DNA Extraction Experiment Discussion Examples | How to Interpret Yield, Purity, and Absorbance Ratios

What Is a DNA Extraction Experiment?

A DNA extraction experiment is an experiment in which DNA is removed from cells or tissues while impurities such as proteins, lipids, RNA, and salts are removed as much as possible.
Because DNA is present in nuclei and cellular organelles, cell membranes and nuclear membranes are first disrupted to release DNA into solution.
Proteins, lipids, and other substances are then removed, and the DNA is recovered by precipitation, washing, and redissolution.

Evaluation of DNA extraction includes the yield, which indicates how much DNA was obtained, the purity, which indicates how few impurities are present, and electrophoresis results, which indicate whether the DNA has been degraded.
Even when the yield is high, low purity may cause subsequent experiments such as PCR to fail.

Main Items to Include in the Results

In the results of a DNA extraction experiment, organize the DNA concentration, total yield, A260/A280 ratio, A260/A230 ratio, electrophoresis bands, presence or absence of smearing, and yield per amount of sample.
By discussing the electrophoresis results together with the absorbance measurements, the amount, purity, and degradation state of DNA can be evaluated more comprehensively.

Main Items to Include in the Results

• Name of the sample used
• Amount of sample used for extraction
• Final elution volume
• A260
• A280
• A230
• A260/A280 ratio
• A260/A230 ratio
• DNA concentration
• Dilution factor
• Total DNA yield
• Yield per amount of sample
• Presence or absence of electrophoresis bands
• Presence or absence of smearing
• Possibility of RNA or protein contamination
• Sources of error and points for improvement

Reference Experimental Values for DNA Extraction and Examples of Yield and Purity Calculations

Here, absorbance, DNA concentration, extraction yield, A260/A280 ratio, and A260/A230 ratio obtained in DNA extraction experiments are organized as reference experimental values that are easy to discuss in reports.

Because DNA shows strong absorption near 260 nm, its concentration can be approximately determined from the A260 value.
In addition, the A260/A280 and A260/A230 ratios can be used to estimate contamination by proteins, phenol, salts, sugars, and other impurities.
In DNA extraction, it is important to evaluate not only yield but also purity and the presence or absence of degradation.

Reference Experimental Conditions

Equation for Calculating DNA Concentration

For double-stranded DNA, A260 = 1.0 can be treated as corresponding to a DNA concentration of 50 μg/mL.

DNA concentration (μg/mL) = A260 × 50 × Dilution factor

For example, if the A260 of a DNA solution diluted 10-fold is 0.240,

DNA concentration = 0.240 × 50 × 10 = 120 μg/mL

Because 1 μg/mL = 1 ng/μL, this DNA solution can also be expressed as 120 ng/μL.

Equation for Calculating Total DNA Yield

Total DNA yield is determined by multiplying the DNA concentration by the final elution volume.

Total DNA yield (μg) = DNA concentration (μg/mL) × Elution volume (mL)

If the DNA concentration is 120 μg/mL and the elution volume is 0.200 mL,

Total DNA yield = 120 × 0.200 = 24.0 μg

Therefore, the total amount of DNA obtained from this extraction is calculated to be 24.0 μg.

Reference Data for Absorbance Measurements

The following is a reference example in which extracted DNA was diluted 10-fold and A230, A260, and A280 were measured.

Sample A has an A260/A280 ratio of 1.82 and an A260/A230 ratio of 2.03 and is considered to be relatively high-purity DNA.
Sample B has low A260/A280 and A260/A230 ratios, suggesting contamination by impurities such as proteins, salts, or phenol.

How to Interpret the A260/A280 Ratio

In general, high-purity double-stranded DNA has an A260/A280 ratio near approximately 1.8.
If the ratio is low, protein contamination is considered, while a high ratio may indicate RNA contamination or measurement error.

How to Interpret the A260/A230 Ratio

The A260/A230 ratio provides an indication of contamination by salts, sugars, phenol, guanidine salts, and similar substances.
Even if the DNA concentration appears high, a low A260/A230 ratio may affect downstream PCR or enzyme reactions.

Example Comparison of Extraction Yields

The following is a reference example in which DNA was extracted from different samples and recovered in an elution volume of 200 μL.

For Plant Leaf A, because the DNA concentration is 120 ng/μL and the elution volume is 200 μL, the total yield is 24.0 μg.
The yield per 0.50 g of sample is 48.0 μg/g.

Differences in DNA Yield and Purity Depending on the Extraction Method

The balance between yield and purity varies depending on the extraction method.
Even if the yield is high, low A260/A280 or A260/A230 ratios may indicate that the sample contains many impurities.

Example Calculations for Different Dilution Factors

In absorbance measurements, an excessively concentrated DNA solution may be diluted before measurement.
If the dilution factor is omitted from the calculation, the DNA concentration will be greatly miscalculated.

Even with the same A260 value, the original DNA concentration changes greatly depending on the dilution factor.
The dilution factor used for measurement must always be stated in the report.

Precautions When Absorbance Is Too High

If the absorbance is too high or too low, the reliability of the measured value may decrease.
It is important to measure using an appropriate dilution factor.

Example When RNA Contamination Is Present

RNA also absorbs near 260 nm, so RNA contamination may cause the DNA concentration to be overestimated.

If A260 decreases after RNase treatment and the A260/A280 ratio approaches approximately 1.8, RNA may have been present before treatment.

Example When Protein Contamination Is Present

Proteins absorb near 280 nm, so protein contamination tends to decrease the A260/A280 ratio.

Additional washing may improve purity, but if DNA is lost during washing, the yield may decrease.

Example When Salts, Phenol, or Sugars Are Present

The A260/A280 ratio may be relatively good even when the A260/A230 ratio is low.
In this case, residual low-molecular-weight impurities or extraction reagents other than proteins should be suspected.

Example of DNA Quality Confirmation by Electrophoresis

Absorbance measurements alone may not sufficiently reveal the degradation state of DNA.
Checking bands and smears by electrophoresis allows DNA fragmentation to be evaluated.

Even if the absorbance ratios are good, smearing in electrophoresis may indicate DNA degradation.
DNA quality is judged by considering concentration, purity, and degradation state together.

Relationship Between Extraction Operations and Results

Guidelines for DNA Quality When PCR Use Is Intended

For DNA to be used in PCR, it is important not only that the concentration be sufficient but also that few inhibitory substances are present and that the DNA has not been extensively degraded.

Example of How to Write the Results

When the extracted DNA solution was diluted 10-fold and its absorbance was measured, A260 was 0.240.
Because A260 = 1.0 can be converted to 50 μg/mL for double-stranded DNA, the DNA concentration was calculated as 0.240 × 50 × 10 = 120 μg/mL, or 120 ng/μL.
Because the elution volume was 200 μL, the total DNA yield was 120 ng/μL × 200 μL = 24.0 μg.

The A260/A280 ratio of this sample was 1.82, which was close to the general guideline of 1.8 for DNA.
The A260/A230 ratio was also 2.03, suggesting that the amount of low-molecular-weight impurities such as salts and organic solvents was relatively small.
Therefore, Sample A can be judged to be a DNA sample with relatively good yield and purity.

On the other hand, Sample B had a high DNA concentration of 130 ng/μL, but its A260/A280 ratio was 1.63 and its A260/A230 ratio was 1.24, both of which were low.
These results suggest that proteins, salts, or extraction reagents may have remained.
Although the yield appears high when only the DNA concentration is considered, low purity may inhibit downstream experiments such as PCR.

Points for Connecting the Results to the Discussion

In a discussion of DNA extraction, it is important to evaluate not only concentration and yield but also absorbance ratios, electrophoresis images, and operating conditions together.

• Can the DNA concentration be calculated from A260?
• Has the dilution factor been reflected in the concentration calculation?
• Can the total yield be calculated from the DNA concentration and elution volume?
• Can the possibility of protein or RNA contamination be discussed from the A260/A280 ratio?
• Can contamination by salts, phenol, sugars, and organic solvents be discussed from the A260/A230 ratio?
• Can it be explained that high yield does not necessarily mean high purity?
• Can it be explained that even if the absorbance ratios are good, DNA degradation must be confirmed by electrophoresis?
• Can the effects of insufficient disruption, insufficient washing, insufficient drying, overdrying, and strong stirring on the results be discussed?
• Can it be judged from concentration, purity, and degradation state whether the DNA is suitable for downstream experiments such as PCR?

Example Discussion

In this experiment, DNA was extracted from a sample and its concentration and purity were evaluated by absorbance measurement.
When DNA Sample A was diluted 10-fold and measured, A260 was 0.240.
Because A260 = 1.0 corresponds to 50 μg/mL for double-stranded DNA, the DNA concentration was calculated to be 120 ng/μL.
Because the elution volume was 200 μL, the total yield was 24.0 μg.

The A260/A280 ratio of Sample A was 1.82, which was a relatively good value for DNA.
Because proteins absorb near 280 nm, protein contamination is suspected when the A260/A280 ratio is low.
Because this ratio was close to 1.8 in Sample A, protein contamination is considered to have been low.
In addition, the A260/A230 ratio was 2.03, so the amount of low-molecular-weight impurities such as salts and phenol was also considered relatively small.

On the other hand, Sample B had a high DNA concentration but low A260/A280 and A260/A230 ratios.
This is considered to have occurred because washing during the extraction process was insufficient and proteins, salts, sugars, extraction reagents, and other substances remained.
In such samples, even if the DNA concentration calculated from absorbance is high, the measured absorbance may actually include absorption by impurities.
Therefore, purity must be evaluated using absorbance ratios in addition to yield.

DNA quality cannot be judged from absorbance ratios alone.
If a clear band is observed on the high-molecular-weight side in electrophoresis, the DNA is considered not to have been extensively degraded.
However, if a smear is observed, the DNA may have been sheared or degraded.
Strong stirring and prolonged processing can cause DNA fragmentation, so gentle mixing is important during extraction.

Possible sources of error include mistakes in recording the dilution factor, insufficient blank correction, measurement under conditions where the absorbance was too high or too low, and pipetting errors.
In particular, forgetting to include the dilution factor in the calculation causes the DNA concentration to be greatly underestimated.
In addition, when the A230 value is high, insufficient washing or drying is suspected, so additional washing or reprecipitation should be considered.

Summary

In DNA extraction, the DNA concentration can be determined from A260 and the total yield can be calculated by multiplying it by the elution volume.
The A260/A280 ratio provides an indication of protein or RNA contamination, while the A260/A230 ratio provides an indication of contamination by salts, phenol, sugars, extraction reagents, and similar substances.

This reference example covered DNA concentration, total yield, A260/A280, A260/A230, differences among extraction methods, dilution factors, RNA contamination, protein contamination, low-molecular-weight impurities, quality confirmation by electrophoresis, and judgment for PCR use.
In a report, it is useful to evaluate yield and purity separately and discuss them in relation to the extraction operations and their effects on downstream experiments.

Why DNA Concentration Is Determined From Absorbance at 260 nm

Nucleic acids such as DNA and RNA absorb ultraviolet light near 260 nm through their base components.
Therefore, by measuring absorbance at 260 nm, the amount of nucleic acid in the sample can be estimated.
For double-stranded DNA, A260 = 1 is commonly converted to a DNA concentration of approximately 50 µg/mL.

DNA concentration = A260 × 50 µg/mL × Dilution factor

However, because RNA as well as DNA absorbs at 260 nm, DNA concentration may be overestimated when RNA is present.
In addition, absorbance measurement assumes that the sample is sufficiently clear and contains few impurities.

How to Determine DNA Yield

DNA yield is the total amount of DNA ultimately obtained by extraction.
It is determined by multiplying the DNA concentration calculated from absorbance by the final elution volume.
If absorbance is measured after dilution, the dilution factor must be reflected in the concentration calculation.

DNA total yield = DNA concentration × Final elution volume

In a report, writing not only the DNA concentration but also the total yield taking the final elution volume into account makes it clear how much DNA was recovered.
In addition, calculating the yield per amount of sample makes comparison with different samples or groups easier.

What Is the A260/A280 Ratio?

The A260/A280 ratio is an indicator commonly used to evaluate nucleic-acid purity.
DNA and RNA absorb near 260 nm, while proteins mainly absorb near 280 nm.
Therefore, the A260/A280 ratio can be used to judge the possibility of protein contamination to some extent.

In general, high-purity DNA often has an A260/A280 ratio near approximately 1.8.
If the value is lower than this, proteins, phenol, or other substances that absorb near 280 nm may be present.
On the other hand, if the value is too high, RNA contamination or measurement error may be present.

Discussion When the A260/A280 Ratio Is Low

When the A260/A280 ratio is low, protein contamination is suspected.
Because proteins absorb near 280 nm due to aromatic amino acids and similar components, an increase in A280 lowers the A260/A280 ratio.
Some organic compounds such as phenol may also absorb near 280 nm and lower the ratio.

If protein removal or washing was insufficient during DNA extraction, the A260/A280 ratio may become low.
Such DNA samples may inhibit PCR or enzyme reactions.

Discussion When the A260/A280 Ratio Is High

When the A260/A280 ratio is high, RNA contamination is possible.
Because RNA, like DNA, absorbs near 260 nm, a large amount of RNA increases A260 and may raise the A260/A280 ratio.
In addition, an excessively low measurement concentration or inappropriate blank correction may also produce an unnatural ratio.

If RNA contamination is suspected, the presence or absence of RNase treatment and the electrophoresis pattern are checked.
Samples containing a large amount of RNA may show broadened bands or smearing on the low-molecular-weight side during electrophoresis.

What Is the A260/A230 Ratio?

The A260/A230 ratio is an indicator used to evaluate contamination by organic compounds, salts, and similar substances in DNA samples.
Phenol, guanidine salts, EDTA, carbohydrates, peptides, salts, and other substances may absorb near 230 nm.
Therefore, a low A260/A230 ratio may indicate that these impurities remain.

High-purity nucleic acids have relatively high A260/A230 ratios.
However, because specific guidelines differ depending on the measurement conditions, instrument, and sample, judgment should follow the instructions in the laboratory manual or those of the instructor.

Discussion When the A260/A230 Ratio Is Low

A low A260/A230 ratio may indicate that salts or organic compounds used during extraction remain.
In column purification, possible causes include insufficient washing, insufficient ethanol removal, or contamination by impurities during elution.
If phenol-chloroform extraction was performed, residual phenol may also be considered.

DNA with a low A260/A230 ratio may inhibit PCR or restriction-enzyme reactions even if the apparent DNA concentration is sufficient.
Therefore, suitability for downstream experiments is discussed from the A260/A230 ratio in addition to yield.

Causes of Low DNA Yield

Causes of low DNA yield include a small amount of sample, insufficient cell disruption, insufficient DNA elution, failure to recover precipitated DNA, loss of the pellet, loss during washing, and DNA degradation.
DNA can be lost at any stage of the extraction operation.

In particular, when the DNA pellet is difficult to see, it may be discarded together with the supernatant.
In column methods, causes include insufficient binding of DNA to the column, insufficient elution after washing, and inappropriate elution volume or elution time.

Discussion When DNA Yield Is Too High

If the DNA yield is higher than expected, a large amount of DNA may have been extracted, but RNA or impurities may also have been overestimated as DNA.
Because A260 is derived not only from DNA but also from RNA, RNA contamination causes the DNA concentration to appear high.
In addition, if phenol or other absorbing substances remain, the concentration determined from absorbance may be higher than the actual value.

Even when the yield is high, unnatural A260/A280 or A260/A230 ratios may indicate a purity problem.
If the intensity of the DNA band in electrophoresis and the concentration determined from absorbance differ greatly, impurity contamination should also be considered.

Causes of Low DNA Purity

Causes of low DNA purity include residual proteins, RNA, phenol, salts, ethanol, surfactants, and cellular components.
If protein removal is insufficient, the A260/A280 ratio tends to decrease, while residual salts or organic compounds tend to lower the A260/A230 ratio.
Residual RNA increases A260 and may cause the DNA concentration to be overestimated.

Low DNA purity may negatively affect downstream experiments such as PCR, restriction enzyme treatment, ligation, and sequencing.
Even when the yield is sufficient, low-purity DNA may be difficult to use in experiments.

Causes of DNA Degradation

DNA may be degraded by physical shearing or nucleases.
Strong pipetting, vigorous stirring, prolonged heating, inappropriate storage, and DNase contamination may cause degradation.
Degraded DNA may appear as a smear rather than a clear high-molecular-weight band in electrophoresis.

DNA degradation affects downstream experiments, such as making it difficult to amplify long fragments by PCR.
Particularly when handling genomic DNA, care must be taken to avoid mechanical shearing because DNA is a long, high-molecular-weight molecule.

How to Interpret Electrophoresis Results

Electrophoresis after DNA extraction can be used to determine whether DNA was extracted, whether it has been degraded, and whether RNA contamination is present.
If high-molecular-weight DNA remains without degradation, a strong band may be visible near the upper part of the gel.
If degradation has progressed, a smear spread throughout the gel may be observed.

If RNA is present, bands or spreading may be visible on the low-molecular-weight side.
However, interpretation of electrophoresis results also depends on gel concentration, electrophoresis conditions, staining method, and sample amount.

When the Band Is Faint in Electrophoresis

Possible causes of a faint DNA band include a small amount of DNA, low extraction yield, a small sample loading amount, insufficient staining, and DNA degradation.
If a sufficient DNA concentration is calculated from absorbance but the band is faint, RNA or impurities may have been overestimated as DNA in the absorbance measurement.

When Smearing Appears in Electrophoresis

A smear is a condition in which DNA appears spread across the gel rather than as a single clear band.
If DNA has been cut into various lengths, fragments ranging from short to long migrate continuously and form a smear.
Possible causes include physical shearing, degradation by DNase, sample deterioration, and excessive sample loading.

If smearing is observed, DNA quality may have decreased.
The effect of degradation is particularly large in experiments requiring long DNA fragments.

Discussion of RNA Contamination

RNA may be extracted together with DNA during DNA extraction.
Because RNA absorbs at 260 nm like DNA, RNA contamination increases A260 and may cause the DNA concentration to be overestimated.
RNA contamination may be suspected when the A260/A280 ratio is high or when a signal is visible on the low-molecular-weight side in electrophoresis.

Depending on the experimental conditions, RNase treatment may be used to remove RNA.
However, the presence or absence and conditions of RNase treatment should follow the laboratory manual.

Discussion of Protein Contamination

During DNA extraction, intracellular proteins are also released.
If protein removal is insufficient, proteins remain in the DNA solution.
Because proteins absorb near 280 nm, they can lower the A260/A280 ratio.

DNA samples contaminated with proteins may inhibit PCR, restriction-enzyme reactions, and similar processes.
They may also become viscous or cloudy.
In a report, protein contamination is discussed in relation to the A260/A280 ratio, electrophoresis results, and insufficient washing during extraction.

Discussion of Residual Salts and Ethanol

In DNA extraction, salts and ethanol may be used to precipitate or wash DNA.
If these remain in the final DNA solution, the A260/A230 ratio may decrease and PCR or enzyme reactions may be inhibited.
Residual ethanol may also affect DNA dissolution and downstream reactions.

If DNA is dissolved before sufficient drying after washing, ethanol may remain.
On the other hand, excessive drying may make DNA difficult to dissolve.

Discussion of Residual Phenol

When phenol-chloroform extraction is performed, phenol may remain in the DNA solution.
Because phenol absorbs in the ultraviolet region, it can worsen absorbance ratios.
Phenol also inhibits enzyme reactions and may negatively affect PCR or restriction enzyme treatment.

If residual phenol is suspected, decreases in the A260/A280 or A260/A230 ratio, the odor of the sample, or insufficient phase separation during extraction can be discussed.

Discussion of Insufficient Cell Disruption

If cell disruption is insufficient, intracellular DNA is not sufficiently released into the solution.
As a result, the yield of extracted DNA becomes low.
If the sample consists of hard tissue or an organism with a cell wall, the disruption conditions may greatly affect the yield.

Insufficient disruption causes low yield, but excessively strong disruption may physically shear DNA.
Therefore, in DNA extraction, a balance between sufficient disruption and prevention of DNA damage is important.

Discussion of Insufficient Pellet Recovery or Elution

In experiments involving DNA precipitation, the DNA pellet is recovered after centrifugation.
DNA pellets may be transparent or white and difficult to see, and may be lost when the supernatant is removed.
The pellet may also become detached and be lost during washing.

In column methods, yield decreases if DNA does not bind sufficiently to the column or if the elution solution does not sufficiently contact the DNA.
Elution-solution volume, temperature, and contact time may also affect recovery efficiency.

Errors in Absorbance Measurement

In absorbance measurement, blank settings, dilution factor, bubbles, contamination, turbidity, and the measurement range affect the results.
If A260 is too high or too low, the measurement may fall outside the linear range of the instrument or be strongly affected by noise.
Before measurement, it is important to mix the sample thoroughly and check for bubbles or precipitates.

In microspectrophotometric measurements such as NanoDrop measurements, sample uniformity, contamination of the measurement surface, and differences from the blank solution may affect the results.
If repeated measurements vary greatly, insufficient sample mixing or contamination of the measurement surface should be considered.

Discussion of Blank Settings

In absorbance measurements, the solvent or buffer in which the DNA is dissolved is used as the blank.
If the blank differs from the sample solvent, absorbance derived from the solvent cannot be correctly subtracted, and the DNA concentration and absorbance ratios may shift.
In particular, A230 is easily affected by buffer components, so blank settings are important.

When the Results Can Be Considered Good

DNA extraction results can be considered good when a sufficient DNA yield is obtained, the A260/A280 and A260/A230 ratios do not deviate greatly, and a clear DNA band is confirmed by electrophoresis.
It is also important that there is little smearing and that the DNA has sufficient purity for use in downstream experiments.

However, a “high yield” alone does not necessarily indicate a good result.
The concentration may appear high because of RNA or impurity contamination.
Yield, purity, and electrophoresis results must be judged comprehensively.

Example Discussion When the Experiment Did Not Go Well

If DNA extraction does not go well, the causes are considered from results such as low yield, a low A260/A280 ratio, a low A260/A230 ratio, a faint electrophoresis band, smearing, or a low-molecular-weight signal that appears to be RNA.
Separating the evaluation into yield, purity, and degradation state makes the discussion easier to write.

How to Write Points for Improvement

In a discussion of a DNA extraction experiment, including points for improvement as well as sources of error makes the report easier to organize.
Improvements are easier to organize when divided into sample disruption, DNA recovery, washing, prevention of degradation, and absorbance measurement.

Points for Improving Yield

• Keep sample amounts accurate and consistent
• Perform sufficient cell disruption
• Carefully remove the supernatant without losing the DNA pellet
• Use appropriate elution conditions in column methods
• Redissolve the DNA sufficiently

Points for Improving Purity

• Remove proteins sufficiently
• Confirm RNA removal when necessary
• Perform washing operations carefully
• Do not leave salts or ethanol
• Do not leave extraction reagents such as phenol
• Use the same solution as the sample solvent for the blank

Points for Preventing Degradation

• Avoid strong pipetting
• Avoid vigorous stirring
• Use clean equipment to prevent DNase contamination
• Store samples at an appropriate temperature
• Avoid leaving samples for long periods

Difference Between a Superficial Discussion and a Good Discussion

In a discussion of a DNA extraction experiment, simply writing that “DNA was obtained” or “the purity was poor” results in a superficial discussion.
Relating yield, absorbance ratios, contaminants, electrophoresis results, and operational causes produces a more persuasive discussion.

Examples of Expressions That Can Be Used in Reports

The following expressions can be used when writing the results and discussion of a DNA extraction experiment.
Adjust the necessary parts according to your own experimental results.

• Because DNA absorbs near 260 nm, the DNA concentration was calculated from A260.
• Because RNA also absorbs near 260 nm, RNA contamination may cause the DNA concentration to be overestimated.
• The low A260/A280 ratio suggests contamination by proteins or phenol.
• The low A260/A230 ratio suggests residual salts, extraction reagents, or organic compounds.
• Possible causes of the low DNA yield include insufficient cell disruption and loss during DNA recovery.
• Because smearing was observed in electrophoresis, the DNA may have been degraded or sheared.
• If a signal is observed on the low-molecular-weight side in electrophoresis, RNA contamination may be present.
• If the blank used for absorbance measurement is inappropriate, errors may occur in the DNA concentration and absorbance ratios.
• Even if the yield is high, poor absorbance ratios may indicate that the DNA sample contains impurities.
• For use in downstream PCR or enzyme reactions, not only the DNA yield but also the purity is important.

Points to Check When Discussing DNA Extraction Experiments

Checking the following points before writing the report makes the discussion easier to write.

• Has the DNA concentration been calculated from A260?
• Has the dilution factor been correctly reflected?
• Has the total yield been calculated from the final elution volume?
• Has the A260/A280 ratio been evaluated?
• Has the A260/A230 ratio been evaluated?
• Has the possibility of RNA contamination been considered?
• Has the possibility of protein contamination been considered?
• Have residual salts and extraction reagents been discussed?
• Have bands and smears been checked by electrophoresis?
• Have the causes of low yield been considered for each stage of the operation?
• Have the effects of the absorbance-measurement blank and bubbles been considered?
• Do the points for improvement correspond to the sources of error?

Summary

In a DNA extraction experiment, DNA is extracted from cells or tissues and its yield, purity, and degradation state are evaluated.
DNA concentration can be determined from A260, but because RNA also absorbs near 260 nm, DNA purity cannot be sufficiently evaluated from A260 alone.
Therefore, it is important to check the A260/A280 and A260/A230 ratios as well.

A low A260/A280 ratio suggests contamination by proteins or phenol.
A low A260/A230 ratio suggests residual salts, extraction reagents, or organic compounds.
Causes of low DNA yield include insufficient cell disruption, loss during DNA recovery, loss during washing, and insufficient elution.

In a report, rather than simply writing that “DNA was extracted,” relate the concentration determined from A260, total yield, A260/A280 ratio, A260/A230 ratio, and electrophoresis results to one another.
Even if the yield is high, low purity may make the DNA unsuitable for downstream experiments.
In evaluating DNA extraction, it is important to make an overall judgment of quantity, purity, and the presence or absence of degradation.