Determination of the Free-Energy Change for Repair of a DNA Phosphodiester Bond
Open accessAbstract
The repair of phosphodiester bonds in nicked DNA is catalyzed by DNA ligases. Ligation is coupled to cleavage of a phosphoanhydride bond in a nucleotide cofactor resulting in a thermodynamically favorable process. A free energy value for phosphodiester bond formation was calculated using the reversibility of the T4 DNA ligase reaction. The relative number of DNA nicks to phosphodiester bonds in a circular plasmid DNA, formed during this reaction at fixed concentrations of ATP to AMP and PP(i), was quantified. At 25 degrees C, pH 7, the equilibrium constant (K(eq)) for the ligation reaction is 3.89 x 10(4) m. This value corresponds to a standard free energy (DeltaG degrees ') of -6.3 kcal mol(-1). By subtracting the known energy contribution due to hydrolysis of ATP to AMP and PP(i), DeltaG degrees ' for the hydrolysis of a DNA phosphodiester bond is -5.3 kcal mol(-1).
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The equilibrium constant estimated from DNA phosphodiester bond formation and NMP likely overestimates the magnitude of the driving force because it ignores the unfavorable entropy change of binding a free NTP monomer.
“This value likely overestimates the magnitude of because it ignores the unfavorable entropy change of binding a free NTP monomer, leading to .”
From Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution (2012) · cites this paper as [36]
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“We may estimate the equilibrium constant from DG0~5:3 kcal=mol of DNA phosphodiester bond formation and DG0~{10:9 kcal=mol of NTP?NMPzPPi (NMP: nucleoside monophosphate), yielding DG0~{5:6 kcal=mol [36,37].”
Background
- Authors
- Dickson, K. S., Burns, C. M., & Richardson, J. P.
- Affiliations
- Indiana University Bloomington (US)
- Corresponding author
- Richardson, John P.
- Venue
- Journal of Biological Chemistry
- Publisher
- Elsevier BV
- Published
- 2000-05
- Volume
- 275
- Issue
- 21
- Pages
- 15828-15831
- ISSN
- 0021-9258 (ISSN-L)
- OpenAlex
- W2059323916
- Cited by
- 78
- References
- 0
- Citations by year
- 2026: 4 · 2024: 4 · 2023: 5 · 2022: 5 · 2021: 3 · 2020: 8 · 2019: 3 · 2018: 3 · 2017: 5 · 2016: 3 · 2015: 3 · 2014: 6 · 2013: 4 · 2012: 5
- FWCI
- 0.36
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Biological Chemistry (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (5r01gm056095-30)
- National Institute of General Medical Sciences (GM56095)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › thermodynamics and calorimetric analyses
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Keywords
- DNA ligase, T4 DNA ligase, ATP hydrolysis, nicked DNA, plasmid DNA
- MeSH terms
- Adenosine Monophosphate, Adenosine Triphosphate, DNA Repair, DNA, Circular, Nucleic Acid Conformation, DNA Ligases, Thermodynamics
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