DNA Calculator

Introduction

DNA Calculator provides a set of online tools to calculate basic physical and chemical parameters of a DNA or RNA molecule.

Sequence Input and Settings

The nucleic acid sequence to be analyzed can be provided by the user either directly - pasted into the sequence text area, or in the form of a text file (plain text file containing the sequence, fasta format file, or GenBank format file) with the "Choose File" button located just above the sequence text area. After the sequence has been loaded, it is necessary to select the desired set of parameters - DNA or RNA, single-stranded or double-stranded, linear or circular, and the exact type of 5' end in case of a linear sequence. Synthetic oligonucleotides and PCR products normally have 5' hydroxyl while fragments obtained with restriction digestion have 5' phosphate at their ends.

Calculated Properties

Besides trivial length and GC-content calculations, DNA Calculator also calculates the exact molecular weight and a predicted molar extinction coefficient (for 260 nm wavelength) of the nucleic acid plus some other values derived thereof. The molecular weight is the sum of molecular weights of all nucleotides making up the sequence corrected for the particular terminus (hydroxyl, phosphate, or triphosphate). The molecular weights used in DNA Calculator are listed in Table 1. Note that molecular weights of nucleotides incorporated in a nucleic acid differ from free nucleoside 5'-monophosphates by a weight of a water molecule (18.015).

Table 1. Molecular weights of nucleotides and 2'-deoxynucleotides

Nucleotide Molecular weight of a free nucleoside 5'-monophosphate Molecular weight of a nucleotide incorporated in a nucleic acid
AMP 347.223 329.208
CMP 323.198 305.183
GMP 363.223 345.207
UMP 324.182 306.166
dAMP 331.222 313.207
dCMP 307.197 289.182
dGMP 347.224 329.209
dTMP 322.209 304.193

The 260 nm molar extinction coefficient of the nucleic acid is calculated with the nearest neighbor method (parameters and description in references [1-3]). Briefly, the nucleic acid is seen as a sequence of overlapping dinucleotides each contributing a specific value to the final extinction coefficient (sum of the contributions). In case of a double-stranded DNA, the value is further corrected for hypochromicity effect.

Absorbance and Concentration

The calculation of the expected absorbance of a solution of a nucleic acid from its concentration or vice versa is based on the Beer-Lambert law:

A = ε · l · c

A - absorbance [unitless]
ε - molar extinction coefficient [l·mol-1·cm-1]
l - optical path length [cm]
c - molar concentration of the nucleic acid [mol·l-1]

For long nucleic acids, average empirical values of the extinction coefficient provide accurate results. For oligonucleotides and oligodeoxynucleotides, the extinction coefficient value is strongly affected by the composition of the oligomer and calculations based on the nearest neighbor method provide the most accurate results.

Note that the linear relationship described by the Beer-Lambert low is valid only in a certain range of concentrations (aprox. 0.2 - 0.8 when l = 1). Outside this range, the dependency becomes non-linear and the calculations inaccurate.

Typical working concentrations of nucleic acids are too high for direct measurements of absorbance and thus need to be diluted by a certain factor, usually 100 or 200. To obtain the original, non-diluted concentration the dilution factor has to be included in the calculation.

Molarity, Mass, and Volume

The calculations of molarity (molar concentration), mass, and dilution volume of nucleic acid solutions are based on the equation:

molar concentration [µmol·l-1] =
mass [µg]
molar mass [g·mol-1] · volume [µl]
· 106

As the molar mass is required for the calculations, a nucleic acid sequence has to be provided and the type of the nucleic acid has to be properly set.

Base-pair Molarity of dsDNA Solutions

The calculations of base-pair molarity (total concentration of base pairs in a solution of double-stranded DNA) are based on the equation:

base-pair concentration [mmol·l-1] =
DNA mass [µg]
617.9 · volume [µl]
· 103

The number 617.9 is the average molar mass of a DNA base pair. As the molar mass of an A-T pair (617.4) is almost the same as that of a G-C pair (618.4) the particular composition of the DNA molecule has only a minor effect on the calculated concentration of base pairs and is neglected in DNA Calculator.

References

1.

Oligonucleotide Interactions. 111. Circular Dichroism Studies of the Conformation of Deoxyoligonucleotides

Cantor, C.R., Warshaw, M.M., Shapiro, H.

Biopolymers. 1970;9(9):1059-77.

Pubmed

2.

Handbook of Biochemistry and Molecular Biology, Volume 1: Nucleic Acids

Fasman, G.D. (Ed.)

CRC Press 1975, 3rd edition, pp 589.

3.

Predicting ultraviolet spectrum of single stranded and double stranded deoxyribonucleic acids

Tataurov, A.V., You, Y., Owczarzy, R.

Biophys Chem. 2008;133(1-3):66-70.

Pubmed