molbiotools

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Molbiotools is a collection of free online apps:

DNA Sequence Tools
Text and Data Tools
Calculators

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Nucleobases

N N N N NH 2

Adenine

N N N NH O NH 2

Guanine

O NH N N 2

Cytosine

O O NH N

Thymine

O O NH N

Uracil

Nucleic Acid Monomer MW

dA313.2
dC289.2
dG329.2
dT304.2
A329.2
C305.2
G345.2
U306.2

DNA base pair ~ 618

DNA Calculator

Sequence input and settings

Open a sequence file (txt, fasta or GenBank format) or paste a sequence in the area bellow.

Set the nucleic acid parameters:

DNA
RNA
single strand
double strand
linear
circular
5' hydroxyl
5' phosphate
5' triphosphate

Calculated properties

Length:

GC content:

Molecular weight:

Molarity of 1 μg/μl solution:

Number of molecules in 1 μg:

Approx. 260 nm extinction coefficient:

A260 of 1 μg/μl solution after 100-fold dilution:

In the following boxes, always fill all but one field and click 'Calculate'. Don't use commas to separate thousands.

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Absorbance and concentration

Nucleic acid:
260 nm absorbance:(in a 1 cm cuvette)
Dilution factor:
Original concentration:μg/μl
For the calculation use:
empirical rules
predicted extinction coefficient
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Calculate

Molarity, mass and volume

Concentration:μM
Mass:μg
Volume:μl
Clear
Calculate

Base-pair molarity of dsDNA solutions

Mass (amount of dsDNA):μg
Volume:μl
Concentration of base pairs:mM

Tool Description

You can use DNA Calculator to:

  • Calculate basic physical and chemical parameters of a nucleic acid molecule.
  • Calculate the mass or volume required to prepare a nucleic acid solution of specified molar concentration. Conversely, you can calculate the molarity of a nucleic acid solution prepared by dissolving a certain amount of it in a specified volume of a solvent.
  • Calculate nucleic acid concentration from absorbance and vice versa.
  • Calculate base-pair molarity of dsDNA solutions.

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Nucleobases

These are structures of the common bases found in nucleic acids (DNA and RNA). Nitrogen atoms forming N-glycosidic bonds with ribose or deoxyribose are highlighted with blue color. Red dotted lines mark the sites of hydrogen bonds responsible for base pairing in double stranded DNA molecules or in complementary regions of RNA molecules.

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Nucleic Acid Monomer MW

These are approximate molecular weights of nucleotides incorporated into a nucleic acid molecule (not dissociated, no counterions). Molecular weights of nucleotides that are a part of a nucleic acid differ from free nucleoside 5'-monophosphates by a weight of a water molecule. For high-precision molecular weights (5 decimal places) of both free and incorporated nucleotides see the user guide.

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Calculated properties

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The text comes here.

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Absorbance and concentration

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Molarity, mass and volume

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Base-pair molarity of dsDNA solutions

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OD260 Calculation

It is recommended to use empricial rules for high molecular weight DNA and RNA. For DNA and RNA oligonucleotides, the calculations based on predicted extinction coefficients give more accurate results.

Empirical rules for the relationship between nucleic acid concentration and 260 nm absorbance (OD260):

260 nm absorbance value 1 (alias "1 OD260 unit") corresponds to the following concentrations:

NOTE: OD260 units are sometimes used to describe quantities of nucleic acids. One OD260 unit is the amount of nucleic acid that will give 260 nm absorbance 1 after dissolution in 1 ml of solvent.

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