Unit 13: DNA-Protein Interactions

True or false: Proteins can bind to DNA both specifically and non-specifically (i.e. regardless of the nucleotide sequence).

True or false: Proteins can bind to DNA both specifically and non-specifically (i.e. regardless of the nucleotide sequence).

True

Specific binding of DNA by DNA-binding proteins is characterized by…

the dissociation constants ranging from ~10^-9 M to ~10^12 M

Where do DNA-protein interactions happen?

In the major groove of B-DNA, where protein’s functional groups can interact with the accessible groups of the nitrogenous bases to ensure specificity

DBA-binding proteins may have the following motifs:

• Helix-Turn-Helix (HTH) motif

• Zinc finger motif

• Leucine zipper motif

What is the helix-turn-helix (HTH) motif?

• A major structural motif capable of binding DNA

• Consists of two α-helices connected by a short loop

• Both DNA bases and groups of DNA sugar-phosphate backbone are involved in hydrogen bonding with the protein groups

Where is zinc finger motif found?

Often found in transcription factors

The zinc finger motif involves…

Zn2+ ion coordinated by Cys and His side chains

• X is any amino acid residue

The protein component of the Zinc finger motif is made of…

• An α-helix connected to a two-stranded antiparallel ß sheet by a short turn

• α-helixes interact with 3-bp segments of DNA through to maintain the zinc finger folded structure, which provides a platform for inserting an α-helix in the major groove of the recognized DNA fragment

The leucine zipper motif is involved in…

Dimerization of transcription factors, but not for the binding of DNA itself

Describe interactions between nucleic acids and proteins.

Define structural requirements for common motifs for DNA-binding proteins (HTH, Zinc finger, Leucine zipper)

Describe the levels of DNA packaging in eukaryotic cells.