Extinction Coefficient Calculator DNA

DNA Extinction Coefficient Equation:

\[ \varepsilon_{DNA} = \frac{(\varepsilon_A \times n_A + \varepsilon_T \times n_T + \varepsilon_G \times n_G + \varepsilon_C \times n_C)}{Length} \]

Adenine Count (n_A):

bases

Thymine Count (n_T):

bases

Guanine Count (n_G):

bases

Cytosine Count (n_C):

bases

DNA Length:

DNA Extinction Coefficient (ε_DNA):

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1. What is DNA Extinction Coefficient?

The DNA extinction coefficient (ε_DNA) is a measure of how strongly DNA absorbs light at 260 nm wavelength. It is used to quantify DNA concentration in solution and is calculated based on the nucleotide composition of the DNA sequence.

2. How Does the Calculator Work?

The calculator uses the DNA extinction coefficient equation:

\[ \varepsilon_{DNA} = \frac{(\varepsilon_A \times n_A + \varepsilon_T \times n_T + \varepsilon_G \times n_G + \varepsilon_C \times n_C)}{Length} \]

Where:

\( \varepsilon_A \) — Adenine extinction coefficient (15,400 M⁻¹ cm⁻¹)
\( \varepsilon_T \) — Thymine extinction coefficient (8,800 M⁻¹ cm⁻¹)
\( \varepsilon_G \) — Guanine extinction coefficient (11,500 M⁻¹ cm⁻¹)
\( \varepsilon_C \) — Cytosine extinction coefficient (7,500 M⁻¹ cm⁻¹)
\( n_A, n_T, n_G, n_C \) — Count of each nucleotide base
\( Length \) — Total DNA length in base pairs

Explanation: The equation calculates the average extinction coefficient per base pair based on the specific nucleotide composition of the DNA sequence.

3. Importance of Extinction Coefficient Calculation

Details: Accurate extinction coefficient calculation is essential for determining DNA concentration using spectrophotometry, which is fundamental in molecular biology, genomics, and biotechnology applications.

4. Using the Calculator

Tips: Enter the count of each nucleotide base (A, T, G, C) and the total DNA length in base pairs. All values must be valid non-negative integers, with length greater than 0.

5. Frequently Asked Questions (FAQ)

Q1: Why is extinction coefficient important for DNA quantification?
A: It allows accurate calculation of DNA concentration from absorbance measurements at 260 nm using the Beer-Lambert law.

Q2: What are typical extinction coefficient values for DNA?
A: For double-stranded DNA, ε is typically around 50-60 M⁻¹ cm⁻¹ per base pair, depending on GC content.

Q3: How does GC content affect extinction coefficient?
A: GC-rich DNA has higher extinction coefficients because guanine and cytosine have higher individual extinction coefficients than adenine and thymine.

Q4: Are these coefficients the same for single-stranded DNA?
A: No, single-stranded DNA typically has higher extinction coefficients due to unstacked bases that absorb more light.

Q5: Can I use this for RNA calculations?
A: No, RNA has different extinction coefficients. Use RNA-specific calculators for accurate RNA quantification.