Protein-DNA Interactions

Proteins that bind DNA have been found to have common folding patterns known as DNA binding motifs. Each DNA binding motif is composed of a recognition region and a stabilization region. Recognition of DNA by protein can take place at two levels: nonspecific binding - between protein sidechains and DNA sugar/phosphate backbone, and specific binding - between protein sidechains and nucleotide bases.

In these examples of proteins recognizing and binding DNA, the protein α-helices make most of the base-specific interactions. In the DNA, base-specific interactions most often occur in the major groove.

Helix-Turn-Helix Motif

The helix-turn-helix (HTH) motif is commonly found in prokaryotic proteins that regulate gene expression (at the level of transcription of DNA to RNA). Examples include the E. coli trp repressor, the 434 Cro repressor (from a bacteriophage), and the E. coli lac repressor.

lac repressor structure
In order to do its job of regulating the genes that control lactose metabolism, the lac repressor binds DNA.

Subunit structure
The lac repressor is a dimer of two identical subunits, each of which has two domains, the N-terminal (NH2) domain and the C-terminal (CO2) domain. The DNA-binding sites are found in the N-terminal domain.

The HTH motif
Each subunit of the lac repressor binds the DNA via a characteristic fold in the protein: the helix-turn-helix motif.

Protein-DNA interactions
One of each motif's two helices, called the recognition helix, enters the major groove of the DNA.

Notice how well the DNA and protein fit together. Amino acid sidechains of this helix form hydrogen bonds to the DNA phosphodiester backbone and the nucleotide bases. The atoms shown in red and blue are oxygen and nitrogen that are within hydrogen bonding distance of each other. The ones most likely to be forming hydrogen bonds are shown with dotted lines.

Leucine Zipper Motif

The leucine zipper is composed of two α-helices that interact with each other at one end, promoting dimerization. The other end of each helix contacts the DNA in the major groove.

Dimerization Region
The dimerization region is characterized by leucines at every seventh position in the helix. They form a tight dimer structure.

DNA recognition
The region that interacts with the DNA features many arginine and lysine residues (shown in blue). Why do you think these might be useful sidechains for binding DNA?

Nonspecific Interactions: lys and arg
The interactions between the phosphodiester backbone of the DNA and the arginines and lysines are nonspecific interactions. They can occur along any strand of DNA, regardless of its sequence, because the interactions are with the DNA backbone only.

Nonspecific Interactions: all
A few additional protein-DNA backbone interactions occur via side chains other than arginine and lysine.

Base-specific interactions:
Specific interactions between protein and DNA take place with the DNA's nucleotide bases rather than its sugar-phosphate backbone. These are the interactions that allow sequence-specific recognition of a gene, which is essential for correct gene regulation.

Zinc Finger Motif

Zinc-finger protein TFIIIA
Zinc fingers are common eukaryotic transcriptional regulators. They usually occur in tandem (next to each other) with several occurring in a row in the protein. The zinc finger motifs we'll be looking at are from Transcription Factor IIIA.

Secondary structure
TFIIIA contains nine zinc fingers, six of which are present in the crystal structure.

Stabilizing the zinc finger
The zinc finger motif consists of an α-helix followed by a turn and two short β-strands. The β-stands form a small loop resembling a finger, and overall the fold sandwiches a zinc ion. The α-helix and the first β-strand contain conserved cysteine and histidine residues that coordinate the zinc metal ion. As you may be able to tell from the following animation, the ion is important for stabilzing the protein fold.

Bear in mind that DNA binding motifs are only part of a protein. The job that a protein must do once it binds to the DNA is often accomplished by another part of the protein that may not have been present when the structure of the DNA binding domain was determined.


The following interactive question(s) require you to interact with the structure to arrive at the correct answer. You may use any of the visualization controls or the dropdown menus to help you to answer the questions - direct manipulation of the structure may be required.

Question 1- Load structure
Based on examining the leucines of a leucine zipper, what kind of interaction enables the dimerization of the protein helices?
View Answer

Question 2 - Load structure
What types of interactions anchor the protein to the DNA backbone?
View Answer

For specific instructions on how to manipulate the 3D images in this tutorial, see Structure Tutorial Help.

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