Intrinsic Properties of Nucleic Acids

Singer, Brett C.; Grünberger, Dezider

doi:10.1007/978-1-4613-3772-0_3

Cited by 10 publications

(5 citation statements)

References 24 publications

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“…Of interest is 3mA, a product of endogenous methyl donors (e.g., S-adenosylmethionine) [67, 68] and alkylating agents used in chemotherapy [69, 70]. Due to the short half-life of 3mA in DNA [71], it has not been possible to prepare purified oligonucleotides containing a single 3mA modification suitable for use in biochemical assays, although methylsulfonate derivatized lexitropsin (Me-Lex) peptides have been useful to study the biological effects of 3mA [72, 73].…”

Section: Discussionmentioning

confidence: 99%

An HPLC–tandem mass spectrometry method for simultaneous detection of alkylated base excision repair products

Mullins

Rubinson

Pereira

et al. 2013

Methods

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DNA glycosylases excise a broad spectrum of alkylated, oxidized, and deaminated nucleobases from DNA as the initial step in base excision repair. Substrate specificity and base excision activity are typically characterized by monitoring the release of modified nucleobases either from a genomic DNA substrate that has been treated with a modifying agent or from a synthetic oligonucleotide containing a defined lesion of interest. Detection of nucleobases from genomic DNA has traditionally involved HPLC separation and scintillation detection of radiolabeled nucleobases, which in the case of alkylation adducts can be laborious and costly. Here, we describe a mass spectrometry method to simultaneously detect and quantify multiple alkylpurine adducts released from genomic DNA that has been treated with N-methyl-N-nitrosourea (MNU). We illustrate the utility of this method by monitoring the excision of N3-methyladenine (3mA) and N7-methylguanine (7mG) by a panel of previously characterized prokaryotic and eukaryotic alkylpurine DNA glycosylases, enabling a comparison of substrate specificity and enzyme activity by various methods. Detailed protocols for these methods, along with preparation of genomic and oligonucleotide alkyl-DNA substrates, are also described.

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Section: Discussionmentioning

confidence: 99%

An HPLC–tandem mass spectrometry method for simultaneous detection of alkylated base excision repair products

Mullins

Rubinson

Pereira

et al. 2013

Methods

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“…The electrophilic methyldiazonium ion (Figure 1B ) derived from NDMA is the biotransformation product of the parent carcinogen by mammalian cytochrome P450s, primarily isoenzyme 2E1 (CYP2E1) ( 16 , 17 ). Reaction of the methyldiazonium ion with DNA produces 7-methylguanine (m7G; ∼70% of all DNA adducts), methyl phosphotriester (a backbone adduct; ∼15%), O 6 -methylguanine (m6G; ∼7%), 3-methyladenine (m3A; ∼3%), and several other quantitatively minor DNA base adducts ( 18–20 ).…”

Section: Introductionmentioning

confidence: 99%

Molecular origins of mutational spectra produced by the environmental carcinogen N-nitrosodimethylamine and SN1 chemotherapeutic agents

et al. 2023

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DNA-methylating environmental carcinogens such as N-nitrosodimethylamine (NDMA) and certain alkylators used in chemotherapy form O6-methylguanine (m6G) as a functionally critical intermediate. NDMA is a multi-organ carcinogen found in contaminated water, polluted air, preserved foods, tobacco products, and many pharmaceuticals. Only ten weeks after exposure to NDMA, neonatally-treated mice experienced elevated mutation frequencies in liver, lung and kidney of ∼35-fold, 4-fold and 2-fold, respectively. High-resolution mutational spectra (HRMS) of liver and lung revealed distinctive patterns dominated by GC→AT mutations in 5’-Pu-G-3’ contexts, very similar to human COSMIC mutational signature SBS11. Commonly associated with alkylation damage, SBS11 appears in cancers treated with the DNA alkylator temozolomide (TMZ). When cells derived from the mice were treated with TMZ, N-methyl-N-nitrosourea, and streptozotocin (two other therapeutic methylating agents), all displayed NDMA-like HRMS, indicating mechanistically convergent mutational processes. The role of m6G in shaping the mutational spectrum of NDMA was probed by removing MGMT, the main cellular defense against m6G. MGMT-deficient mice displayed a strikingly enhanced mutant frequency, but identical HRMS, indicating that the mutational properties of these alkylators is likely owed to sequence-specific DNA binding. In sum, the HRMS of m6G-forming agents constitute an early-onset biomarker of exposure to DNA methylating carcinogens and drugs.

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“…m 1 A is a non-mutagenic cytotoxic DNA lesion that acts as a strong replication blocker ( 45 ). It is generated by external and endogenous alkylating agents that modify single- and double-stranded DNA ( 46 ). The N 1-methyl group knocks out a WC H-bond and sterically destabilizes WC pairing (Figure 1B ) ( 19 , 22 , 33 , 34 ).…”

Section: Introductionmentioning

confidence: 99%

Insights into Watson–Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A

Sathyamoorthy

Shi

Zhou

et al. 2017

Nucleic Acids Research

123

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In the canonical DNA double helix, Watson–Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02–0.4%) and short-lived (lifetimes ∼0.2–2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair.

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Intrinsic Properties of Nucleic Acids

Cited by 10 publications

References 24 publications

An HPLC–tandem mass spectrometry method for simultaneous detection of alkylated base excision repair products

An HPLC–tandem mass spectrometry method for simultaneous detection of alkylated base excision repair products

Molecular origins of mutational spectra produced by the environmental carcinogen N-nitrosodimethylamine and SN1 chemotherapeutic agents

Insights into Watson–Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A

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