# DNA Concentration Calculator

Knowing the concentration of the DNA in a sample is fundamental in many experiments and laboratory techniques: with our DNA concentration calculator, you will learn how to determine that quantity using the **absorbance**.

Here you will learn:

- What is DNA concentration, and how do we calculate it;
- How to calculate the DNA concentration from A
_{260}values; - The DNA concentration equation (
**both for nucleic acid samples and oligonucleotides**).

## Spectrophotometry for the calculation of the DNA concentration

The measurement of the concentration of DNA (or RNA) is obtained through various techniques: the choice depends on the desired sensitivity or purposes. Our DNA concentration calculator will analyze the **spectrophotometric technique**, commonly used since it **doesn't require additional reagents** and its relative simplicity, it **lacks sensitivity at low concentrations**, and it **can't distinguish** between the two nucleic acids.

The only instrument required for the measurement of the DNA concentration is a **spectrophotometer**. Place the sample in a quartz cuvette, and measure its **absorbance** at the ultraviolet wavelength of $260\ \text{nm}$: we call this quantity $\text{A}_{260}$.

## How to calculate the DNA concentration from the absorbance

The calculation of the DNA concentration from A_{260} values uses the **Beer-Lambert Law**. The equation for the DNA concentration is:

Here we can identify:

- $c_{\text{DNA}}$, the DNA concentration;
- $b$, the
**length of the optical path**; - $\text{df}$, the
**dilution****factor**; and - $c$, the
**conversion factor**.

The **conversion factor** depends on the type of nucleic acid under analysis. Its value is:

- $33\ \text{µg}/\text{mL}$ for single-stranded DNA (ssDNA);
- $50\ \text{µg}/\text{mL}$ for double-stranded DNA (dsDNA); and
- $40\ \text{µg}/\text{mL}$ for RNA.

The dilution factor is nothing but a measurement of the quantity of acid nucleic per unit volume of water.

## How to calculate the concentration of any nucleotide sequence

The formula for the DNA concentration can be slightly modified to consider any short sequence of nucleotides (oligonucleotide), given that we know the composition of the sequence.

Where we introduced the quantity:

- $e_{260}$, the
**extinction coefficient**; and - $w_{\text{M}}$, the
**molecular weight**of the nucleotide strand.

To compute the molecular weight of the oligonucleotide, sum the weights of the nucleotides making up the sequence. First, use the data in the following table:

Nucleotide | ssDNA | dsDNA | RNA |
---|---|---|---|

| $313.21\ \text{Da}$ | $616\ \text{Da}$ | $329\ \text{Da}$ |

| $329.21\ \text{Da}$ | $617.88\ \text{Da}$ | $345.21\ \text{Da}$ |

| $289.18\ \text{Da}$ | $617.88\ \text{Da}$$$ | $305.18\ \text{Da}$ |

| $304.20\ \text{Da}$ | $616.78\ \text{Da}$ | N/A |

| N/A | N/A | $306.20\ \text{Da}$ |

The weights are expressed in **Daltons**, a unit defined by $$\text{N}*{\text{A}}\ \text{Da}\simeq 1\ \text{g}/\text{mol}$where$\text{N}*{\text{A}}$$ is the **Avogadro's number**.

To refine the calculations for the weight of the oligonucleotide, you need to apply the following modifications:

- Subtract $61.96\ \text{Da}$ for ssDNA or $123.38\ \text{Da}$ for dsDNA if you are using
**unmodified nucleotides**. - Add $17.04\ \text{Da}$ for ssDNA or $34.08\ \text{Da}$ for dsDNA in
**nucleic acids with added phosphate groups**.

*Add $159.0\ \text{Da}$ for RNA with added phosphate groups.

To calculate the absorption coefficient $\epsilon_{260}$ at $260\ \text{nm}$, we use the **nearest neighbour model** for nucleotides. Use the formula:

And substitute the vales of absorption for the individual basis:

Adenine | Guanine | Cytosine | Thymine | Uracil |
---|---|---|---|---|

$15,400$ | $11,500$ | $7,400$ | $8,700$ | $9,900$ |

And for the nearest neighbour in the **5'/3' direction**, use the following table:

5'/3' position | Adenine | Guanine | Cytosine | Thymine | Uracil |
---|---|---|---|---|---|

Adenine | $27,400$ | $25,000$ | $21,200$ | $22,800$ | $24,600$ |

Guanine | $25,200$ | $21,600$ | $17,600$ | $20,000$ | $20,000$ |

Cytosine | $21,200$ | $18,000$ | $14,600$ | $15,200$ | $17,200$ |

Thymine | $23,400$ | $19,000$ | $16,200$ | $16,800$ | N/A |

Uracil | $24,000$ | $21,200$ | $16,200$ | N/A | $19,600$ |

Use these values (expressed in **M ^{-1}cm^{-1}**, the inverse of molarity per centimeter) in the DNA concentration formula to calculate the value of the DNA concentration from A

_{260}values also in short sequences of nucleotides.