DNA Copy Number Calculator

Our dna copy number calculator is used in molecular biology and genetics to determine the quantity of specific DNA sequences present in a sample.

DNA Conc. (ng/µL)	DNA Length (bp)	Sample Volume (µL)	Copy Number
10	1000	1	9.26 x 10^9
50	5000	2	3.71 x 10^10
100	10000	0.5	4.63 x 10^9
5	500	5	9.26 x 10^10
200	20000	0.1	9.26 x 10^8
30	1500	3	1.39 x 10^10
75	3000	1.5	1.73 x 10^10
150	2500	2.5	2.88 x 10^10
20	8000	4	3.71 x 10^9
60	4000	1.2	1.38 x 10^10
90	6000	2.2	2.59 x 10^10
120	3500	3.5	4.42 x 10^10
15	1200	6	1.16 x 10^10
250	10000	0.2	3.85 x 10^8
40	9000	5.5	3.56 x 10^9

DNA Copy Number Formula

The formula for calculating DNA copy number is based on the relationship between the mass of DNA, its length, and Avogadro’s number.

The equation is:

Copy Number = (DNA amount (ng) * 6.022 x 10^23) / (DNA length (bp) * 1 x 10^9 * 650)

Where:

6.022 x 10^23 is Avogadro’s number
1 x 10^9 converts ng to g
650 is the average molecular weight of a DNA base pair in g/mol

For instance, if you have 10 ng of a 1000 bp DNA fragment, the calculation would be:

Copy Number = (10 * 6.022 x 10^23) / (1000 * 1 x 10^9 * 650) ≈ 9.26 x 10^9 copies

This means there are approximately 9.26 billion copies of the DNA fragment in the sample.

How do you calculate the number of copies of DNA?

To calculate the number of copies of DNA, follow these steps:

Determine the DNA concentration using spectrophotometry or fluorometry.

Measure the length of the DNA sequence in base pairs.

Apply the DNA Copy Number Formula as explained above.

Suppose you have a plasmid with a concentration of 50 ng/µL and a length of 5000 bp.

To calculate the copy number in 1 µL of this solution:

Copy Number = (50 ng * 6.022 x 10^23) / (5000 bp * 1 x 10^9 * 650)
             ≈ 9.26 x 10^9 copies/µL

This result indicates that each microliter of the plasmid solution contains about 9.26 billion copies of the DNA sequence.

How to estimate gene copy number?

Here’s a basic workflow:

Extract genomic DNA from your samples.
Design primers specific to your target gene and a single-copy reference gene.
Perform qPCR on both genes in parallel.
Analyze the results using the ΔΔCt method or absolute quantification.

Estimating gene copy number typically involves quantitative PCR (qPCR) or digital PCR (dPCR) techniques.

For example, if you’re investigating the HER2 gene in breast cancer:

Extract DNA from tumor and normal tissue samples.

Use primers for HER2 and a single-copy gene like RNase P.

Run qPCR for both genes on all samples.

Calculate the ratio of HER2 to RNase P amplification.

If the ratio in tumor tissue is significantly higher than in normal tissue (e.g., > 2), it suggests HER2 amplification, which is associated with certain types of aggressive breast cancer.

What is the copy number of DNA?

The copy number of DNA refers to the number of times a particular DNA sequence appears in a genome or sample.

In a diploid organism, most genes have two copies – one from each parent. Copy numbers can vary due to genetic events such as:

Duplications
Deletions
Insertions
Translocations

In humans, the AMY1 gene, which codes for salivary amylase, can have copy numbers ranging from 2 to 15 or more. Higher copy numbers of AMY1 are associated with improved starch digestion and have been linked to populations with high-starch diets.

Another example is the CCL3L1 gene, which influences HIV susceptibility. Individuals with lower copy numbers of this gene tend to be more susceptible to HIV infection and faster progression to AIDS.

References

National Center for Biotechnology Information (NCBI): https://www.ncbi.nlm.nih.gov/probe/docs/techrealtime/
Nature Education: https://www.nature.com/scitable/topicpage/gene-copy-number-variations-in-complex-phenotypes-824/
Cold Spring Harbor Protocols: http://cshprotocols.cshlp.org/content/2015/9/pdb.top083659.full

Related Tools:

DNA Copy Number Calculator – Calculating Genetic Abundance