(1) Protein removal

Phenol-chloroform extraction, salting-out, proteinase K digestion, and silica membrane washing can all reduce protein contamination. A low A260/A280 ratio usually indicates protein or phenolic contamination.

(2) RNA removal

RNase A can degrade RNA, preventing RNA from causing overestimation of DNA concentration or interfering with gel interpretation. If accurate concentration and clear bands are required in genomic DNA extraction, RNase treatment should be included.

(3) Removal of polysaccharides and polyphenols

In plant samples, polysaccharides can make DNA solutions viscous, while oxidized polyphenols can bind DNA and inhibit PCR. CTAB, PVP, high-salt conditions, and β-mercaptoethanol are commonly used to improve plant DNA purity.

(4) Removal of humic acids and bile salts

Humic acids and bile salts in soil, fecal, and environmental samples inhibit PCR. Silica columns, magnetic bead purification, and dedicated inhibitor removal steps are more suitable for these complex matrices.

2.3 DNA Enrichment, Washing, and Elution

(1) Precipitation-based enrichment

Ethanol or isopropanol can precipitate DNA in the presence of salts. Precipitation methods are suitable for larger-volume samples and high-molecular-weight DNA recovery, but residual salts and organic solvents must be thoroughly removed.

(2) Silica binding

Under high-salt or chaotropic salt conditions, DNA can bind to silica membranes or silica particles. After washing, DNA is eluted with low-salt buffer or nuclease-free water. This approach is suitable for rapid and standardized extraction.

(3) Magnetic bead binding

The magnetic bead method enables automated purification through reversible DNA binding. It is suitable for high-throughput samples and automated platforms. By adjusting PEG, salt concentration, and bead ratio, the recovered DNA fragment range can be controlled.

(4) Elution control

Elution volume affects DNA concentration, while elution temperature and incubation time affect recovery rate. For restriction digestion, PCR, and sequencing, residual salts, ethanol, and chelators in the eluent should be kept within downstream reaction tolerance.

3 Comparison of Common DNA Extraction Methods

3.1 Phenol-Chloroform Extraction

(1) Principle and workflow

Phenol-chloroform extraction uses organic solvents to denature proteins and drive them into the organic phase or interphase, while DNA remains in the aqueous phase. DNA is then recovered by ethanol or isopropanol precipitation. This method is suitable for obtaining relatively high-purity and intact DNA.

(2) Advantages

The phenol-chloroform method has strong protein removal capacity and is suitable for tissues, cells, some microorganisms, and samples requiring high-molecular-weight DNA. If performed gently, it can preserve relatively long DNA fragments.

(3) Limitations

Phenol and chloroform are toxic and corrosive, requiring strict operational safety and waste disposal. The extraction process is time-consuming; improper aspiration at the interphase can cause protein contamination or DNA loss, and residual phenol can inhibit PCR and enzymatic reactions.

3.2 Salting-Out Method

(1) Principle and workflow

The salting-out method uses high-salt conditions to aggregate and precipitate proteins, while DNA remains in the supernatant and is then recovered by alcohol precipitation. It is commonly used for genomic DNA extraction from blood, cells, and tissue samples.

(2) Advantages

The salting-out method avoids phenol and chloroform, making it safer than organic extraction. It is low cost and suitable for batch extraction of medium- to high-quality genomic DNA.

(3) Limitations

Protein removal depends on salt concentration, mixing, and centrifugation conditions. In complex matrices, residual proteins, salts, and RNA may affect purity. This method has limited ability to remove inhibitors such as polyphenols, polysaccharides, and humic acids.

3.3 Silica Column Method

(1) Principle and workflow

The silica column method allows DNA to bind to a silica membrane under high-salt or chaotropic salt conditions. Impurities are removed with wash buffers, and DNA is then eluted with low-salt buffer or nuclease-free water.

(2) Advantages

The silica column method is rapid, reproducible, and highly standardized. It is suitable for DNA preparation before PCR, qPCR, routine sequencing, and molecular cloning. Most sample types can be accommodated using different lysis buffers and silica membrane systems.

(3) Limitations

The binding capacity of the column membrane is limited. Excessive sample input or high DNA content can reduce recovery. Centrifugal column operation may shear longer DNA fragments and is not suitable for all high-molecular-weight DNA applications.

3.4 Magnetic Bead Method

(1) Principle and workflow

The magnetic bead method purifies nucleic acids through reversible binding between DNA and the surface of magnetic particles under specific salt and PEG conditions. Magnetic separation replaces centrifugation and can be adapted to automated platforms.

(2) Advantages

The magnetic bead method offers high throughput, a high degree of automation, and good reproducibility. It is suitable for clinical samples, micro-volume samples, PCR product purification, NGS library construction, and batch extraction of multiple samples. Fragment selection can also be achieved by adjusting the bead ratio.

(3) Limitations

Residual magnetic beads, ethanol residues, or insufficient washing can affect PCR and sequencing. The magnetic bead method is usually more expensive than traditional methods and requires strict control of mixing, magnetic separation time, and consistency of automated programs.

3.5 CTAB Method

(1) Principle and workflow

The CTAB method is commonly used for plant DNA extraction. CTAB helps separate polysaccharides and other impurities, and under high-salt conditions supports DNA retention in the solution phase or subsequent precipitation recovery. PVP and reducing agents can further reduce polyphenol interference.

(2) Advantages

The CTAB method is well suited for plant samples rich in polysaccharides, polyphenols, and secondary metabolites, especially leaves, seeds, fruits, and woody plant tissues.

(3) Limitations

The method involves many steps and requires a longer operating time. It depends strongly on sample grinding, temperature, high-salt conditions, and extraction steps. If polyphenols are not sufficiently removed, DNA may turn brown and inhibit PCR.

3.6 Rapid Lysis Method

(1) Principle and workflow

Rapid lysis methods directly release DNA through heating, alkaline lysis, Chelex resin, or simplified lysis buffers, usually omitting complex purification steps. This method emphasizes speed rather than high purity.

(2) Advantages

Rapid lysis methods are simple, fast, and low cost. They are suitable for colony PCR, preliminary genotyping, field rapid screening, and sample prescreening.

(3) Limitations

The extracted DNA has relatively low purity, with more residual proteins, salts, cell debris, and inhibitors. This method is not suitable for high-quality sequencing, restriction digestion, long-term storage, or high-accuracy quantification.

Table 2 Comparison of common DNA extraction methods

Method	Core Principle	Main Advantages	Main Limitations	Applicable Scenarios
Phenol-chloroform extraction	Organic phase removes proteins while DNA remains in aqueous phase	High purity and relatively intact DNA	Toxic and hazardous, complex operation	High-quality genomic DNA, tissue and cell samples
Salting-out method	High salt precipitates proteins, alcohol precipitates DNA	Low cost and relatively safe	Limited inhibitor removal capacity	Blood, cells, animal tissues
Silica column method	DNA binds to silica membrane under high-salt conditions	Rapid, standardized, reproducible	Limited binding capacity; long DNA may be sheared	PCR, qPCR, routine sequencing
Magnetic bead method	Reversible binding between DNA and magnetic beads	High throughput, automated, suitable for micro-samples	Higher cost; bead and ethanol residues need control	Automated extraction, NGS, clinical samples
CTAB method	Removes plant polysaccharides and polyphenols	Suitable for complex plant samples	Many steps and longer processing time	Plant tissues, polysaccharide-rich samples
Rapid lysis method	Heating, alkaline lysis, or resin adsorption of inhibitors	Fast and low cost	Low DNA purity and high inhibitor residue	Colony PCR, rapid screening

4 DNA Extraction Strategies for Different Sample Types

4.1 Animal Tissues and Cells

Animal tissue samples should first be fully minced, ground, or homogenized, followed by SDS and proteinase K lysis. For ordinary PCR and qPCR, silica column and magnetic bead methods are efficient. For high-molecular-weight DNA extraction, vortexing and vigorous pipetting should be reduced to avoid shearing long DNA fragments.

4.2 Blood Samples

The main goal of blood DNA extraction is to obtain genomic DNA from leukocytes. Red blood cell lysis, proteinase K digestion, and anticoagulant residue control are critical steps. Heparin-anticoagulated samples may inhibit PCR, whereas EDTA-anticoagulated samples are more commonly used for molecular testing.

4.3 Plant Samples

Plant tissues should be thoroughly ground at low temperature or in liquid nitrogen to reduce nuclease activity and polyphenol oxidation. The CTAB method is suitable for samples with high polysaccharide and polyphenol content, while the silica column method is suitable for higher-throughput plant materials with lower matrix complexity.

4.4 Bacterial and Fungal Samples

Bacterial DNA extraction requires adjustment of lysis conditions according to cell wall structure. Gram-negative bacteria are relatively easy to lyse, while Gram-positive bacteria often require lysozyme or mechanical disruption. Fungal samples usually require bead beating, liquid nitrogen grinding, or enzymatic assistance.

4.5 Soil, Feces, and Environmental Samples

The key issue for environmental samples is inhibitor removal. Soil humic acids, fecal bile salts, and complex organic compounds can inhibit PCR. These samples are preferably processed using silica column or magnetic bead workflows that include inhibitor removal steps, and inhibition should be evaluated by spike-in amplification.

Table 3 Key considerations for DNA extraction from different sample types

Sample Type	Main Challenges	Recommended Strategy	Quality Control Focus
Animal tissue	High protein and lipid content	Proteinase K lysis, silica column, or phenol-chloroform method	A260/A280, integrity
Cultured cells	Limited sample amount, nuclease contamination	Gentle lysis, column method, or magnetic bead method	Yield, PCR amplification efficiency
Blood	Heme and anticoagulant interference	Red blood cell lysis, proteinase K digestion	Inhibitor residue, purity
Plant tissue	Polysaccharides, polyphenols, cell wall	CTAB method, PVP assistance, low-temperature grinding	A260/A230, PCR inhibition
Bacteria	Cell wall differences	Enzymatic lysis, mechanical disruption, column method	Lysis efficiency, DNA integrity
Fungi	Robust cell wall	Bead beating, liquid nitrogen grinding, enzymatic lysis	Yield, fragment integrity
Soil/feces	Humic acids, bile salts, complex inhibitors	Inhibitor removal columns, magnetic bead purification	Spike-in amplification, A260/A230
FFPE samples	DNA crosslinking and fragmentation	Deparaffinization, proteinase K digestion, crosslink reversal	Fragment length, qPCR amplifiability

5 DNA Quality Assessment Methods

5.1 UV Spectrophotometry

UV spectrophotometry estimates DNA concentration using A260 and evaluates purity using A260/A280 and A260/A230. A low A260/A280 ratio often indicates protein, phenol, or other organic contamination; a low A260/A230 ratio often indicates residual salts, guanidine salts, phenol, polysaccharides, or humic acids.

5.2 Fluorescence Quantification

Fluorescent dyes can selectively bind double-stranded DNA, and the quantitative results are usually more suitable than A260 for low-concentration samples and complex matrices. If samples contain RNA, free nucleotides, or absorbance background, fluorescence quantification is more suitable for assessing true double-stranded DNA concentration.

5.3 Agarose Gel Electrophoresis

Gel electrophoresis can be used to observe DNA integrity, fragment size, and degradation. High-quality genomic DNA usually appears as a high-molecular-weight major band, while degraded samples show smearing or diffuse bands. RNA contamination can also be assessed by low-molecular-weight bands or background.

5.4 Downstream Amplification Validation

PCR or qPCR is an effective method to assess whether DNA contains inhibitors. If DNA concentration is normal but amplification fails, residual salts, ethanol, phenol, humic acids, heme, or polysaccharides should be investigated.

Table 4 Quality assessment methods for DNA extraction results

Method	Main Use	Advantages	Limitations
A260 UV quantification	Measures total nucleic acid amount and purity ratios	Fast, no dye required	RNA and contaminants can overestimate concentration
Fluorescence quantification	Measures double-stranded DNA concentration	High specificity, suitable for low-concentration samples	Requires dedicated dyes and instruments
Agarose gel electrophoresis	Evaluates integrity and degradation	Direct visualization of fragment status	Limited quantitative accuracy
PCR/qPCR validation	Evaluates template usability and inhibitors	Strong relevance to downstream applications	Affected by primers and amplification system
Automated fragment analysis	Evaluates fragment distribution and integrity	Suitable for sequencing sample QC	Higher cost

6 Common Problems and Optimization Strategies

6.1 Low DNA Yield

(1) Insufficient lysis

Incomplete tissue grinding, insufficient cell wall disruption, or inadequate proteinase K digestion can result in incomplete DNA release. Grinding, enzymatic lysis, or lysis duration should be adjusted according to sample type.

(2) Low binding or precipitation efficiency

In silica column methods, ethanol ratio, guanidine salt concentration, and loading amount affect binding efficiency. In precipitation methods, salt concentration, alcohol ratio, and low-temperature incubation affect DNA recovery.

(3) Incomplete elution

Too small an elution volume, insufficient incubation time, or incomplete contact between elution buffer and membrane can reduce recovery. Elution time can be extended or a second elution can be performed.

6.2 Poor DNA Purity

(1) Protein contamination

When A260/A280 is low, possible causes include insufficient proteinase K digestion, improper aspiration at the phenol-chloroform interphase, or inadequate washing. Increasing protein digestion or optimizing extraction steps can improve results.

(2) Salt and organic residue

Low A260/A230 is commonly caused by residual guanidine salts, ethanol, phenol, polysaccharides, or humic acids. Washing should be extended, drying time increased, or secondary purification used.

(3) RNA contamination

Residual RNA can cause overestimation of A260 readings and interfere with gel band interpretation. RNase A treatment can be added during genomic DNA extraction.

6.3 DNA Degradation or Fragmentation

(1) Nuclease activity

Improper sample storage, delayed lysis, or insufficient EDTA may lead to DNA degradation. Samples should be stored at low temperature, and lysis and nuclease inactivation should be completed as soon as possible.

(2) Mechanical shearing

Vigorous vortexing, repeated pipetting, excessive bead beating, and pipetting through narrow-bore tips can break high-molecular-weight DNA. Wide-bore tips and gentle mixing should be used for long-fragment DNA extraction.

(3) Repeated freeze-thaw cycles

Repeated freeze-thaw cycles increase the risk of DNA fragmentation. DNA should be aliquoted for long-term storage to avoid repeated freeze-thaw.

6.4 Downstream PCR Failure

PCR failure despite normal DNA concentration usually indicates residual inhibitors or poor template quality. Plant, soil, fecal, and blood samples especially require attention to polysaccharides, polyphenols, humic acids, bile salts, and heme inhibition. Template dilution, secondary purification, or spike-in amplification can be used to locate the issue.

Table 5 Common problems in DNA extraction and troubleshooting directions

Problem	Possible Cause	Impact	Optimization Direction
Low DNA yield	Insufficient lysis, low binding efficiency, incomplete elution	Insufficient downstream template	Enhance grinding or enzymatic lysis; optimize binding and elution
Low A260/A280	Protein, phenol, or organic contamination	Enzymatic reactions inhibited	Strengthen protein digestion or perform secondary purification
Low A260/A230	Residual salts, guanidine salts, polysaccharides, humic acids	PCR and sequencing affected	Increase washing, drying, or inhibitor removal
DNA smearing	Degradation or mechanical shearing	Limited long-fragment applications	Operate at low temperature; reduce vortexing and freeze-thaw
RNA contamination	No RNase treatment	Overestimated concentration and complex gel background	Add RNase A digestion
PCR failure	Residual inhibitors or template degradation	No amplification or abnormal Ct values	Dilute template, perform secondary purification, or validate by spike-in
DNA difficult to dissolve	Over-dried pellet or salt residue	Uneven concentration and sampling error	Dry appropriately and dissolve fully in low-salt buffer

7 Related Product and Material Selection

Table 6 DNA extraction-related kits and supporting materials

Cat. No.	Product Name	Grade/Use	Application Module	Application Positioning
D1121516	Universal Plant Genomic DNA Extraction Kit	BioReagent, for DNA and RNA applications	Plant DNA extraction	Used for genomic DNA extraction from routine plant tissues
D1121524	Plant Genomic DNA Extraction Kit	BioReagent, for DNA and RNA applications	Plant DNA extraction	Used to improve lysis and DNA recovery efficiency from plant samples
P1522831	Polysaccharide & Polyphenol Rich Plants DNA Kit	BioReagent, Suitable for molecular biology, for DNA and RNA applications	DNA extraction from complex plant samples	Used for DNA extraction from plant tissues rich in polysaccharides and polyphenols
D1372310	Magnetic Plant DNA Kit	BioReagent, for DNA and RNA applications	Magnetic bead-based plant DNA extraction	Used for automated or high-throughput DNA extraction from plant samples
M1373546	Magnetic Bead-Based DNA Extraction Kit for Polysaccharide- and Polyphenol-Rich Plant Samples	BioReagent, for DNA and RNA applications	Magnetic bead-based complex plant DNA extraction	Used for magnetic bead-based DNA extraction from plant samples with high polysaccharide and polyphenol content
B1522827	Bacteria Genomic DNA Kit	BioReagent, Suitable for molecular biology, for DNA and RNA applications	Bacterial DNA extraction	Used for bacterial sample lysis and genomic DNA purification
M1373368	Magnetic Bacterial Genomic DNA Kit	BioReagent, for DNA and RNA applications	Magnetic bead-based bacterial DNA extraction	Used for automated or high-throughput genomic DNA extraction from bacterial samples
F1522818	Fungal Genomic DNA Kit	BioReagent, Suitable for molecular biology, for DNA and RNA applications	Fungal DNA extraction	Used for fungal cell wall lysis and genomic DNA extraction
Y1522816	Yeast Genomic DNA Kit	BioReagent, Suitable for molecular biology, for DNA and RNA applications	Yeast DNA extraction	Used for genomic DNA extraction from yeast samples
M1522636	Magnetic Pathogen DNA/RNA Kit	BioReagent, Suitable for molecular biology, for DNA and RNA applications	Pathogenic microorganism nucleic acid extraction	Used for DNA/RNA extraction and magnetic bead-based nucleic acid purification from pathogenic microorganism samples
M665559	Blood/Cell/Tissue Genomic DNA Extraction Kit (Spin Column)	BioReagent	Animal sample DNA extraction	Used for genomic DNA extraction from blood, cells, and tissue samples
B1522828	Blood DNA Kit	Bioactive, Suitable for molecular biology, for DNA and RNA applications	Blood DNA extraction	Used for genomic DNA extraction from whole blood or leukocytes
D1372302	Magnetic Blood Genomic DNA Kit	BioReagent, for DNA and RNA applications	Magnetic bead-based blood DNA extraction	Used for automated or high-throughput genomic DNA extraction from blood samples
M1522695	Magnetic Blood Spots DNA Kit	BioReagent, Suitable for molecular biology, for DNA and RNA applications	Dried blood spot DNA extraction	Used for DNA extraction from dried blood spot samples and genetic testing sample pretreatment
M666110	Magbead Blood Spots DNA Kit		Blood spot DNA extraction	Used for magnetic bead-based DNA extraction from blood spot samples
O1522835	Oral Swab DNA Kit	BioReagent, Suitable for molecular biology, for DNA and RNA applications	Buccal swab DNA extraction	Used for genomic DNA extraction from buccal swab samples
M1372312	Magnetic Oral Swab Genomic DNA Rapid Kit	For DNA and RNA applications, BioReagent	Magnetic bead-based buccal swab DNA extraction	Used for rapid magnetic bead-based DNA extraction from buccal swab samples
M1522830	Marine Animals Tissue DNA Kit	BioReagent, Suitable for molecular biology, for DNA and RNA applications	Animal tissue DNA extraction	Used for genomic DNA extraction from marine animal tissue samples
N665859	NuClean FFPE DNA Kit		Fixed tissue DNA extraction	Used for DNA extraction from fixed tissue samples
M1522715	Magnetic FFPE DNA Kit	BioReagent, Suitable for molecular biology, for DNA and RNA applications	FFPE sample DNA extraction	Used for DNA extraction from paraffin-embedded tissues and purification of fragmented samples
F1522829	Stool DNA Kit	BioReagent, Suitable for molecular biology, for DNA and RNA applications	Fecal DNA extraction	Used for DNA extraction from fecal samples and inhibitor removal
S1522826	Soil Genomic DNA Kit	BioReagent, Suitable for molecular biology, for DNA and RNA applications	Soil DNA extraction	Used for microbial DNA extraction from soil samples and removal of humic acid inhibitors
D1372280	Magnetic Soil/Stool DNA Kit	BioReagent, for DNA and RNA applications	Magnetic bead-based soil/fecal DNA extraction	Used for high-throughput DNA extraction from soil and fecal samples
M1522592	Magnetic Water DNA Kit	BioReagent, Suitable for molecular biology, for DNA and RNA applications	Water sample DNA extraction	Used for microbial or environmental DNA extraction from water samples
M1522683	Magnetic Deeply Processed Food DNA Kit	BioReagent, Suitable for molecular biology, for DNA and RNA applications	Food DNA extraction	Used for extraction of degraded or low-abundance DNA from deep-processed food
M1522674	Magnetic Cell-free DNA Kit	BioReagent, DNase- and RNase-free, Suitable for molecular biology	Cell-free DNA extraction	Used for cell-free DNA extraction from plasma, body fluids, and related samples
F1456624	cfDNA Extraction Magnetic Beads	BioReagent, DNase- and RNase-free, for DNA and RNA applications, 50 mg/mL	Cell-free DNA magnetic bead material	Used for cell-free DNA magnetic bead extraction systems, fragment recovery, and method development
M1522624	Micro Sample Genomic DNA Kit	BioReagent, Suitable for molecular biology, for DNA and RNA applications	Micro-sample DNA extraction	Used for DNA extraction from low-input cells, tissues, or clinical samples
M1522612	Magnetic Micro Sample DNA Kit	BioReagent, Suitable for molecular biology, for DNA and RNA applications	Magnetic bead-based micro-sample DNA extraction	Used for automated or high-recovery DNA extraction from low-input samples
D1372306	Magnetic Universal Genomic DNA Kit	BioReagent, for DNA and RNA applications	Universal magnetic bead-based DNA extraction	Used for genomic DNA extraction from multiple sample types and adaptation to automated platforms
D669986	DNALyse Amplification Kit		Rapid lysis/direct amplification	Used for rapid DNA release and sample processing before amplification, suitable for screening experiments
D1518314	DNA Phenol Reagent	BioReagent, Suitable for molecular biology	Phenol-chloroform extraction	Used for protein denaturation and DNA purification in traditional organic extraction methods

8 Frequently Asked Questions

8.1 Should DNA extraction use a kit or a traditional method?

Routine PCR, qPCR, and batch samples are more suitable for kits or magnetic bead methods. When high-molecular-weight DNA is required or method cost needs to be controlled, phenol-chloroform extraction, salting-out, or optimized manual protocols can be selected.

8.2 Does a normal A260/A280 ratio mean DNA quality is definitely good?

Not necessarily. A260/A280 mainly reflects protein contamination and cannot fully evaluate salts, polysaccharides, humic acids, ethanol residues, or DNA integrity. A260/A230, gel electrophoresis, and downstream amplification results should be evaluated together.

8.3 Why does PCR fail when DNA concentration is high?

Common causes include residual inhibitors such as phenol, salts, ethanol, polysaccharides, polyphenols, humic acids, heme, or bile salts. Template dilution, secondary purification, or spike-in amplification validation can be attempted.

8.4 Why does plant DNA extraction easily produce viscous or brown DNA?

Viscosity is often related to polysaccharide residues, while browning is usually associated with polyphenol oxidation. CTAB, PVP, β-mercaptoethanol, and low-temperature grinding can improve plant DNA extraction quality.

8.5 What should be considered for long-fragment DNA extraction?

Vortexing, vigorous pipetting, and excessive mechanical disruption should be reduced. Gentle mixing, wide-bore tips, and low-shear operations are preferred. Sample storage and lysis should also minimize nuclease activity.

8.6 Why can magnetic bead-based DNA extraction affect PCR?

Residual magnetic beads, ethanol, salts, or incomplete elution can affect PCR. During operation, complete magnetic separation, thorough washing, sufficient ethanol evaporation, and avoidance of bead carryover should be ensured.

8.7 How should DNA be stored after extraction?

DNA can be stored at 4°C or -20°C for short-term use, and at -20°C or -80°C for long-term storage. DNA should be dissolved in low-salt buffer or nuclease-free water, repeated freeze-thaw cycles should be avoided, and important samples should be aliquoted.

DNA extraction method selection should be based on sample type, DNA integrity, inhibitor removal, and downstream experimental requirements. Phenol-chloroform extraction is suitable for high-purity and high-molecular-weight DNA, the silica column method is suitable for rapid standardized extraction, the magnetic bead method is suitable for high-throughput and automated workflows, the CTAB method is suitable for plant samples, and the rapid lysis method is suitable for preliminary screening experiments.

For more related articles, please see below:

[1] RNA Extraction

[2] RNA Extraction and Reverse Transcription Protocol

[3] RNA Extraction Technologies: Method Systems, Operational Workflows, and Key Quality-Control Considerations

[4] How to Choose Plasma Cell-Free RNA (cfRNA) Extraction Reagents