Thermodynamic Additivity for Impacts of Base-Pair Substitutions on Association of the Egr-1 Zinc-Finger Protein with DNA

Abhijnan Chattopadhyay, Levani Zandarashvili, Ross H. Luu, Junji Iwahara

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

The transcription factor Egr-1 specifically binds as a monomer to its 9 bp target DNA sequence, GCGTGGGCG, via three zinc fingers and plays important roles in the brain and cardiovascular systems. Using fluorescence-based competitive binding assays, we systematically analyzed the impacts of all possible single-nucleotide substitutions in the target DNA sequence and determined the change in binding free energy for each. Then, we measured the changes in binding free energy for sequences with multiple substitutions and compared them with the sum of the changes in binding free energy for each constituent single substitution. For the DNA variants with two or three nucleotide substitutions in the target sequence, we found excellent agreement between the measured and predicted changes in binding free energy. Interestingly, however, we found that this thermodynamic additivity broke down with a larger number of substitutions. For DNA sequences with four or more substitutions, the measured changes in binding free energy were significantly larger than predicted. On the basis of these results, we analyzed the occurrences of high-affinity sequences in the genome and found that the genome contains millions of such sequences that might functionally sequester Egr-1.

Original languageEnglish (US)
Pages (from-to)6467-6474
Number of pages8
JournalBiochemistry
Volume55
Issue number47
DOIs
StatePublished - Nov 29 2016

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Zinc Fingers
Thermodynamics
Base Pairing
Zinc
Substitution reactions
Free energy
DNA sequences
DNA
Nucleotides
Genome
Proteins
Competitive Binding
Cardiovascular System
Transcription Factors
Genes
Fluorescence
Cardiovascular system
Brain
Assays
Monomers

ASJC Scopus subject areas

  • Biochemistry

Cite this

Thermodynamic Additivity for Impacts of Base-Pair Substitutions on Association of the Egr-1 Zinc-Finger Protein with DNA. / Chattopadhyay, Abhijnan; Zandarashvili, Levani; Luu, Ross H.; Iwahara, Junji.

In: Biochemistry, Vol. 55, No. 47, 29.11.2016, p. 6467-6474.

Research output: Contribution to journalArticle

Chattopadhyay, Abhijnan ; Zandarashvili, Levani ; Luu, Ross H. ; Iwahara, Junji. / Thermodynamic Additivity for Impacts of Base-Pair Substitutions on Association of the Egr-1 Zinc-Finger Protein with DNA. In: Biochemistry. 2016 ; Vol. 55, No. 47. pp. 6467-6474.
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