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Fleming AM, Guerra Castañaza Jenkins BL, Buck BA, Burrows CJ. DNA Damage Accelerates G-Quadruplex Folding in a Duplex-G-Quadruplex-Duplex Context. J Am Chem Soc 2024; 146. [PMID: 38602473 PMCID: PMC11046481 DOI: 10.1021/jacs.4c00960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
Molecular details for the impact of DNA damage on folding of potential G-quadruplex sequences (PQSs) to noncanonical DNA structures involved in gene regulation are poorly understood. Here, the effects of DNA base damage and strand breaks on PQS folding kinetics were studied in the context of the VEGF promoter sequence embedded between two DNA duplex anchors, termed a duplex-G-quadruplex-duplex (DGD) motif. This DGD scaffold imposes constraints on the PQS folding process that more closely mimic those found in genomic DNA. Folding kinetics were monitored by circular dichroism (CD) to find folding half-lives ranging from 2 s to 12 min depending on the DNA damage type and sequence position. The presence of Mg2+ ions and G-quadruplex (G4)-binding protein APE1 facilitated the folding reactions. A strand break placing all four G runs required for G4 formation on one side of the break accelerated the folding rate by >150-fold compared to the undamaged sequence. Combined 1D 1H NMR and CD analyses confirmed that isothermal folding of the VEGF-DGD constructs yielded spectral signatures that suggest the formation of G4 motifs and demonstrated a folding dependency on the nature and location of DNA damage. Importantly, the PQS folding half-lives measured are relevant to replication, transcription, and DNA repair time frames.
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Affiliation(s)
- Aaron M. Fleming
- Department of Chemistry, University
of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112-0850, United States
| | | | - Bethany A. Buck
- Department of Chemistry, University
of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University
of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112-0850, United States
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2
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Fleming AM, Jenkins BLGC, Buck BA, Burrows CJ. DNA Damage Accelerates G-Quadruplex Folding in a Duplex-G-Quadruplex-Duplex Context. bioRxiv 2024:2024.01.20.576387. [PMID: 38293204 PMCID: PMC10827223 DOI: 10.1101/2024.01.20.576387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Molecular details for DNA damage impact on the folding of potential G-quadruplex sequences (PQS) to non-canonical DNA structures that are involved in gene regulation are poorly understood. Here, the effects of DNA base damage and strand breaks on PQS folding kinetics were studied in the context of the VEGF promoter sequence embedded between two DNA duplex anchors, referred to as a duplex-G-quadruplex-duplex (DGD) motif. This DGD scaffold imposes constraints on the PQS folding process that more closely mimic those found in genomic DNA. Folding kinetics were monitored by circular dichroism (CD) to find folding half-lives ranging from 2 s to 12 min depending on the DNA damage type and sequence position. The presence of Mg2+ ions and the G-quadruplex (G4)-binding protein APE1 facilitated the folding reactions. A strand break placing all four G runs required for G4 formation on one side of the break accelerated the folding rate by >150-fold compared to the undamaged sequence. Combined 1D 1H-NMR and CD analyses confirmed that isothermal folding of the VEGF-DGD constructs yielded spectral signatures that suggest formation of G4 motifs, and demonstrated a folding dependency with the nature and location of DNA damage. Importantly, the PQS folding half-lives measured are relevant to replication, transcription, and DNA repair time frames.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850 United States
| | | | - Bethany A Buck
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850 United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850 United States
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3
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Fleming AM, Zhu J, Done VK, Burrows CJ. Advantages and challenges associated with bisulfite-assisted nanopore direct RNA sequencing for modifications. RSC Chem Biol 2023; 4:952-964. [PMID: 37920399 PMCID: PMC10619145 DOI: 10.1039/d3cb00081h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/23/2023] [Indexed: 11/04/2023] Open
Abstract
Nanopore direct RNA sequencing is a technology that allows sequencing for epitranscriptomic modifications with the possibility of a quantitative assessment. In the present work, pseudouridine (Ψ) was sequenced with the nanopore before and after the pH 7 bisulfite reaction that yields stable ribose adducts at C1' of Ψ. The adducted sites produced greater base call errors in the form of deletion signatures compared to Ψ. Sequencing studies on E. coli rRNA and tmRNA before and after the pH 7 bisulfite reaction demonstrated that using chemically-assisted nanopore sequencing has distinct advantages for minimization of false positives and false negatives in the data. The rRNA from E. coli has 19 known U/C sequence variations that give similar base call signatures as Ψ, and therefore, are false positives when inspecting base call data; however, these sites are refractory to reacting with bisulfite as is easily observed in nanopore data. The E. coli tmRNA has a low occupancy Ψ in a pyrimidine-rich sequence context that is called a U representing a false negative; partial occupancy by Ψ is revealed after the bisulfite reaction. In a final study, 5-methylcytidine (m5C) in RNA can readily be observed after the pH 5 bisulfite reaction in which the parent C deaminates to U and the modified site does not react. This locates m5C when using bisulfite-assisted nanopore direct RNA sequencing, which is otherwise challenging to observe. The advantages and challenges of the overall approach are discussed.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah 315 S. 1400 East Salt Lake City UT 84112-0850 USA
| | - Judy Zhu
- Department of Chemistry, University of Utah 315 S. 1400 East Salt Lake City UT 84112-0850 USA
| | - Vilhelmina K Done
- Department of Chemistry, University of Utah 315 S. 1400 East Salt Lake City UT 84112-0850 USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah 315 S. 1400 East Salt Lake City UT 84112-0850 USA
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Fleming AM, Omaga CA, Burrows CJ. NEIL3 promoter G-quadruplex with oxidatively modified bases shows magnesium-dependent folding that stalls polymerase bypass. Biochimie 2023; 214:156-166. [PMID: 37437684 PMCID: PMC10592359 DOI: 10.1016/j.biochi.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023]
Abstract
Oxidative stress unleashes reactive species capable of oxidizing 2'-deoxyguanosine (G) nucleotides in G-rich sequences of the genome, such as the potential G-quadruplex forming sequencing (PQS) in the NEIL3 gene promoter. Oxidative modification of G yields 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG) that can be further oxidized to hydantoin products. Herein, OG was synthesized into the NEIL3 PQS that was allowed to fold to a G-quadruplex (G4) in K+ ion solutions with varying amounts of Mg2+ in the physiological range. The Mg2+ dependency in the oxidatively modified NEIL3 G4 to stall a replicative DNA polymerase was evaluated. The polymerase was found to stall at the G4 or OG, as well as continue to full-length extension with dependency on the location of the modification and the concentration of Mg2+. To provide some clarity on these findings, OG or the hydantoins were synthesized in model NEIL3 G4 folding sequences at the positions of the polymerase study. The model G4 sequences were allowed to fold in K+ ion solutions with varying levels of Mg2+ to identify how the presence of the divalent metal impacted G4 folding depending on the location of the modification. The presence of Mg2+ either caused the transition of the NEIL3 G4 folds from an antiparallel to parallel orientation of the strands or had no impact. Structural models are proposed to understand the findings using the literature as a guide. The biological significance of the results is discussed.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112-0850, USA
| | - Carla A Omaga
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112-0850, USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112-0850, USA.
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Fleming AM, Bommisetti P, Xiao S, Bandarian V, Burrows CJ. Direct Nanopore Sequencing for the 17 RNA Modification Types in 36 Locations in the E. coli Ribosome Enables Monitoring of Stress-Dependent Changes. ACS Chem Biol 2023; 18:2211-2223. [PMID: 37345867 PMCID: PMC10594579 DOI: 10.1021/acschembio.3c00166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023]
Abstract
The bacterium Escherichia coli possesses 16S and 23S rRNA strands that have 36 chemical modification sites with 17 different structures. Nanopore direct RNA sequencing using a protein nanopore sensor and helicase brake, which is also a sensor, was applied to the rRNAs. Nanopore current levels, base calling profile, and helicase dwell times for the modifications relative to unmodified synthetic rRNA controls found signatures for nearly all modifications. Signatures for clustered modifications were determined by selective sequencing of writer knockout E. coli and sequencing of synthetic RNAs utilizing some custom-synthesized nucleotide triphosphates for their preparation. The knowledge of each modification's signature, apart from 5-methylcytidine, was used to determine how metabolic and cold-shock stress impact rRNA modifications. Metabolic stress resulted in either no change or a decrease, and one site increased in modification occupancy, while cold-shock stress led to either no change or a decrease. The double modification m4Cm1402 resides in 16S rRNA, and it decreased with both stressors. Using the helicase dwell time, it was determined that the N4 methyl group is lost during both stressors, and the 2'-OMe group remained. In the ribosome, this modification stabilizes binding to the mRNA codon at the P-site resulting in increased translational fidelity that is lost during stress. The E. coli genome has seven rRNA operons (rrn), and the earlier studies aligned the nanopore reads to a single operon (rrnA). Here, the reads were aligned to all seven operons to identify operon-specific changes in the 11 pseudouridines. This study demonstrates that direct sequencing for >16 different RNA modifications in a strand is achievable.
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Affiliation(s)
- Aaron M. Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake
City, Utah 84112-0850, United States
| | - Praneeth Bommisetti
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake
City, Utah 84112-0850, United States
| | - Songjun Xiao
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake
City, Utah 84112-0850, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake
City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake
City, Utah 84112-0850, United States
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Burrows CJ, Fleming AM. Bisulfite and Nanopore Sequencing for Pseudouridine in RNA. Acc Chem Res 2023; 56:2740-2751. [PMID: 37700703 PMCID: PMC10911771 DOI: 10.1021/acs.accounts.3c00458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Nucleophilic addition of bisulfite to pyrimidine bases has been known for a half century, and the reaction has been in use for at least a quarter of a century for identifying 5-methylcytidine in DNA. This account focuses on the chemistry of bisulfite with pseudouridine, an isomer of the RNA nucleoside uridine in which the uracil base is connected to C1' of ribose via C5 instead of N1. Pseudouridine, Ψ, is the most common nucleotide modification found in cellular RNA overall, in part due to its abundance in rRNAs and tRNAs. It has a stabilizing influence on RNA structure because N1 is now available for additional hydrogen bonding and because the heterocycle is slightly better at π stacking. The isomerization of U to Ψ in RNA strands is catalyzed by 13 different enzymes in humans and 11 in E. coli; some of these enzymes are implicated in disease states which is testament to the biological importance of pseudouridine in cells. Recently, pseudouridine came into the limelight as the key modification that, after N1 methylation, enables mRNA vaccines to be delivered efficiently into human tissue with minimal generation of a deleterious immunogenic response. Here we describe the bisulfite reaction with pseudouridine which gives rise to a chemical sequencing method to map the modified base in the epitranscriptome. Unlike the reaction with cytidine, the addition of bisulfite to Ψ leads irreversibly to form an adduct that is bypassed during cDNA synthesis by reverse transcriptases yielding a characteristic deletion signature. Although there were hints to the structure of the bisulfite adduct(s) 30 to 50 years ago, it took modern spectroscopic and computational methods to solve the mystery. Raman spectroscopy along with extensive NMR, ECD, and computational work led to the assignment of the major product as the (R) diastereomer of an oxygen adduct at C1' of a ring-opened pseudouridine. Mechanistically, this arose from a succession of conjugate addition, E2 elimination, and a [2,3] sigmatropic rearrangement, all of which are stereodefined reactions. A minor reaction with excess bisulfite led to the (S) isomer of a S-adducted SO3- group. Understanding structure and mechanism aided the design of a Ψ-specific sequencing reaction and guided attempts to improve the utility and specificity of the method. Separately, we have been investigating the use of nanopore direct RNA sequencing, a single-molecule method that directly analyzes RNA strands isolated from cells after end-ligation of adaptor sequences. By combining the electrical current and base-calling data from the nanopore with dwell-time analysis from the helicase employed to deliver RNA to the nanopore, we were able to map Ψ sites in nearly all sequence contexts. This analysis was employed to find Ψ residues in the SARS-CoV-2 vRNA, to analyze the sequence context effects of mRNA vaccine synthesis via in vitro transcription, and to evaluate the impact of stress on chemical modifications in the E. coli ribosome. Most recently, we found that bisulfite treatment of RNA leading to Ψ adducts could modulate the nanopore signal to help in mapping modifications of low occupancy.
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Affiliation(s)
- Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112-0850, United States
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Xiao S, Fleming AM, Burrows CJ. Sequencing for oxidative DNA damage at single-nucleotide resolution with click-code-seq v2.0. Chem Commun (Camb) 2023; 59:8997-9000. [PMID: 37401666 PMCID: PMC10909242 DOI: 10.1039/d3cc02699j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Oxidative damage to DNA nucleotides has many cellular outcomes that could be aided by the development of sequencing methods. Herein, the previously reported click-code-seq method for sequencing a single damage type is redeveloped to enable the sequencing of many damage types by making simple changes to the protocol (i.e., click-code-seq v2.0).
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Affiliation(s)
- Songjun Xiao
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA.
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Howpay Manage SA, Zhu J, Fleming AM, Burrows CJ. Promoters vs. telomeres: AP-endonuclease 1 interactions with abasic sites in G-quadruplex folds depend on topology. RSC Chem Biol 2023; 4:261-270. [PMID: 37034403 PMCID: PMC10074553 DOI: 10.1039/d2cb00233g] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
The DNA repair endonuclease APE1 is responsible for the cleavage of abasic sites (AP) in DNA as well as binding AP in promoter G-quadruplex (G4) folds in some genes to regulate transcription. The present studies focused on the topological properties of AP-bearing G4 folds and how they impact APE1 interaction. The human telomere sequence with a tetrahydrofuran model (F) of an AP was folded in K+- or Na+-containing buffers to adopt hybrid- or basket-folds, respectively. Endonuclease and binding assays were performed with APE1 and the G4 substrates, and the data were compared to prior work with parallel-stranded VEGF and NEIL3 promoter G4s to identify topological differences. The APE1-catalyzed endonuclease assays led to the conclusion that telomere G4 folds were slightly better substrates than the promoter G4s, but the yields were all low compared to duplex DNA. In the binding assays, G4 topological differences were observed in which APE1 bound telomere G4s with dissociation constants similar to single-stranded DNA, and promoter G4s were bound with nearly ten-fold lower values similar to duplex DNA. An in-cellulo assay with the telomere G4 in a model promoter bearing a lesion failed to regulate transcription. These data support a hypothesis that G4 topology in gene promoters is a critical feature that APE1 recognizes for gene regulation.
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Affiliation(s)
| | - Judy Zhu
- Department of Chemistry, University of Utah 315 S. 1400 E. Salt Lake City UT 84112-0850 USA
| | - Aaron M Fleming
- Department of Chemistry, University of Utah 315 S. 1400 E. Salt Lake City UT 84112-0850 USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah 315 S. 1400 E. Salt Lake City UT 84112-0850 USA
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Fleming AM, Burrows CJ. Nanopore sequencing for N1-methylpseudouridine in RNA reveals sequence-dependent discrimination of the modified nucleotide triphosphate during transcription. Nucleic Acids Res 2023; 51:1914-1926. [PMID: 36727474 PMCID: PMC9976907 DOI: 10.1093/nar/gkad044] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/21/2022] [Accepted: 01/16/2023] [Indexed: 02/03/2023] Open
Abstract
Direct RNA sequencing with a commercial nanopore platform was used to sequence RNA containing uridine (U), pseudouridine (Ψ) or N1-methylpseudouridine (m1Ψ) in >100 different 5-nucleotide contexts. The base calling data for Ψ or m1Ψ were similar but different from U allowing their detection. Understanding the nanopore signatures for Ψ and m1Ψ enabled a running start T7 RNA polymerase assay to study the selection of UTP versus ΨTP or m1ΨTP competing mixtures in all possible adjacent sequence contexts. A significant sequence context dependency was observed for T7 RNA polymerase with insertion yields for ΨTP versus UTP spanning a range of 20-65%, and m1ΨTP versus UTP producing variable yields that differ by 15-70%. Experiments with SP6 RNA polymerase, as well as chemically-modified triphosphates and DNA templates provide insight to explain the observations. The SP6 polymerase introduced m1ΨTP when competed with UTP with a smaller window of yields (15-30%) across all sequence contexts studied. These results may aid in future efforts that employ RNA polymerases to make therapeutic mRNAs with sub-stoichiometric amounts of m1Ψ.
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Affiliation(s)
- Aaron M Fleming
- Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA
| | - Cynthia J Burrows
- Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA.
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Fleming AM, Tran R, Omaga CA, Manage SAH, Burrows CJ, Conboy JC. Second Harmonic Generation Interrogation of the Endonuclease APE1 Binding Interaction with G-Quadruplex DNA. Anal Chem 2022; 94:15027-15032. [PMID: 36269876 PMCID: PMC9945475 DOI: 10.1021/acs.analchem.2c02951] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The binding interaction between the DNA repair enzyme apurinic/apyrimidinic endonuclease-1 (APE1) with promoter G-quadruplex (G4) folds bearing an abasic site (AP) can serve as a gene regulatory switch during oxidative stress. Prior fluorescence-based analysis in solution suggested APE1 binds the VEGF promoter G4 but whether this interaction was specific or not remained an open question. Second harmonic generation (SHG) was used in this work to measure the noncanonical DNA-protein binding interaction in a label-free assay with high sensitivity to demonstrate the interaction is ordered and specific. The binding of APE1 to the VEGF promoter G4 with AP sites modeled by a tetrahydrofuran analogue produced dissociation constants of ∼100 nM that differed from duplex and single-stranded DNA control studies. The SHG measurements confirmed APE1 binds the VEGF G4 folds in a specific manner resolving a remaining question regarding how this endonuclease with gene regulatory features engages G4 folds. The studies demonstrate the power of SHG to interrogate noncanonical DNA-protein interactions providing a foundational example for the use of this analytical method in future biochemical analyses.
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Affiliation(s)
- Aaron M. Fleming
- 315 S 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT United States, 84112-0850
| | - Renee Tran
- 315 S 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT United States, 84112-0850
| | - Carla A. Omaga
- 315 S 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT United States, 84112-0850
| | - Shereen A. Howpay Manage
- 315 S 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT United States, 84112-0850
| | - Cynthia J. Burrows
- 315 S 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT United States, 84112-0850
| | - John C. Conboy
- 315 S 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT United States, 84112-0850
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Fleming AM, Xiao S, Chabot MB, Burrows CJ. Fluorophore-mediated Photooxidation of the Guanine Heterocycle. J PHYS ORG CHEM 2022; 35:e4325. [PMID: 36388261 PMCID: PMC9642976 DOI: 10.1002/poc.4325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/11/2022] [Indexed: 11/09/2022]
Abstract
Fluorescent dyes are routinely used to visualize DNA or RNA in various experiments, and some dyes also act as photosensitizers capable of catalyzing oxidation reactions. The present studies explored whether the common labeling dyes fluorescein, rhodamine, BODIPY, or cyanine3 (Cy3) can function as photosensitizers to oxidize nucleic acid polymers. Photoirradiation of each dye in the presence of the guanine (G) heterocycle, which is the most sensitive toward oxidation, identified slow rates of nucleobase oxidation in the nucleoside and DNA contexts. For all four fluorophores studied, the only product detected was spiroiminodihydantoin (Sp) suggesting the dyes functioned as Type II photosensitizers and generate singlet oxygen (1O2). The nucleoside reactions were then conducted in D2O solutions, known to increase the lifetime of 1O2, which resulted in a ~6-fold increase in the Sp yield, further supporting the classification of these dyes as Type II photosensitizers. Lastly, we inspected the pattern of G reactivity with the dyes upon photoirradiation in the context of a parallel-stranded G-quadruplex. The G nucleotides in the two exterior G-tetrads were found to be oxidation prone, providing the third line of evidence that the dyes are Type II photooxidants. The present work found that the common dyes fluorescein, rhodamine, BODIPY, or Cy3 can drive G oxidation but with a slow rate and low overall yield. This will likely not impact many experiments using dyes to study nucleic acids except for those that have long exposures with high-intensity lights, such as sequencing-by-synthesis experiments using fluorescence as the readout.
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Affiliation(s)
- Aaron M. Fleming
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850
| | - Songjun Xiao
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850
| | - Michael B. Chabot
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850
| | - Cynthia J. Burrows
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850
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Abstract
Apurinic/apyrimidinic endonuclease-1 (APE1) is a base excision repair (BER) enzyme that is also engaged in transcriptional regulation. Previous work demonstrated that the enzymatic stalling of APE1 on a promoter G-quadruplex (G4) recruits transcription factors during oxidative stress for gene regulation. Also, during oxidative stress, cysteine (Cys) oxidation is a post-translational modification (PTM) that can change a protein's function. The current study provides a quantitative survey of cysteine oxidation to sulfenic acid in APE1 and how this PTM at specific cysteine residues affects the function of APE1 toward the NEIL3 gene promoter G4 bearing an abasic site. Of the seven cysteine residues in APE1, five (C65, C93, C208, C296, and C310) were prone to carbonate radical anion oxidation to yield sulfenic acids that were identified and quantified by mass spectrometry. Accordingly, five Cys-to-serine (Ser) mutants of APE1 were prepared and found to have attenuated levels of endonuclease activity, depending on the position, while KD values generally decreased for G4 binding, indicating greater affinity. These data support the concept that cysteine oxidation to sulfenic acid can result in modified APE1 that enhances G4 binding at the expense of endonuclease activity during oxidative stress. Cysteine oxidation to sulfenic acid residues should be considered as one of the factors that may trigger a switch from base excision repair activity to transcriptional modulation by APE1.
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Affiliation(s)
- Shereen A. Howpay Manage
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
| | - Aaron M. Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
| | - Hsiao-Nung Chen
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
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Abstract
In RNA, pseudouridine (Ψ) and 5-methylcytidine (m5C) are located by their differential reactions with NaHSO3 at pH 5. The pyrimidines were allowed to react with NaHSO3, NaN3, NaCN, or NaSCN at pH 5 to find that NaHSO3 was unique in achieving quantitative yields. Pseudouridine reaction selectivity with NaHSO3 was found at pH 7 supported by the reaction rate constants. The Ψ derivative N1-methylpseudouridine found in mRNA vaccines reacts similarly with bisulfite to yield ribose adducts.
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Affiliation(s)
- Aaron M. Fleming
- Dept. of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT, 84112-0850
| | - Songjun Xiao
- Dept. of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT, 84112-0850
| | - Cynthia J. Burrows
- Dept. of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT, 84112-0850
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15
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Chabot MB, Fleming AM, Burrows CJ. Insights into the 5-Carboxamido-5-Formamido-2-Iminohydantoin Structural Isomerization Equilibria. J Org Chem 2022; 87:11865-11870. [PMID: 35960780 DOI: 10.1021/acs.joc.2c01371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Exposure of DNA to oxidants results in modification of the electron-rich guanine heterocycle including formation of the mutagenic 5-carboxamido-5-formamido-2-iminohydantoin (2Ih) lesion. Previously thought to exist solely as a pair of diastereomers, we found under biologically relevant conditions that 2Ih reversibly closes to a formerly hypothetical intermediate and opens into a newly discovered regioisomer. In a nucleoside model, only ∼80% of 2Ih existed as the structure studied over the last 20 years with significant isomeric products persisting in buffered aqueous solution.
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Affiliation(s)
- Michael B Chabot
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, Utah 84112-0850, United States
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16
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Abstract
Ozonolysis of guanosine formed the 5-carboxamido-5-formamido-2-iminohydantoin (2Ih) nucleoside along with trace spiroiminodihydantoin (Sp). On the basis of literature precedent, we propose an unconventional ozone mechanism involving incorporation of only one oxygen atom of O3 to form 2Ih with evolution of singlet oxygen responsible for Sp formation. The increased yield of Sp in the buffered 1O2-stabilizing solvent D2O, formation of 2Ih in a short oligodeoxynucleotide, and 18O-isotope labeling provided evidence to support this mechanism. The elusiveness and challenges of working with 2Ih are described in a series of studies on the significant context effects on the half-life of the 2Ih glycosidic bond.
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Affiliation(s)
- Michael B Chabot
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, Utah 84112-0850, United States
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17
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Fleming AM, Chabot MB, Nguyen NLB, Burrows CJ. Collateral Damage Occurs When Using Photosensitizer Probes to Detect or Modulate Nucleic Acid Modifications. Angew Chem Int Ed Engl 2022; 61:e202110649. [PMID: 34919767 PMCID: PMC8810719 DOI: 10.1002/anie.202110649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Indexed: 12/23/2022]
Abstract
Nucleic acids are chemically modified to fine-tune their properties for biological function. Chemical tools for selective tagging of base modifications enables new approaches; the photosensitizers riboflavin and anthraquinone were previously proposed to oxidize N6 -methyladenine (m6 A) or 5-methylcytosine (5mdC) selectively. Herein, riboflavin, anthraquinone, or Rose Bengal were allowed to react with the canonical nucleosides dA, dC, dG, and dT, and the modified bases 5mdC, m6 A, 8-oxoguanine (dOG), and 8-oxoadenine (dOA) to rank their reactivities. The nucleoside studies reveal that dOG is the most reactive and that the native nucleoside dG is higher or similar in reactivity to 5mdC or m6 A; competition in both single- and double-stranded DNA of dG vs. 5mdC or 6mdA for oxidant confirmed that dG is favorably oxidized. Thus, photosensitizers are promiscuous nucleic acid oxidants with poor chemoselectivity that will negatively impact attempts at targeted oxidation of modified nucleotides in cells.
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Affiliation(s)
- Aaron M. Fleming
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, UT 84112-0850
| | - Michael B. Chabot
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, UT 84112-0850
| | - Ngoc L. B. Nguyen
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, UT 84112-0850
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, UT 84112-0850
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18
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Affiliation(s)
- Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112-0850, United States
| | - Jason B Harper
- School of Chemistry, University of New South Wales, Sydney 2052, Australia
| | - Wolfram Sander
- Lehrstuhl für Organische Chemie II, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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19
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Abstract
![]()
The G-quadruplex
is a noncanonical fold of DNA commonly found at
telomeres and within gene promoter regions of the genome. These guanine-rich
sequences are highly susceptible to damages such as base oxidation
and depurination, leading to abasic sites. In the present work, we
address whether a vacancy, such as an abasic site, in a G-quadruplex
serves as a specific ligand recognition site. When the G-tetrad is
all guanines, the vacant (abasic) site is recognized and bound by
free guanine nucleobase. However, we aim to understand whether the
preference for a specific ligand recognition changes with the presence
of a guanine oxidation product 8-oxo-7,8-dihydroguanine (OG) adjacent
to the vacancy in the tetrad. Using molecular dynamics simulation,
circular dichroism, and nuclear magnetic resonance, we examined the
ability for riboflavin to stabilize abasic site-containing G-quadruplex
structures. Through structural and free energy binding analysis, we
observe riboflavin’s ability to stabilize an abasic site-containing
G-quadruplex only in the presence of an adjacent OG-modified base.
Further, when compared to simulation with the vacancy filled by free
guanine, we observe that the free guanine nucleobase is pushed outside
of the tetrad by OG to interact with other parts of the structure,
including loop residues. These results support the preference of riboflavin
over free guanine to fill an OG-adjacent G-quadruplex abasic vacancy.
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Affiliation(s)
- Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States
| | - Lauren Winkler
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States
| | - Jingwei Ma
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Fatjon Hanelli
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States
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20
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Abstract
PURPOSE One outcome of DNA damage from hydroxyl radical generated by ionizing radiation (IR) or by the Fenton reaction is oxidation of the nucleobases, especially guanine (G). While 8-oxo-7,8-dihydroguanine (OG) is a commonly studied oxidized lesion, several others are formed in high abundance, including 5-carboxamido-5-formamido-2-iminohydantoin (2Ih), a prevalent product in in vitro chemistry that is challenging to study from cellular sources. In this short review, we have a goal of explaining new insights into hydroxyl radical-induced oxidation chemistry of G in DNA and comparing it to endogenous DNA damage, as well as commenting on the biological outcomes of DNA base damage. CONCLUSIONS Pathways of oxidation of G are discussed and a comparison is made between IR (hydroxyl radical chemistry) and endogenous oxidative stress that largely forms carbonate radical anion as a reactive intermediate. These pathways overlap with the formation of OG and 2Ih, but other guanine-derived lesions are more pathway specific. The biological consequences of guanine oxidation include both mutagenesis and epigenetics; a new mechanism of gene regulation via the base excision repair pathway is described for OG, whereas the impact of IR in forming guanine modifications may be to confound this process in addition to introduction of mutagenic sites.
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21
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Fleming AM, Chabot MB, Nguyen NLB, Burrows CJ. Collateral Damage Occurs When Using Photosensitizer Probes to Detect or Modulate Nucleic Acid Modifications. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Aaron M. Fleming
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City Ut84112-0850 USA
| | - Michael B. Chabot
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City Ut84112-0850 USA
| | - Ngoc L. B. Nguyen
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City Ut84112-0850 USA
| | - Cynthia J. Burrows
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City Ut84112-0850 USA
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22
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Fleming AM, Manage SAH, Burrows CJ. Binding of AP endonuclease-1 to G-quadruplex DNA depends on the N-terminal domain, Mg 2+ and ionic strength. ACS Bio Med Chem Au 2021; 1:44-56. [PMID: 35005714 DOI: 10.1021/acsbiomedchemau.1c00031] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The base excision repair enzyme apurinic/apyrimidinic endonuclease-1 (APE1) is also engaged in transcriptional regulation. APE1 can function in both pathways when the protein binds to a promoter G-quadruplex (G4) bearing an abasic site (modeled with tetrahydrofuran, F) that leads to enzymatic stalling on the non-canonical fold to recruit activating transcription factors. Biochemical and biophysical studies to address APE1's binding and catalytic activity with the vascular endothelial growth factor (VEGF) promoter G4 are lacking, and the present work provides insight on this topic. Herein, the native APE1 was used for cleavage assays, and the catalytically inactive mutant D210A was used for binding assays with double-stranded DNA (dsDNA) versus the native G4 or the G4 with F at various positions, revealing dependencies of the interaction on the cation concentrations K+ and Mg2+ and the N-terminal domain of the protein. Assays in 0, 1, or 10 mM Mg2+ found that dsDNA and G4 substrates required the cation for both binding and catalysis, in which G4 binding increased with [Mg2+]. Studies with 50 versus physiological 140 mM K+ ions showed that F-containing dsDNA was bound and cleaved by APE1; whereas, the G4s with F were poorly cleaved in low salt and not cleaved at all at higher salt while the binding remained robust. Using Δ33 or Δ61 N-terminal truncated APE1 proteins, the binding and cleavage of dsDNA with F was minimally impacted; in contrast, the G4s required the N-terminus for binding and catalysis is nearly abolished without the N-terminus. With this knowledge, we found APE1 could remodel the F-containing VEGF promoter dsDNA→G4 folds in solution. Lastly, the addition of the G4 ligand pyridostatin inhibited APE1 binding and cleavage of F-containing G4s but not dsDNA. The biological and medicinal chemistry implications of the results are discussed.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
| | - Shereen A Howpay Manage
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
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23
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Fleming AM, Mathewson NJ, Howpay Manage SA, Burrows CJ. Nanopore Dwell Time Analysis Permits Sequencing and Conformational Assignment of Pseudouridine in SARS-CoV-2. ACS Cent Sci 2021; 7:1707-1717. [PMID: 34729414 PMCID: PMC8554835 DOI: 10.1021/acscentsci.1c00788] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Indexed: 05/08/2023]
Abstract
Direct RNA sequencing for the epitranscriptomic modification pseudouridine (Ψ), an isomer of uridine (U), was conducted with a protein nanopore sensor using a helicase brake to slowly feed the RNA into the sensor. Synthetic RNAs with 100% Ψ or U in 20 different known human sequence contexts identified differences during sequencing in the base-calling, ionic current, and dwell time in the nanopore sensor; however, the signals were found to have a dependency on the context that would result in biases when sequencing unknown samples. A solution to the challenge was the identification that the passage of Ψ through the helicase brake produced a long-range dwell time impact with less context bias that was used for modification identification. The data analysis approach was employed to analyze publicly available direct RNA sequencing data for SARS-CoV-2 RNA taken from cell culture to locate five conserved Ψ sites in the genome. Two sites were found to be substrates for pseudouridine synthase 1 and 7 in an in vitro assay, providing validation of the analysis. Utilization of the helicase as an additional sensor in direct RNA nanopore sequencing provides greater confidence in calling RNA modifications.
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Affiliation(s)
- Aaron M. Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake
City, Utah 84112-0850, United States
| | - Nicole J. Mathewson
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake
City, Utah 84112-0850, United States
| | - Shereen A. Howpay Manage
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake
City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake
City, Utah 84112-0850, United States
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24
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Fleming AM, Burrows CJ. Oxidative stress-mediated epigenetic regulation by G-quadruplexes. NAR Cancer 2021; 3:zcab038. [PMID: 34541539 PMCID: PMC8445369 DOI: 10.1093/narcan/zcab038] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/20/2021] [Accepted: 09/06/2021] [Indexed: 02/06/2023] Open
Abstract
Many cancer-associated genes are regulated by guanine (G)-rich sequences that are capable of refolding from the canonical duplex structure to an intrastrand G-quadruplex. These same sequences are sensitive to oxidative damage that is repaired by the base excision repair glycosylases OGG1 and NEIL1–3. We describe studies indicating that oxidation of a guanosine base in a gene promoter G-quadruplex can lead to up- and downregulation of gene expression that is location dependent and involves the base excision repair pathway in which the first intermediate, an apurinic (AP) site, plays a key role mediated by AP endonuclease 1 (APE1/REF1). The nuclease activity of APE1 is paused at a G-quadruplex, while the REF1 capacity of this protein engages activating transcription factors such as HIF-1α, AP-1 and p53. The mechanism has been probed by in vitro biophysical studies, whole-genome approaches and reporter plasmids in cellulo. Replacement of promoter elements by a G-quadruplex sequence usually led to upregulation, but depending on the strand and precise location, examples of downregulation were also found. The impact of oxidative stress-mediated lesions in the G-rich sequence enhanced the effect, whether it was positive or negative.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA
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25
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Fleming AM, Burrows CJ. Iron Fenton oxidation of 2'-deoxyguanosine in physiological bicarbonate buffer yields products consistent with the reactive oxygen species carbonate radical anion not the hydroxyl radical. Chem Commun (Camb) 2021; 56:9779-9782. [PMID: 32716425 DOI: 10.1039/d0cc04138f] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Product analysis from the iron Fenton oxidation of 2'-deoxyguanosine found reactions in bicarbonate buffer yield 8-oxo-2'-deoxyguanosine and spiroiminodihyantoin consistent with CO3˙-. Reactions in phosphate buffer furnished high yields of sugar oxidation products consistent with HO˙. These observations change the view of DNA oxidation products from the iron-Fenton reaction.
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Affiliation(s)
- Aaron M Fleming
- Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA.
| | - Cynthia J Burrows
- Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA.
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26
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Burrows CJ. Kool chemistry of DNA and RNA biopolymers. Biopolymers 2021; 112:e23417. [PMID: 33493362 DOI: 10.1002/bip.23417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Cynthia J Burrows
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
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27
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Burrows CJ. Welcoming Our New Sister Journal, Accounts of Materials Research. Acc Chem Res 2020; 53:2495. [PMID: 33141571 DOI: 10.1021/acs.accounts.0c00676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Abstract
Contrary to frequent reports in the literature, hydroxyl radical is not a key species participating in endogenous oxidative DNA damage. Instead, carbonate radical anion is formed from the Fenton reaction under cellular conditions and from decomposition of nitrosoperoxycarbonate generated during inflammation. Carbonate radical anion is a potent one-electron oxidant capable of generating base radical cations that can migrate over long distances in duplex DNA, ultimately generating 8-oxo-7,8-dihydroguanine at a redox-sensitive sequence such as GGG. Such a mechanism enables G-quadruplex-forming sequences to act as long-range sensors of oxidative stress, impacting gene expression via the DNA repair mechanism that reads and ultimately erases the oxidized base. With a writing, reading and erasing mechanism in place, oxidative 'damage' to DNA might be relabeled as 'epigenetic' modifications.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA.
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29
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. ACS Pharmacol Transl Sci 2020; 3:559-561. [DOI: 10.1021/acsptsci.0c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Indexed: 11/29/2022]
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30
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. J Proteome Res 2020; 19:2911-2913. [DOI: 10.1021/acs.jproteome.0c00436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. ACS Nano 2020; 14:7675-7677. [PMID: 32558540 DOI: 10.1021/acsnano.0c05013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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32
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. J Chem Inf Model 2020; 60:3325-3327. [DOI: 10.1021/acs.jcim.0c00683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. ACS Chem Health Saf 2020. [DOI: 10.1021/acs.chas.0c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. J Nat Prod 2020; 83:2057-2059. [PMID: 32559070 DOI: 10.1021/acs.jnatprod.0c00670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. ACS Sens 2020; 5:1858-1860. [PMID: 32558548 DOI: 10.1021/acssensors.0c01217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. ACS Cent Sci 2020; 6:1012-1014. [PMID: 32724833 PMCID: PMC7379059 DOI: 10.1021/acscentsci.0c00794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. ACS Macro Lett 2020; 9:1004-1006. [PMID: 35648598 DOI: 10.1021/acsmacrolett.0c00459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. Acc Chem Res 2020; 53:1257-1259. [PMID: 32558553 DOI: 10.1021/acs.accounts.0c00383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. ACS Appl Bio Mater 2020; 3:3925-3927. [DOI: 10.1021/acsabm.0c00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Burrows CJ, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Aldrich CC, Rowan S, Bin Liu, Liotta D, Weiss PS, Zhang D, Ganesh KN, Sexton P, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, McCoy A, Shea JE, Zanni M, Murphy C, Scholes G, Loo JA. Update to Our Reader, Reviewer, and Author Communities-April 2020. Chem Res Toxicol 2020; 33:1509-1510. [PMID: 32320611 DOI: 10.1021/acs.chemrestox.0c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. Chem Res Toxicol 2020; 33:1511-1513. [DOI: 10.1021/acs.chemrestox.0c00245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Rogers RA, Meyer MR, Stewart KM, Eyring GM, Fleming AM, Burrows CJ. Hysteresis in poly-2'-deoxycytidine i-motif folding is impacted by the method of analysis as well as loop and stem lengths. Biopolymers 2020; 112:e23389. [PMID: 33098582 DOI: 10.1002/bip.23389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/06/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023]
Abstract
In DNA, i-motif (iM) folds occur under slightly acidic conditions when sequences rich in 2'-deoxycytidine (dC) nucleotides adopt consecutive dC self base pairs. The pH stability of an iM is defined by the midpoint in the pH transition (pHT ) between the folded and unfolded states. Two different experiments to determine pHT values via circular dichroism (CD) spectroscopy were performed on poly-dC iMs of length 15, 19, or 23 nucleotides. These experiments demonstrate two points: (1) pHT values were dependent on the titration experiment performed, and (2) pH-induced denaturing or annealing processes produced isothermal hysteresis in the pHT values. These results in tandem with model iMs with judicious mutations of dC to thymidine to favor particular folds found the hysteresis was maximal for the shorter poly-dC iMs and those with an even number of base pairs, while the hysteresis was minimal for longer poly-dC iMs and those with an odd number of base pairs. Experiments to follow the iM folding via thermal changes identified thermal hysteresis between the denaturing and annealing cycles. Similar trends were found to those observed in the CD experiments. The results demonstrate that the method of iM analysis can impact the pHT parameter measured, and hysteresis was observed in the pHT and Tm values.
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Affiliation(s)
- R Aaron Rogers
- Department of Chemistry, University of Utah, Salt Lake City, Utah, U.S.A
| | - Madeline R Meyer
- Department of Chemistry, University of Utah, Salt Lake City, Utah, U.S.A
| | - Kayla M Stewart
- Department of Chemistry, University of Utah, Salt Lake City, Utah, U.S.A
| | - Gabriela M Eyring
- Department of Chemistry, University of Utah, Salt Lake City, Utah, U.S.A
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, Utah, U.S.A
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, Salt Lake City, Utah, U.S.A
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. ACS Synth Biol 2020; 9:1487-1489. [PMID: 32558550 DOI: 10.1021/acssynbio.0c00320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. ACS Chem Biol 2020; 15:1719-1721. [PMID: 32558538 DOI: 10.1021/acschembio.0c00489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. Bioconjug Chem 2020; 31:1693-1695. [DOI: 10.1021/acs.bioconjchem.0c00358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. J Chem Theory Comput 2020; 16:4003-4005. [DOI: 10.1021/acs.jctc.0c00614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. Biomacromolecules 2020; 21:2543-2545. [DOI: 10.1021/acs.biomac.0c00924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Burrows CJ, Huang J, Wang S, Kim HJ, Meyer GJ, Schanze K, Lee TR, Lutkenhaus JL, Kaplan D, Jones C, Bertozzi C, Kiessling L, Mulcahy MB, Lindsley CW, Finn MG, Blum JD, Kamat P, Choi W, Snyder S, Aldrich CC, Rowan S, Liu B, Liotta D, Weiss PS, Zhang D, Ganesh KN, Atwater HA, Gooding JJ, Allen DT, Voigt CA, Sweedler J, Schepartz A, Rotello V, Lecommandoux S, Sturla SJ, Hammes-Schiffer S, Buriak J, Steed JW, Wu H, Zimmerman J, Brooks B, Savage P, Tolman W, Hofmann TF, Brennecke JF, Holme TA, Merz KM, Scuseria G, Jorgensen W, Georg GI, Wang S, Proteau P, Yates JR, Stang P, Walker GC, Hillmyer M, Taylor LS, Odom TW, Carreira E, Rossen K, Chirik P, Miller SJ, Shea JE, McCoy A, Zanni M, Hartland G, Scholes G, Loo JA, Milne J, Tegen SB, Kulp DT, Laskin J. Confronting Racism in Chemistry Journals. ACS Biomater Sci Eng 2020; 6:3690-3692. [DOI: 10.1021/acsbiomaterials.0c00901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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