ArticleThe journal of physical chemistry. B2010
Thermodynamic characterization of DNA with 3-deazaadenine and 3-methyl-3-deazaadenine substitutions: the effect of placing a hydrophobic group in the minor groove of DNA.
Article in The journal of physical chemistry. B, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 16 citations in OpenAlex.
- Elucidating the Role of Groove Hydration on Stability and Functions of Biased DNA Duplexes in Cell-Like Chemical Environments.Journal of the American Chemical Society · 2024Article
- Impact of 3-deazapurine nucleobases on RNA properties.Nucleic acids research · 2021Article
- Structural Comparisons of PEI/DNA and PEI/siRNA Complexes Revealed with Molecular Dynamics Simulations.The journal of physical chemistry. B · 2017Article
- Specific minor groove solvation is a crucial determinant of DNA binding site recognition.Nucleic acids research · 2014Article
- Looking for Waldo: a potential thermodynamic signature to DNA damage.Accounts of chemical research · 2014Article
- Thermodynamic profiles and nuclear magnetic resonance studies of oligonucleotide duplexes containing single diastereomeric spiroiminodihydantoin lesions.Biochemistry · 2013Article
- Exploring purine N7 interactions via atomic mutagenesis: the group I ribozyme as a case study.RNA (New York, N.Y.) · 2012Article
- Thermodynamic signature of DNA damage: characterization of DNA with a 5-hydroxy-2'-deoxycytidine·2'-deoxyguanosine base pair.Biochemistry · 2012Article
- 3-Methyl-3-deazaadenine, a stable isostere of N3-methyl-adenine, is efficiently bypassed by replication in vivo and by transcription in vitro.DNA repair · 2011Article
- Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
In many high-resolution structures of DNA there are ordered waters associated with the floor of the minor groove and extending outward in several layers. It is thought that this hydration structure, along with cations, reduces the Coulombic repulsion of the interstrand phosphates. In previous studies, the replacement of the 3-N atom of adenine with a C-H to afford 3-deazaadenine was shown to decrease the thermodynamic stability of DNA via a reduction in the enthalpic term. Using spectroscopic and calorimetric methods, we report herein a rigorous examination of the thermodynamics of DNA with 3-deazaadenine modifications, and report for the first time how the presence of a minor groove methyl group, i.e., 3-methyl-3-deazaadeine, affects DNA stability, hydration, and cation binding. The methylation of adenine at the N3-position to yield N3-methyladenine represents an important reaction in the toxicity of many anticancer compounds. This minor groove lesion is unstable and cannot be readily studied in terms of its effect on DNA stability or structure. Our studies show that 3-methyl-3-deazaadenine, an isostere of N3-methyladenine, significantly destabilizes DNA (DeltaDeltaG > 4 kcal x mol(-1)) due to a significant drop in the enthalpy (DeltaH) term, which is associated with a lower hydration of the duplex relative to the unfolded state.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.