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Molecules of Life
Illustration of a DNA double helix.

DNA

Molecules of life

Deoxyribonucleic acid (DNA) forms the genetic basis of every organism on this planet. Whether unicellular organism, plant or animal – as the carrier of genetic information, this macromolecule shapes appearance, life expectancy, state of health and biological sex, together with environmental influences. The unbelievable diversity of our earth as we know it today has developed from only four individual building blocks, the nucleotides, through billions of years of evolution – all the way back to the last universal common ancestor (LUCA) of all living cells.

  • Structural formula of adenine, a purine base.
    Adenine
  • Structural formula of thymine, a pyrimidine base.
    Thymine
  • Structural formula of guanine, a purine base.
    Guanine
  • Structural formula of cytosine, a pyrimidine base.
    Cytosine
Nucleobases
Structural formula of a nucleotide: three phosphate groups bound to the C5 atom of a deoxyribose sugar, which carries a nucleobase at its C1 atom.
Nucleotide

Chemical basis

The basic structure of DNA consists of the four bases adenine, thymine, guanine and cytosine. Adenine and guanine belong to the group of purines, thymine and cytosine are pyrimidines. Each nucleobase is connected to the C1′ atom of a C5 sugar, deoxyribose, via an N-glycosidic bond. At its C5′ atom, the sugar carries a phosphate residue bound by an ester bond. When a nucleotide is incorporated, pyrophosphate (two phosphate residues) is cleaved off and the remaining phosphate binds to the 3′-OH group of the growing strand. Through these phosphodiester bonds, millions of nucleotides line up along the sugar-phosphate backbone to form a single DNA strand containing specific information.

Double-stranded DNA, unwound: the upper strand reads C-A-A-C-G-T-G-A from 3′ to 5′, the lower strand G-T-T-G-C-A-C-T from 5′ to 3′. Adenine pairs with thymine, guanine with cytosine.3′5′5′3′CGATATCGGCTAGCAT

Animation: the double strand twists into a helix.

Biological design

Physiologically, DNA is found in the form of a right-handed double strand. In each case, complementary base pairs are coupled: adenine (A) is stabilized by two hydrogen bonds with thymine (T), guanine (G) forms three hydrogen bonds with cytosine (C). As Erwin Chargaff found out in the middle of the 20th century, double-stranded DNA always contains as much adenine as thymine and as much guanine as cytosine (Chargaff’s first rule). Both strands run antiparallel, one from 5′ to 3′, the other from 3′ to 5′. The stacking of the flat base pairs on top of each other and the geometry of the sugar-phosphate backbone make the double strand twist around its own axis, creating the typical double helix.

Annotated DNA double helix: one turn spans about 10 base pairs and 3.4 nm; the major groove is about 2.2 nm wide, the minor groove about 1.2 nm. Both strands run antiparallel from 5′ to 3′.

Key figures

One helix turn has a length of 3.4 nm or 34 Ångström. With a twist angle of about 36° between neighbouring base pairs, about 10 base pairs form a complete turn (10.5 in solution). The sugar-phosphate backbone is located on the outside. Because the two sugars of a base pair are not attached exactly opposite each other, the backbones form two grooves of different size: a major groove about 2.2 nm wide and a minor groove about 1.2 nm wide. They enable proteins to bind to the DNA – for example transcription factors that read the base sequence in the major groove to transcribe a specific gene, or histone proteins that further package the double strand.

A-DNA viewed along the helix axis: wide helix with an open centre.
A-DNA
B-DNA viewed along the helix axis: compact helix.
B-DNA
Z-DNA viewed along the helix axis: zigzag-shaped backbone.
Z-DNA

Physiological variations

In aqueous solution, as in human cells, and at a relative humidity above about 92%, DNA is present in the B form. Its base pairs lie almost perpendicular to the helix axis, right at its centre. If hydration drops to around 75%, the conformation changes to the A form: the sugar switches from C2′-endo to C3′-endo conformation, and the base pairs are tilted and shifted away from the axis, leaving an open channel in the centre. A-DNA is about 25–30% shorter per base pair and wider than B-DNA. Z-DNA is left-handed and forms preferentially in sequences of alternating purines and pyrimidines, at high salt concentrations or under negative supercoiling. In cells it occurs transiently, for example behind a transcribing RNA polymerase, and is recognised by proteins such as ADAR1 and ZBP1, which play a role in innate immunity.

Credits

Research, design and publication by Peter Schönhammer, M. Sc. Biochemistry, University of Bayreuth, 2019.

Licence: CC BY-NC-SA 4.0

References

  • Knippers, Rolf (2006): Molekulare Genetik. 9th, fully revised edition. Stuttgart: Thieme. ISBN 978-3-13-477009-4
  • Berg, Jeremy M.; Tymoczko, John L.; Stryer, Lubert (2013): Stryer Biochemie. Springer, Berlin/Heidelberg. ISBN 978-3-8274-2988-9