ArticleBiochemistry2013
Structural destabilization of DNA duplexes containing single-base lesions investigated by nanopore measurements.
Article in Biochemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- DNA glycosylase NEIL2 functions in multiple cellular processes.Progress in biophysics and molecular biology · 2021Review
- RNA Editing of the Human DNA Glycosylase NEIL1 Alters Its Removal of 5-Hydroxyuracil Lesions in DNA.Biochemistry · 2021Article
- Removal of oxidatively generated DNA damage by overlapping repair pathways.Free radical biology & medicine · 2017Review
- Interrogation of Base Pairing of the Spiroiminodihydantoin Diastereomers Using the α-Hemolysin Latch.Biochemistry · 2017Article
- Kinetics of T3-DNA Ligase-Catalyzed Phosphodiester Bond Formation Measured Using the α-Hemolysin Nanopore.ACS nano · 2016Article
- Energetics of base flipping at a DNA mismatch site confined at the latch constriction of α-hemolysin.Faraday discussions · 2016Article
- Article
- Base and Nucleotide Excision Repair of Oxidatively Generated Guanine Lesions in DNA.The Journal of biological chemistry · 2016Article
- Base Flipping within the α-Hemolysin Latch Allows Single-Molecule Identification of Mismatches in DNA.Journal of the American Chemical Society · 2016Article
- Unzipping of A-Form DNA-RNA, A-Form DNA-PNA, and B-Form DNA-DNA in the α-Hemolysin Nanopore.Biophysical journal · 2016Article
- Characterization of Interstrand DNA-DNA Cross-Links Using the α-Hemolysin Protein Nanopore.ACS nano · 2015Article
- Identification of DNA lesions using a third base pair for amplification and nanopore sequencing.Nature communications · 2015Article
- Article
- Smooth DNA transport through a narrowed pore geometry.Biophysical journal · 2014Article
- Internal vs fishhook hairpin DNA: unzipping locations and mechanisms in the α-hemolysin nanopore.The journal of physical chemistry. B · 2014Article
- Effect of an Electrolyte Cation on Detecting DNA Damage with the Latch Constriction of α-Hemolysin.The journal of physical chemistry letters · 2014Article
- Base-excision repair activity of uracil-DNA glycosylase monitored using the latch zone of α-hemolysin.Journal of the American Chemical Society · 2013Article
- The shaping of a molecular linguist: How a career studying DNA energetics revealed the language of molecular communication.The Journal of biological chemistryArticle
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5 authors.
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Abstract
The influence of DNA duplex structural destabilization introduced by a single base-pair modification was investigated by nanopore measurements. A series of 11 modified base pairs were introduced into the context of an otherwise complementary DNA duplex formed by a 17-mer and a 65-mer such that the overhanging ends comprised poly(dT)23 tails, generating a representative set of duplexes that display a range of unzipping mechanistic behaviors and kinetic stabilities. The guanine oxidation products 8-oxo-7,8-dihydroguanine (OG), guanidinohydantoin (Gh), and spiroiminodihydantoin (Sp) were paired with either cytosine (C), adenine (A), or 2,6-diaminopurine (D) to form modified base pairs. The mechanism and kinetic rate constants of duplex dissociation were determined by threading either the 3' or 5' overhangs into an α-hemolysin (α-HL) channel under an electrical field and measuring the distributions of unzipping times at constant force. In order of decreasing thermodynamic stability (as measured by duplex melting points), the rate of duplex dissociation increases, and the mechanism evolves from a first-order reaction to two sequential first-order reactions. These measurements allow us to rank the kinetic stability of lesion-containing duplexes relative to the canonical G:C base pair in which the OG:C, Gh:C, and Sp:C base pairs are, respectively, 3-200 times less stable. The rate constants also depend on whether unzipping was initiated from the 3' versus 5' side of the duplex. The kinetic stability of these duplexes was interpreted in terms of the structural destabilization introduced by the single base-pair modification. Specifically, a large distortion of the duplex backbone introduced by the presence of the highly oxidized guanine products Sp and Gh leads to a rapid two-step unzipping. The number of hydrogen bonds in the modified base pair plays a lesser role in determining the kinetics of duplex dissociation.
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