Handling DNA

Working with DNA: Good laboratory practice

DNA is a relatively stable molecule. However, introduction of nucleases to DNA solutions should be avoided as these enzymes will degrade DNA. Genomic DNA consists of very large DNA molecules, which are fragile and can break easily. To ensure the integrity of genomic DNA, excessive and rough pipetting and vortexing should be avoided. DNA is subject to acid hydrolysis when stored in water, and should therefore be stored in TE buffer, see table TE buffer, pH 7.4.
TE Buffer, pH 7.4
Component Volume
1 M Tris·Cl, pH7.4 10 ml
0.5 M EDTA, pH 8.0 2 ml

Molecular weight conversions for DNA
  • MW of a double-stranded DNA molecule (sodium salt) = (number of base pairs) x (662 daltons/base pair)
  • MW of a single-stranded DNA molecule (sodium salt) = (number of base pairs) x (331 daltons/base pair)
  • MW of a DNA oligonucleotide (sodium salt, pH ≥7):
  • MW = (NA x 335.2) + (NC x 311.2) + (NC x 351.2) + (NT x 326.2) + P

Where NX = the number of residues of the respective nucleotide within the oligonucleotide (the MW listed for each nucleotide is the MW of that nucleotide, with associated sodium, incorporated in the oligonucleotide)

For dephosphorylated oligonucleotides: P = –84.0

For phosphorylated oligonucleotides: P = 40.0


Molecular conversions for DNA

Molar conversions for DNA can be found in the tables Microgram DNA conversions and Picomole DNA conversions. Protein/DNA conversions can be found in the table Protein/DNA conversions.

Microgram DNA conversions
1 µg pmol Molecules
20 b oligonucleotide 152 9.1 x 1013
1000 bp DNA 1.52 9.1 x 1011
pUC 19 DNA (2686 bp) 0.57 3.4 x 1011
pBR322 DNA (4363 bp) 0.35 2.1 x 1011
Lambda DNA (48,502 bp) 0.03 1.8 x 1010

Picomole DNA conversions
1 pmol Micrograms
20 b oligonucleotide 0.0066
1000 bp DNA 0.66
pUC 19 DNA (2686 bp) 1.77
pBR322 DNA (4363 bp) 2.88
Lambda DNA (48,502 bp) 32.01

Protein/DNA conversions
1 pmol DNA
10,000 Da 270 bp
30,000 Da 810bp
100,000 Da 2.7 kb
X
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