Publications
2024
A. M. Fleming, J. C. Dingman, and C. J. Burrows, “CO2 protects cells from iron-Fenton oxidative DNA damage in E. coli and humans,” bioRxiv, https://biorxiv.org/cgi/content/short/2024.08.26.609766v1.
A. M. Fleming, B. L. Guerra Castañaza Jenkins, B. A. Buck and C. J. Burrows, “DNA damage accelerates G-quadruplex folding in a duplex-G-quadruplex-duplex context,” J. Am. Chem. Soc. 2024, 146, 11364–11370. https://doi.org/10.1021/jacs.4c00960.
A. M. Fleming, J. C. Dingman, Y. Wu, S. S. Hoon, and C. J. Burrows, “Nanopore Direct RNA Sequencing for Modified Uridine Nucleotides Yields Signals Dependent on the Physical Properties of the Modified Base,” Israel J. Chem.2024, 64,online. DOI: 10.1002/ijch.202300177.
A. Bellina, M. C. Malfatti, A. M. Fleming, G. Antoniali, N. Gualandi, D. Marasco, E. Dassi, C. J. Burrows, and G. Tell, “Apurinic/Apyrimidinic Endoribonuclease APE1 binds and regulates the expression of G-quadruplex-containing miRNAs with clinical significance,” bioRxiv, www.biorxiv.org/content/10.1101/2024.02.22.581538 .
2023
C.J. Burrows and A. M. Fleming, “Bisulfite and Nanopore Sequencing for Pseudouridine in RNA,” Acc. Chem. Res. 2023, 56, 2740-2751. https://doi.org/10.1021/acs.accounts.3c00458
M. Fleming, J. Zhu, V. K. Done, and C. J. Burrows, “Advantages and challenges associated with bisulfite-assisted nanopore direct RNA sequencing for modifications,” RSC Chem. Biol. 2023, 4, 952-964.
M. Fleming, C. A. Omaga, and C. J. Burrows, “NEIL3 promoter G-quadruplex with oxidatively modified bases shows magnesium-dependent folding that stalls polymerase bypass,” Biochimie2023,214, 156-166. https://doi.org/10.1016/j.biochi.2023.07.001
S. Xiao, A. M. Fleming and C. J. Burrows, “Sequencing for oxidative DNA damage at single-nucleotide resolution with click-code-seq v2.0,” Chem. Commun.2023, 59, 8997 - 9000. https://doi.org/10.1039/D3CC02699J
A. M. Fleming, P. Bommasetti, S. Xiao, V. Bandarian and C. J. Burrows, “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. https://doi.org/10.1021/acschembio.3c00166.
A. M. Fleming and C. J. Burrows, Fleming, A.M., Burrows, C.J. “DNA Damage and Repair in G-Quadruplexes Impact Gene Expression”. In: Sugimoto, N. (ed) Handbook of Chemical Biology of Nucleic Acids, 2023. Springer, Singapore. https://doi.org/10.1007/978-981-16-1313-5_38-1.
A. M. Fleming and C. J. Burrows, “DNA modifications walk a fine line between epigenetics and mutagenesis,” Nat. Rev. Mol. Cell Biol. 2023, https://doi.org/10.1038/s41580-023-00590-2.
S. A. Howpay Manage, J. Zhu, A. M. Fleming, and C. J. Burrows, “Promoters vs. Telomeres: AP-Endonuclease 1 interactions with abasic sites in G-quadruplex folds depend on topology,” RSC Chem. Biol. 2023, 4, 261-270. https://doi.org/10.1039/D2CB00233G.
A. M. Fleming and C. J. Burrows, “Nanopore sequencing for N1-methylpseudouridine in RNA reveals sequence-dependent discrimination of the modified nucleotide triphosphate during transcription,” NAR 2023, 51, 1914-1926.https://doi.org/10.1093/nar/gkad044.
A. M. Fleming, S. Xiao and C. J. Burrows, “Nanopore sequencing for the 17 modification types in 36 locations in E. coli ribosomal RNA enables monitoring of stress-dependent changes,” bioRxiv, BIORXIV/2023/532289. www.biorxiv.org/content/10.1101/2023.03.12.532289v1.
2022
A. M. Fleming and C. J. Burrows, “Chemistry of ROS-Mediated Oxidation of the Guanine Base in DNA and its Biological Consequences,“ Intl. J. Radiat. Biol. 2022, 98, 452-460. DOI: 10.1080/09553002.2021.2003464.
A. M. Fleming, M. B. Chabot, N. L. B. Nguyen, and C. J. Burrows, “Collateral damage occurs when using photosensitizer probes to detect or modulate nucleic acid modifications,” Angew. Chem. Int. Ed. Eng. 2022, 61, e202110649. DOI: 10.1002/anie.202110649.
R. Galindo-Murillo, L. Winkler, J. Ma, F. Hanelli, A. M. Fleming, C. J. Burrows and T. E. Cheatham, III, “Riboflavin stabilizes abasic, oxidized G-quadruplex structures,” Biochemistry 2022, 61, 265-275. DOI: 10.1021/acs.biochem.1c00598
M. B. Chabot, A. M. Fleming and C. J. Burrows, “Identification of the major product of guanine oxidation in DNA by ozone,” Chem. Res. Toxicol. 2022, 35, 1809-1813. DOI: 10.1021/acs.chemrestox.2c00103. Selected for Editor’s Choice.
A. M. Fleming, S. Xiao, M. B. Chabot and C. J. Burrows, “Fluorophore-mediated Photooxidation of the Guanine Heterocycle,” J. Phys. Org. Chem. 2022, in press. DOI: 10.1002/poc.4325. (Special issue in honor of B. K. Carpenter.)
C. J. Burrows and A. M. Fleming, “Response to ‘Hydroxyl radical is predominantly involved in oxidatively generated base damage to cellular DNA exposed to ionizing radiation,’ by Cadet et al.” Int. J. Rad. Biol. 2022, online. DOI: 10.1080/09553002.2022.2094024
S. A. Howpay Manage, A. M. Fleming, H.-N. Chen, and C. J. Burrows, “Cysteine oxidation to sulfenic acid in APE1 aids G-quadruplex binding while compromising DNA repair,” ACS Chem. Biol. 2022, 17, 2583-2594. DOI: 10.1021/acschembio.2c00511.
M. B. Chabot, A. M. Fleming, and C. J. Burrows, “Insights into the 5-carboxamido-5-formamido-2-iminohydantoin structural isomerization equilibria,” J. Org. Chem. 2022, 87, 11865–11870. DOI: 10.1021/acs.joc.2c01371.
A. M. Fleming, S. Xiao, and C. J. Burrows, “Pseudouridine and N1-methylpseudouridine display pH-independent reaction rates with bisulfite yielding ribose adducts,” Org. Lett. 2022, 24, 6182–6185. DOI: 10.1021/acs.orglett.2c02427.
A. M. Fleming, R. Tran, C. A. Omaga, S. A. Howpay Manage, C. J. Burrows, and J. C. Conboy, “Second harmonic generation interrogation of the endonuclease APE1 binding interaction with G-quadruplex DNA,” Anal. Chem. 2022, 94, 15027-15031. DOI: 10.1021/acs.analchem.2c02951.
Q. Zhu, Y.Kapon, A. M. Fleming, S. Mishra, K. Santra, F. Tassinari, S. R. Cohen, Y. Sang, D. Bhowmick, C. J. Burrows, Y. Paltiel, R. Naaman, “The Role of Electrons’ Spin in DNA Oxidative Damage Recognition,” Cell Rep. Phys. Sci. 2022, 3, 3, 101157. DOI: 10.1016/j.xcrp.2022.101157
2021
A. M. Fleming, S. A. Howpay Manage, and C. J. Burrows, “Binding of AP endonuclease 1 to G-quadruplex DNA depends on the N-terminal domain, Mg2+ and ionic strength,” ACS Bio. & Med. Chem. Au2021, 1, xxxx. DOI: 10.1021/acsbiomedchemau.1c00031.
A. M. Fleming and C. J. Burrows, “Chemistry of ROS-Mediated Oxidation of the Guanine Base in DNA and its Biological Consequences, “ Intl. J. Radiat. Biol., in press.
A. M. Fleming and C. J. Burrows, “Oxidative stress-mediated epigenetic regulation by G-quadruplexes,” NAR Cancer2021, 3, zcab038. DOI: 10.1093/narcan/zcab038.
A. M. Fleming, N. J. Mathewson, S. A. Howpay Manage and C. J. Burrows, “Nanopore dwell-time analysis permits sequencing and conformational assignment of pseudouridine in SARS-CoV-2,” ACS Cent. Sci.2021, 7, 1707-1717. DOI: 10.1021/acscentsci.1c00788.
R.A. Rogers, M. Meyer, K. M. Stewart, G. M. Eyring, A. M. Fleming, and C. J. Burrows, “Hysteresis in poly-2`-deoxycytidine i-motif folding is impacted by the method of analysis as well as loop and stem lengths,” Biopolymers, 2021, 112, e23389. DOI: 10.1002/bip.23389.
2020
A. M. Fleming and C. J. Burrows, “Iron Fenton oxidation of 2′-deoxyguanosine in physiological bicarbonate buffer yields products consistent with the reactive oxygen species carbonate radical anion not hydroxyl radical,” Chem. Commun. 2020, 56, 9779-9782. DOI: 10.1039/D0CC04138F.
A. M. Fleming and C. J. Burrows, “On the irrelevancy of hydroxyl radical to DNA damage from oxidative stress and implications for epigenetics,” Chem. Soc. Rev.2020, 49, 6524-6528. DOI: 10.1039/d0cs00579g
A. M. Fleming, J. Zhu, M. Jara-Espejo and C. J. Burrows, "Cruciform DNA sequences in gene promoters can impact transcription upon oxidative modification of 2′-deoxyguanosine,” Biochemistry 2020, 59, 2616–2626. DOI: 10.1021/acs.biochem.0c00387.
M. Jara-Espejo, A. M. Fleming, and C. J. Burrows, “Potential G-quadruplex forming sequences and N6-methyladenosine co-localize at human pre-mRNA intron splice sites” ACS Chem. Biol. 2020, 15, 1292-1300. DOI: 10.1021/acschembio.0c00260.
J. Oh, A. M. Fleming, J. Xu, J. Chong, C. J. Burrows, and D. Wang, “RNA polymerase II stalls on oxidative DNA damage via a "torsion-latch" mechanism involving
lone pair-pi and CH-pi interactions,” PNAS 2020, 117, 9338-9348. DOI: 10.1073/pnas.1919904117
A. M. Fleming, S. C. J. Redstone, and C. J. Burrows, “Oxidative DNA Damage and Repair in G-Quadruplexes,” DNA Damage, DNA Repair and Disease, M. Dizdaroglu and R. S. Lloyd, Eds., RSC (London), 2020, vol. 1, 61-85.
A. M. Fleming, and C. J. Burrows "Interplay of Guanine Oxidation and G-Quadruplex Folding in Gene Promoters," J. Am. Chem. Soc. 2020, 142, 1115-1136. DOI:10.1021/jacs.9b11050
2019
B. Thapa, S. P. Hebert, B. H. Munk, C. J. Burrows, and H. B. Schlegel, “Computational Study of the Formation of C8, C5 and C4 Guanine:Lysine Adducts via Oxidation of Guanine by Sulfate Radical,” J. Phys. Chem. A 2019, 123, 5150-5163. DOI: 10.1021/acs.jpca.9b03598.
A. M. Fleming, A. Alenko, J. P. Kitt, A. M. Orendt, P. F. Flynn, J. M. Harris, and C. J. Burrows, “Structural elucidation of bisulfite adducts to pseudouridine that result in deletion signatures during reverse transcription of RNA,” J. Am. Chem. Soc.2019, 141,16450-16460. DOI: 10.1021/jacs.9b08630.
A. M. Fleming, J. Zhu, S. A. Howpay Manage, and C. J. Burrows “Human NEIL3 gene expression is regulated by epigenetic-like oxidative DNA modification,” J. Am. Chem. Soc. 2019, 141, 11036-11049. DOI: 10.1021/jacs.9b01847.
A. M. Fleming, J. Zhu, Y. Ding, and C. J. Burrows, “Location dependence of the transcriptional response of G-quadruplexes in gene promoters under oxidative stress,” Nucleic Acids Res.2019, 47(10):5049–5060,. DOI: 10.1093/nar/gkz207.
A. M. Fleming, J. Zhu, Y. Ding, S. Esders, and C. J. Burrows, “Oxidative modification of guanine in a potential Z-DNA-forming sequence of a gene promoter impacts gene expression,” Chem. Res. Toxicol.2019, 32(5):899-909. DOI: 10.1021/acs.chemrestox.9b00041.
J. Wu, S. J. Sturla, C. J. Burrows, and A. M. Fleming, ”Impact of DNA oxidation on toxicology: From quantification to genomics,” Chem. Res. Toxicol.2019, 32, 345-347. DOI: 10.1021/acs.chemrestox.9b00046.
A. M. Fleming, N. L. B. Nguyen, and C. J. Burrows, “Colocalization of m6A and G-quadruplex-forming sequences in viral RNA (HIV, Zika, hepatitis B, and SV40) suggests topological control of adenosine N6-methylation,” ACS Cent. Sci.2019, 5, 218-228. DOI: 10.1021/acscentsci.8b00963.
S.C. J. Redstone, A. M. Fleming, and C. J. Burrows, “Oxidative modification of the potential G-quadruplex sequence in the PCNA gene promoter can turn on transcription,” Chem. Res. Toxicol.2019, 32, 437-446. DOI: 10.1021/acs.chemrestox.8b00332.
V. Khoddami, A. Yerra, T. L. Mosbruger, A. M. Fleming, C. J. Burrows, and B. R. Cairns, “Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution,” Proc. Natl. Acad. Sci. 2019, 118, 6784-6789. DOI: 10.1073/pnas.1817334116.
S. Mishra, V. S. Poonia, C.Fontanesi, R. Naaman, A. M. Fleming, and C. J. Burrows “Effect of oxidative damage on charge and spin transport in DNA,” J. Am. Chem. Soc. 2019, 141, ASAP. DOI: 10.1021/jacs.8b12014.
N. An, A. M. Fleming, N. C. Rosecrans, Y. Liao, C. J. Burrows “Synthesis of Site-specific Crown Ether Adducts to DNA Abasic Sites, 8-Oxoguanosine and Cytidine,” Methods in Mol. Biol. 2019, 1973, 15-25. DOI: 10.1007/978-1-4939-9216-4_2
2018
Y. Ding, A. M. Fleming, and C. J. Burrows, “Case studies on potential G-quadruplex-forming sequences from the bacterial orders Deinococcales and Thermales derived from a survey of published genomes,” Sci. Rep. 2018, 8, 15679. DOI:10.1038/s41598-018-33944-4.
C. S. Tan, A. M. Fleming, H. Ren, C. J. Burrows and H. S. White, “γ-Hemolysin nanopore is sensitive to guanine-to-inosine substitutions in double-stranded DNA at the single-molecule level,” J. Am. Chem. Soc.2018, 139, in press. DOI: 10.1021/jacs.8b08153
W. A. Vinyard, A. M. Fleming, and C. J. Burrows, “Characterization of G-quadruplexes in the Chlamydomonas reinhardtii genome and effects of polyamines and magnesium on stability,” Biochemistry, 2018, 57, 6551-6561. DOI: 10.1021/acs.biochem.8b00749
R. A. Rogers, A. M. Fleming, and C. J. Burrows, “A Rapid Screen of Potential i-Motif Forming Sequences in DNA Repair Gene Promoters,” ACS Omega 2018, 3, 9630–9635. DOI: 10.1021/acsomega.8b01551.
J. Zhu, A. M. Fleming, and C. J. Burrows, “The RAD17 promoter sequence contains a potential G-quadruplex that folds in a tail-dependent fashion,” ACS Chem. Biol. 2018, 13, 2577-2584. DOI: 10.1021/acschembio.8b00522.
A. M. Fleming, K. M. Stewart, G. M. Eyring, T. E. Ball, and C. J. Burrows, “Unraveling the 4n − 1 rule for DNA i-motif stability: base pairs vs. loop lengths,” Org. Biomol. Chem., 2018, 16, 4537-4546. DOI: 10.1039/C8OB01198B
C. A. Omaga, A. M. Fleming, and C. J. Burrows, “The fifth domain in the G-quadruplex sequence motif of the human NEIL3 promoter locks DNA folding in response to oxidative damage,” Biochemistry, 2018, 57 (20), 2958-2970. DOI: 10.1021/acs.biochem.8b00226
T. Zeng, A. M. Fleming, Y. Ding, H. Ren, H. S. White, and C. J. Burrows, “Nanopore Analysis of the 5-Guanidinohydantoin to Iminoallantoin Isomerization in Duplex DNA,” J. Org. Chem.2018, 83, 3973-3978. DOI: 10.1021/acs.joc.8b00317.
R. A. Rogers, A. M. Fleming and C. J. Burrows, “Unusual isothermal hysteresis in DNA i-motif pH transitions: A study of the RAD17 promoter sequence,” Biophys. J. 2018, 114, 1804-1814. DOI: 10.1016/j.bpj.2018.03.012
H. Ren, C. G. Cheyne, A. M. Fleming, C. J. Burrows, and H. S. White, “Single-Molecule Titration in a Protein Nanoreactor Reveals the Protonation/Deprotonation Mechanism of a C:C Mismatch in DNA,” J. Am. Chem. Soc.2018, 140, 5153-5160. DOI: 10.1021/jacs.8b00593.
A. M. Fleming, J. Zhu, J. A. Visser, Y. Ding, J. Zhu, and C. J. Burrows, "Human DNA Repair Genes Possess Potential G-Quadruplex Sequences in Their Promoters and 5′-Untranslated Regions," Biochemistry, 2018, 57 (6), 991–1002. DOI: 10.1021/acs.biochem.7b01172.
2017
A. M. Fleming and C. J. Burrows, "8-Oxo-7,8-dihydro-2'-deoxyguanosine and abasic site tandem lesions are oxidation prone yielding hydantoin products that strongly destabilize duplex DNA," Org. Biomol. Chem. 2017, 15, 8341-8353. DOI: 10.1039/C7OB02096A.
A. M. Fleming, Y. Ding, J. Zhu, and C. J. Burrows, "8-Oxo-7,8-dihydroguanine in the cotext of a gene promoter G-quadruplex is an on-off switch for transcription," ACS Chem. Biol. 2017, 12, 2417-2426. DOI:10.1021/acschembio.7b00636.
A. Alenko, A. M. Fleming and C. J. Burrows, "Reverse Transcription Past Products of Guanine Oxidation in RNA Leads to Insertion of A and C opposite 8-Oxo-7,8-dihydroguanine and A and G opposite 5-Guanidinohydantoin and Spiroiminodihydantoin Diastereomers," Biochemistry, 2017, 56, 5053-5064. DOI:10.1021/acs.biochem.7b00730.
A. M. Fleming and C. J. Burrows, "8-Oxo-7,8-dihydroguanine, friend and foe: Epigenetic-like regulator versus initiator of mutagenesis," DNA Repair, 2017, 56, 75-83. DOI:10.1016/j.dnarep.2017.06.009.
A. M. Fleming, Y. Ding, and C. J. Burrows, "Oxidative DNA Damage is Epigenetic by Regulating Gene Transcription Via Base Excision Repair," Proc. Natl. Acad. Sci. 2017, 114, 2604-2609. DOI: 10.1073/pnas.1619809114. (Featured on the cover.)
R. P. Johnson, A. M. Fleming, R. Perera, C. J. Burrows, and H. S. White, "Dynamics of a DNA Mismatch Site Held in Confinement Discriminate Epigenetic Modifications of Cytosine," J. Am. Chem. Soc., 2017, 139, 2750-2756. DOI: 10.1021/jacs.6b12284.
Y. Ding, A. M. Fleming, and C. J. Burrows, “Sequencing the mouse genome for the oxidatively modified base 8-oxo-7,8-dihydroguanine by OG-Seq,” J. Am. Chem. Soc. 2017, 139, 2569-2572. DOI: 10.1021/jacs.6b12604.
A. M. Fleming, Y. Ding, R. A. Rogers, J. Zhu, J. Zhu, A. Burton, C. Carlisle, C. J. Burrows, “4n-1 is a “Sweet Spot” in DNA i-Motif Folding of 2’-Deoxycytidine Homopolymers,”J. Am. Chem. Soc. 2017, 139, 4682-4689. DOI: 10.1021/jacs.6b10117.
T. Zeng, A. M. Fleming, Y. Ding, H. S. White, and C. J. Burrows, “Interrogation of Base Pairing of the Spiroiminodihydantoin Diastereomers Using the α-Hemolysin Latch,”Biochemistry, 2017, 56, 1596-1603. DOI: 10.1021/acs.biochem.6b01175.
A. M. Fleming, Y. Ding, and C. J. Burrows, “Sequencing DNA for the oxidatively modified base 8-oxo-7,8-dihydroguanine,”Meth. Enzymol. 2017, 591, 187-210. DOI: 10.1016/bs.mie.2017.03.004.
V. Khoddami, T. L. Mosbruger, A. Yerra, A. M. Fleming, C. J. Burrows, and B. R. Cairns, “Transcriptome-wide Profiling of Multiple RNA Modifications Simultaneously at Base-Pair Resolution,” submitted.
B. Thapa, B. H. Munk, C. J. Burrows, and H. B. Schlegel, “Theoretical Study of Oxidation of Guanine by Singlet Oxygen (1∆g) and Formation of Guanine:Lysine Cross-Links,”Chem. Euro. J. 2017, 23, 2804-2813. DOI: 10.1002/chem.201700231.
A. M. Fleming and C. J. Burrows, "Formation and Processing of DNA Damage Substrates for the hNEIL Enzymes," Free Radic. Biol. Med. 2017, 107, 35-52. DOI: 10.1016/j.freeradbiomed.2016.11.030.
2016
A. M. Fleming, Y. Ding, and C. J. Burrows, “Zika virus genomic RNA possesses conserved G-quadruplexes characteristic of the Flaviviridae family,” ACS Infectious Disease, 2016, 2, 674-681. DOI: 10.1021/acsinfecdis.6b00109. Selected for “Editors’ Choice”. Cover art for October 2016 issue.
Y. Zhang, X.-B. Li, A. M. Fleming, J. Dood, A. A. Beckstead, A. M. Orendt, C. J. Burrows, and B. Kohler, “UV-Induced Proton-Coupled Electron Transfer in Cyclic DNA Miniduplexes,” J. Am. Chem. Soc. 2016, 138, 7395–7401. DOI: 10.1021/jacs.6b03216. Highlighted in J. Am. Chem. Soc. 2016, 138, 7446.
R. P. Johnson, R. Perrera, A. M. Fleming, C. J. Burrows, and H. S. White, “Energetics of Base Flipping at a DNA Mismatch Site Confined at the Latch Constriction of α-Hemolysin,” Faraday Disc. 2016,193, 471-485. DOI: 10.1039/C6FD00058D.
B. Thapa, B. Munk, C. J. Burrows, and H. B. Schlegel, “Computational Study of the Radical Mediated Mechanism of the Formation of C8, C5 and C4 Guanine-Lysine Adducts in Presence of the Benzophenone Photosensitizer," Chem. Res. Toxicol.2016, 29, 1396-1409. DOI: 10.1021/acs.chemrestox.6b00057.
J. Riedl, A. M. Fleming and C. J. Burrows, “Sequencing of DNA lesions facilitated by site-specific excision via base excision repair DNA glycosylases yielding ligatable gaps,” J. Am. Chem. Soc. 2016, 138, 491-494. DOI: 10.1021/jacs.5b11563.
N. An, A. M. Fleming, and C. J. Burrows, “Human telomere G-quadruplexes with five repeats accommodate 8-oxo-7,8-dihydroguanine by looping out the DNA damage,”ACS Chem. Biol. 2016, 11, 500–507. DOI: 10.1021/acschembio.5b00844
R. P. Johnson, A. M. Fleming, L. R. Beuth, C. J. Burrows and H. S. White, “Base Flipping within the α-Hemolysin Latch Allows Single-Molecule Identification of Mismatches in DNA,” J. Am. Chem. Soc. 2016, 138, 594-603. DOI: 10.1021/jacs.5b10710.
R. T. Perera, A. M. Fleming, A. M. Peterson, J. M. Heemstra, C. J. Burrows, and H. S. White, “Unzipping of A-form DNA-RNA or DNA-PNA duplexes and B-form DNA-DNA duplexes in the alpha-hemolysin nanopore,” Biophys. J.2016, 183, 973-979, 110, 306-314. DOI: 10.1016/j.bpj.2015.11.020.
Y. Ding, A. M. Fleming and C. J. Burrows, “Interactions between Biogenic Polyamines and DNA Hairpins Studied by the alpha-Hemolysin Nanopore,” Microchimica Acta, 2016, 183, 973-979. DOI: 10.1007/s00604-015-1516-6
Zhu, A. M. Fleming, A. M. Orendt, and C. J. Burrows, “pH-Dependent Equilibrium between 5-Guanidinohydantoin and Iminoallantoin affects Nucleotide Insertion Opposite the DNA Lesion,” J. Org. Chem.2016, 81, 351–359. DOI: 10.1021/acs.joc.5b02180. (Featured Article; cover art for issue 2, 2016.)
C. S. Tan, J. Riedl, A. M. Fleming, C. J. Burrows, H. S. White, “Kinetics of T3 DNA Ligase-Catalyzed Phosphodiester bond Formation Measured using the α-Hemolysin Nanopore,” ACS Nano2016, 10, 11127–11135. DOI: 10.1021/acsnano.6b05995.
2015
Y. Ding, A. M. Fleming, H. S. White, and C. J. Burrows, “Differentiation of G:C vs. A:T and G:C vs. G:mC base pairs in the latch zone of alpha-hemolysin,” ACS Nano 2015, 9, 11325–11332. DOI: 10.1021/acsnano.5b05055
J. Riedl, Y. Ding, A. M. Fleming, and C. J. Burrows, “Identification of DNA Lesions Using a Third Base Pair for Amplification and Nanopore Sequencing,” Nature Comm. 2015, 6, 8807. DOI: 10.1038/ncomms9807
O. R. Alshykhly, A. M. Fleming, and C. J. Burrows, “Guanine oxidation product 5-carboxamido-5-formamido-2-iminohydantoin induces mutations when bypassed by DNA polymerases and is a substrate for base excision repair,” Chem. Res. Toxicol. 2015, 28, 1861-1871. DOI: 10.1021/acs.chemrestox.5b00302
A. M. Fleming, J. Zhou, S. S. Wallace, and C. J. Burrows, “A role for the fifth G-track in G-quadruplex forming oncogene promoter sequences during oxidative stress: Do these “spare tires” have an evolved function?” ACS Central Science 2015, 1, 226-233. DOI: 10.1021/acscentsci.5b00202
Y. Ding, A. M. Fleming, L. He, and C. J. Burrows, “Unfolding kinetics of the human telomere i-motif under a 10 pN force imposed by the alpha-hemolysin nanopore identify transient folded-state lifetimes at physiological pH,” J. Am. Chem. Soc. 2015, 137, 9053-9060. DOI: 10.1021/jacs.5b03912
O. R. Alshykhly, A. M. Fleming, and C. J. Burrows, “5-Carboxamido-5-formamido-2-iminohydantoin, in addition to 8-oxo-7,8-dihydroguanine, is the major product of the iron-Fenton or X-ray radiation-induced oxidation of guanine under aerobic reducing conditions in the nucleoside context,” J. Org. Chem. 2015, 80, 6996–7007. DOI: 10.1021/acs.joc.5b00689.
R. T. Perera, A. M. Fleming, R. P. Johnson, C. J. Burrows, and H. S. White, “Detection of benzo[a]pyrene-guanine adducts in single-stranded DNA using the α-hemolysin nanopore,” Nanotechnology, 2015, 26, 074002. DOI:10.1088/0957-4484/26/7/074002.
Y. Zhang, J. Dood, A. Beckstead, X.-B. Li, K. V. Nguyen, C. J. Burrows, R. Improta, and B. Kohler, “Photoinduced Electron Transfer in DNA: Charge Shift Dynamics Between 8-Oxo-Guanine Anion and Adenine,” J. Phys. Chem. 2015, 119, 7491–7502. DOI: 10.1021/jp511220x. (Festschrift for Norman Sutin and John Miller.
A. M. Fleming, E. I. Armentrout, J. Zhu, J. G. Muller, and C. J. Burrows, “Spirodi(iminohydantoin) Products from Oxidation of 2’-Deoxyguanosine in the Presence of NH4Cl in Nucleoside and Oligodeoxynucleotide Contexts,” J. Org. Chem. 2015, 80, 711-721 (Featured Article). DOI:10.1021/jo502665p
A. M. Fleming, O. Alshykhly, A. M. Orendt, C. J. Burrows, “Computational studies of electronic circular dichroism spectra predict absolute configuration assignments for the guanine oxidation product 5-carboxamido-5-formamido-2-iminohydantoin,” Tetrahedron Lett.2015, 56, 3191-3196. DOI: 10.1016/j.tetlet.2014.12.052. (Special issue in memory of Harry Wasserman).
J. Zhou, A. M. Fleming, A. M. Averill, C. J. Burrows, and S. S. Wallace, “The NEIL glycosylases remove oxidized guanine lesions from telomeric and promoter quadruplex DNA structures,” Nucleic Acids Res. 2015, 43, 4039-4054. DOI: 10.1093/nar/gkv252
An, A. M. Fleming, H. S. White, and C. J. Burrows, “Nanopore Detection of 8-Oxoguanine in the Human Telomere Repeat Sequence,” ACS Nano 2015, 9, 4296–4307. DOI: 10.1021/acsnano.5b00722
Y. Ding, A. M. Fleming and C. J. Burrows, “Interactions between Biogenic Polyamines and DNA Hairpins Studied by the alpha-Hemolysin Nanopore,” Microchimica Acta, 2015, 10.1007/s00604-015-1516-6.
A. M. Fleming, O. Alshykhly, J. Zhu, J. G. Muller, and C. J. Burrows, “Rates of chemical cleavage of DNA and RNA oligomers containing guanine oxidation products,” Chem. Res. Toxicol. 2015, 28, 1292-1300. DOI: 10.1021/acs.chemrestox.5b00096.
J. Riedl and C. J. Burrows, “Site-specific labeling of DNA base modifications for amplification of DNA damage,” Coll. Czech Chem. Commun. 2015, 14, 91-92.
2014
R. P. Johnson, A. M. Fleming, C. J. Burrows and H. S. White, “The Effect of Electrolyte Cation on Detecting DNA Damage with the Latch Constriction of α-Hemolysin,” J.Phys. Chem. Lett. 2014, 5, 3781–3786; DOI: 10.1021/jz502030e.
A. H. Wolna, A. M. Fleming, and C. J. Burrows, “Single-molecule analysis of thymine-dimer containing G-quadruplexes formed from the human telomere sequence,” Biochemistry2014, 53, 7484-7493. DOI: 10.1021/bi501072m.
Y. Ding, A. M. Fleming, H. S. White, and C. J. Burrows, “Internal and Terminal Hairpins: Unzipping Positions and Mechanisms in the α-Hemolysin Nanopore,” J. Phys. Chem. B, 2014, 118, 12873-12882. DOI: 10.1021/jp5101413.
R. P, Johnson, A. M. Fleming, Q. Jin, C. J. Burrows, and H. S. White, “Temperature and Electrolyte Optimization of the α-Hemolysin Latch Sensing Zone for Detection of Base Modification in Double-Stranded DNA,” Biophys. J.2014, 107, 924-931. DOI: 10.1016/j.bpj.2014.07.006.
N. An, A. M. Fleming, E. G. Middleton, and C. J. Burrows, “Single-Molecule Investigation of G-Quadruplex Folds of the Human Telomere Sequence in a Protein Nanocavity,” Proc. Natl. Acad. Sci. 2014, 111, 14325–14331. DOI: 10.1073/pnas.1415944111.
Y. Zhang, J. Dood, A. Beckstead, X.-B. Li, K. V. Nguyen, C. J. Burrows, R. Improta, and B. Kohler, “Efficient UV-induced charge separation and recombination in an 8-oxoguanine-containing dinucleotide,” PNAS, 2014, 111, 11612-11617. DOI: 10.1073/pnas.1404411111.
B. E. Eckenroth, A. M. Fleming, J. B. Sweasy, C. J. Burrows, and S. Doublié, “Crystal Structure of DNA Polymerase β with DNA Containing the Base Lesion Spiroiminodihydantoin in Templating Position,” Biochemistry.2014, 53, 2075–2077; DOI:10.1021/bi500270e.
A. H. Wolna, A. M. Fleming, H. S. White, and C. J. Burrows, "Single-molecule detection of guanine(C8)-thymine(N3) cross-link using ion channel
recording," J. Phys. Org. Chem. 2014, 27, 247-251
N. An, A. M. Fleming, N. C. Rosecrans, Y. Liao, C. J. Burrows, "Synthesis of Site-specific Crown Ether Adducts to DNA Abasic Sites, 8-Oxoguanosine and Cytidine," Methods in Mol. Biol. 2014, in press
2013
Y. Zhang, J. Dood, A. Beckstead, J. Chen, X.-B. Li, C. J. Burrows, Z. Lu, S. Matsika, and B. Kohler, "Ultrafast Excited-State Dynamics and Vibrational Cooling of 8-oxo-7,8-dihydro-2'-deoxyguanosine in D2O," J. Phys. Chem. A, 2013, 117, 12851-12857.
Q. Jin, A. M. Fleming, R. P. Johnson, Y. Ding, C. J. Burrows, and H. S. White, "Base-Excision Repair Activity of Uracil-DNA Glycosylase Monitored Using the Latch Zone of α-Hemolysin," J. Am. Chem. Soc. 2013, 135, 19347-19353.
A. M. Fleming, A. M. Orendt, Y. He, J. Zhu, R. K. Dukkor, and C. J. Burrows, "Reconciliation of chemical, enzymatic, spectroscopic and computational data to assign the absolute configuration of the DNA base lesion spiroiminodihydantoin,"J. Am. Chem. Soc.2013, 135, 18191-18204.
C. J. Burrows, "Ribozyme takes its vitamins,"Nature Chem. 2013,5, 900-901.
Q. Jin, A. M. Fleming, Y. Ding, C. J. Burrows, and H. S. White, "Structural Destabilization of DNA Duplexes Containing Single-Base Lesions Investigated by Nanopore Measurements,"Biochemistry2013,52, 7870-7877.
J. Zhou, M. Liu, A. M. Fleming, C. J. Burrows, and S. S. Wallace, "Neil3 and NEIL1 DNA glycosylases remove oxidative damages from quadruplex DNA and exhibit preferences for lesions in the telomeric sequence context,"J. Biol. Chem. 2013, 288, 27263-27272.
P. L. McKibbin, A. M. Fleming, M. A. Towheed, B. V. Houten, C. J. Burrows, S. S. David, "Repair of Hydantoin Lesions and Their Amine Adducts in DNA by Base and Nucleotide Excision Repair,"J. Am. Chem. Soc.2013, 135, 13851-13861.
S. Z. Krokeide, J. K. Laerdahl, M. Salah, L. Luna, F. H. Cederkvist, A. M. Fleming, C. J. Burrows, B. Dalhus, M. Bjørås, "Human NEIL3 is Mainly a Monofunctional DNA Glycosylase Removing Spiroimindiohydantoin and Guanidinohydantoin,"DNA Repair2013, 12, 1159-1164.
X. Chen, A. M. Fleming, J. G. Muller, C. J. Burrows, "Endonuclease and Exonuclease Activities on Olligodeoxynucleotides Containing Spiroiminodihydantoin Depend on the Sequence Context and the Lesion Stereochemistry,"New J. Chem.2013, 37, 3440-3449 (special issue in honor of Bernard Meunier).
A. H. Wolna, A. M. Fleming, N. An, L. He, H. S. White, C. J. Burrows, "Electrical Current Signatures of DNA Base Modifications in Single Molecules Immobilized in the alpha-Hemolysin Ion Channel,"Israel J. Chem. (special issue)2013, 53, 417-430.
N. An, A. M. Fleming, and C. J. Burrows, "Interactions of the Human Telomere Sequence with the Nanocavity of the ?-Hemolysin Ion Channel Reveal Structure-Dependent Electrical Signatures for Hybrid Folds,"J. Am. Chem. Soc. 2013, 135, 8562-8570.
A. M. Fleming and C. J. Burrows, "G-Quadruplex Folds of the Human Telomere Sequence Alter the Site Reactivity and Reaction Pathway of Guanine Oxidation Compared to Duplex DNA,"Chem. Res. Toxicol.2013, 26, 593-607.
2012
N. An, H. S. White, and C. J. Burrows, "Modulation of the current signatures of DNA abasic site adducts in the alpha-hemolysin ion channel,"Chem. Commun.2012, 48, 11410-11412.
U. Ghanty, E. Fostvedt, R. A. Valenzuela, P. A. Beal, and C. J. Burrows, "Promiscuous 8-Alkoxyadenosines in the Guide Strand of an SiRNA: Modulation of Silencing Efficacy and Off-Pathway Protein Binding,"J. Am. Chem. Soc.2012, 134, 17643-17652.
A. M. Fleming, J. G. Muller, A. C. Dlouhy, and C. J. Burrows, "Structural Context Effects in the Oxidation of 8-Oxo-7,8-dihydro-2'-deoxyguanosine to Hydantaoin Products: Electrostatics, Base Stacking, and Base Pairing,"J. Am. Chem. Soc.2012, 134, 15091-15102.
K. V. Nguyen and C. J. Burrows, "Whence Flavins? Redox-Active Ribonucleotides Link Metabolism and Genome Repair to the RNA World,"Acc. Chem. Res.2012, 45, 2151-2159.
Q. Jin, A. M. Fleming, C. J. Burrows, and H. S. White, "Unzipping Kinetics of Duplex DNA Containing Oxidized Lesions in an alpha-Hemolysin Nanopore,"J. Am. Chem. Soc.2012, 134, 11006-11011.
N. An, A. M. Fleming, H. S. White, and C. J. Burrows, "Crown ether-electrolyte interactions permit nanopore detection of individual DNA abasic sites in single molecules,"PNAS, 2012, 109, 11504-11509.
K. V. Nguyen and C. J. Burrows, "Photorepair of cyclobutane pyrimidine dimers by 8-oxopurine nucleosides,"J. Phys. Org. Chem. 2012, 25, 574-577.
2011
A. M. Fleming, A. Kannan, J. G. Muller, Y. Liao, and C. J. Burrows, "Copper/H2O2-mediated oxidation of 2'-deoxyguanosine in the presence of 2-naphthol leads to the formation of two distinct isomeric adducts,"J. Org. Chem.2011, 76, 7953-7963.
K. V. Nguyen and C. J. Burrows, "A prebiotic role for 8-oxo-7,8-dihydroguanosine as a flavin mimic in pyrimidine dimer repair,"J. Am. Chem. Soc.2011, 133, 14586-14589.
H. Peacock, A. Kannan, P. A. Beal, and C. J. Burrows, "Chemical modification of siRNA bases to probe and enhance RNA interference,"J. Org. Chem.2011, 76, 7295-7300.
A. E. P. Schibel, A. M. Fleming, Q. Jin, N. An, J. Liu, C. P. Blakemore, H. S. White, and C. J. Burrows, "Sequence-specific single-molecule analysis of 8-oxo-7,8-dihydroguanine lesions in DNA based on unzipping kinetics of complementary probes in ion channel recordings,"J. Am. Chem. Soc.2011, 133, 14778-14784.
Y. Sefersted, G. Hildrestrand, D. Kunke, V. Rolseth, S. Krokeide, C. Neurater, R. Suganthan, M. Atneosen-Åsegg, A. Fleming, O. Saugstad, C. Burrows, L. Luna, M. Bjørås, "Endonuclease VIII-like 3 (Neil3) DNA glycosylase promotes neurogenesis induced by hypoxia-ischemia,"Proc. Natl. Acad. Sci., USA, 2011, 12, 60-67.
N. An, A. M. Fleming, and C. J. Burrows, "Nanopore detection of DNA damage in single molecules," Coll. Symp. Series2011, 12, 60-67.
A. M. Fleming, I. Ji, J. G. Muller and C. J. Burrows, “Characterization of 2’-deoxyguanosine oxidation products observed in the Fenton-like system Cu(II)/H2O2/reductant in nucleoside and oligodeoxynucleotide contexts,”Org. Biomolec. Chem, 2011, 9, 3338-3348.
A. Kannan, E. Fostvedt, P. A. Beal, and C. J. Burrows, “8-Oxoguanosine switches modulate the activity of alkylated siRNAs by controlling steric effects in the major vs. minor grooves,”J. Am. Chem. Soc. 2011, 133, 6343-6351.
K. V. Nguyen and C. J. Burrows, “Oxidation of 9-b-D-ribofuranosyl uric acid by one-electron oxidants vs. singlet oxygen and its implications for the oxidation of 8-oxo-7,8-dihydroguanosine,”Tetrahedron Lett. 2011, 52, 2176-2180.
A. Kannan and C. J. Burrows, “Synthesis of N2-alkyl-8-oxo-7,8-dihydro-2’-deoxyguanosine analogues and effects of these modifications on RNA duplex stability,”J. Org. Chem.2011, 76, 720-723.
P. Ghude, M. A. Schallenberger, A. M. Fleming, J. G. Muller, and C. J. Burrows, “Comparison of transition metal-mediated oxidation reactions of guanine in nucleoside and single-stranded oligodeoxynucleotide contexts,”Inorg. Chim. Acta, 2011, 369, 240-246.
2010
A. E. P. Schibel, N. An, Q. Jin, A. M. Fleming, C. J. Burrows, and H. S. White, “Nanopore detection of 8-oxo-7,8-dihydro-2’-deoxyguanosine in immobilized single-stranded DNA via adduct formation to the DNA damage site,”J. Am. Chem. Soc. 2010, 132, 17992-17995.
P. Aller, Y. Ye, S. Wallce, C. J. Burrows, and S. Doublié, “Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin,”Biochemistry, 2010, 49, 2502-2509..
X. Zhao, N. Krishnamurthy, C. J. Burrows, and S. S. David, “Mutation versus repair: NEIL1 removal of hydantoin lesions in single-stranded, bulge, bubble and duplex DNA contexts,”Biochemistry 2010, 49, 1658-1666..
Y. Guo, V. Bandaru, P. Jaruga, X. Zhao, C. J. Burrows, S. Iwai, M. Dizdaroglu, J. P. Bond, and S. S. Wallace, “The DNA glycosylases of Mycobacterium tuberculosis exhibit different substrate specificities from their Escherichia coli counterparts,”DNA Repair 2010, 9, 177-190..
M. Liu, V. Bandaru, J. P. Bond, P. Jaruga, X. Zhao, P. P. Christov, C. J. Burrows, M. Dizdaroglu, C. J. Rizzo, and S. S. Wallace, “The mouse ortholog of NEIL3 is a functional DNA glycosylase in vitro and in vivo,”Proc. Natl. Acad. Sci. (USA)2010, 107, 4925-4930..
2009
C. J. Burrows and A. M. Fleming, “Finding needles in DNA stacks,” Proc. Natl. Acad. Sci. (USA)2009, 106, 16010-16011..
C. J. Burrows, “Surviving an Oxygen Atmosphere: DNA Damage and Repair,” in Chemical Evolution II: From Origins of Life to Modern Society, Zaikowski, L.; Friedrich, J. M.; Seidel, S. R.; Eds. ACS Symposium Series, Washington, DC, 2009..
S. D. Kathe, R. Barrantes-Reynolds, P. Jarugal, M. R. Newton, C. J. Burrows, V. Bandaru, M. Dizdaroglu, J. P. Bond, and S. S. Wallace, “Plant and fungal Fpg homologs are formamidopyrimidine DNA glycosylases but not 8-oxoguanine DNA glycosylases,” DNA Repair 2009, 8, 643-653. .
Y. Ye, B. H. Munk, J. G. Muller, A. Cogbill, C. J. Burrows, and H. B. Schlegel, “Mechanistic and kinetic aspects of the formation of guanidinohydantoin from spiroiminodihydantoin under acid conditions,”Chem. Res. Toxicol. 2009, 22, 526-535.
T. Markus, S. Daube, R. Naaman, A. M. Fleming, J. G. Muller, C. J. Burrows, "The electronic structure of DNA: The unique properties of 8-oxoguanosine,"J. Am. Chem. Soc. 2009, 131, 89-95.
2008
N. Krishnamurthy, X. Zhao, C. J. Burrows, and S. S. David, “Superior removal of hydantoin lesions relative to other oxidized bases by the human DNA glycosylase hNEIL1,”Biochemistry 2008, 47, 7137-7146.
X. Xu, A. Fleming, J. G. Muller, and C. J. Burrows, “Formation of Tricyclic [4.3.3.0] Adducts Between 8-Oxoguanosine and Tyrosine under Conditions of Oxidative DNA-Protein Cross-linking,”J. Am. Chem. Soc. 2008, 130, 10080-10081.
B. H. Munk, C. J. Burrows, and H. B. Schlegel, “An exploration of mechanisms for the transformation of 8-oxoguanine to guanidinohydantoin and spiroiminodihydantoin by density functional theory,” J. Am. Chem. Soc. 2008, 130, 5245-5256.
X. Xu, J. G. Muller, Y. Ye and C. J. Burrows, “DNA-protein cross-links between guanine and lysine depend on the mechanism of oxidation for formation of C5 vs. C8 adducts,”J. Am. Chem. Soc. 2008, 130, 703-709.
2007
V. Bandaru, X. Zhao, M. R. Newton, C. J. Burrows, and S. S. Wallace, “Human Endonuclease VIII-like (NEIL) proteins in the giant DNA Mimivirus,” DNA Repair2007, 6, 1629-1641.
N. Krishnamurthy, J. G. Muller, C. J. Burrows, and S. S. David, “Unusual structural features of hydantoin lesions translate into efficient recognition by Escherichia coli Fpg,”Biochemistry2007, 46, 9355-9365. (Selected as a “hot article”.)
X. Zhao, J. G. Muller, M. Halasyam, S. S. David, and C. J. Burrows, “In vitro DNA ligation of oligodeoxynucleotides containing oxidized purine lesions by bacteriophage T4 DNA ligase,”Biochemistry 2007, 46, 3734-3744. (Selected as a “hot article”.)
B. H. Munk, C. J. Burrows, and H. B. Schlegel, “An exploration of mechanisms for the transformation of 8-hydroxyguanine radical to FAPy-G by density functional theory,”Chem. Res. Toxicol.2007,19, 432-444.
2001-2006
Y. Ye, J. G. Muller, and C. J. Burrows, “Synthesis and Characterization of the Oxidized dGTP Lesions Spiroiminodihydantoin-2'-deoxynucleoside-5'-triphosphate and Guanidinohydantoin-2'-deoxynucleoside-5'-triphosphate,”J. Org. Chem.2006, 71, 2181-2184.
M. E. Johansen, X. Xu, J. G. Muller, and C. J. Burrows, “Oxidatively Induced DNA-Protein Cross-linking between Single-Stranded Binding Protein (SSB) and Oligodeoxynucleotides containing 8-Oxo-7,8-dihydro-2’-deoxyguanosine,” Biochemistry,2005, 44, 5660-5671. (Selected as a “hot article”.)
O. Kornyushyna, A. J. Stemmler, D. M. Graybosch, I. Bergenthal, and C. J. Burrows, “Synthesis of a Metallopeptide-PNA Conjugate and its Oxidative Cross-linking to a DNA Target,”Bioconj. Chem. 2005, 17, 178-183.
M. E. Hosford, J. G. Muller, and C. J. Burrows, “Spermine Participates in Oxidative Damage of Guanosine and 8-Oxoguanosine Leading to Deoxyribosylurea Formation,”J. Am. Chem. Soc. 2004, 126, 9540-9541.
S. Choi, R. B. Cooley, A. S. Hakemian, Y. C. Larrabee, R. C. Bunt, S. D. Maupas, J. G. Muller, and C. J. Burrows, “Mechanism of Two-Electron Oxidation of Deoxyguanosine-5'-monophosphate by a Platinum(IV) Complex,”J. Am. Chem. Soc. 2004, 126, 591-598.
S. E. Rokita and C. J. Burrows, “Salen-Metal Complexes”, in Small Molecule DNA and RNA Binders, Demeunynck, M.; Bailly, C.; Wilson, W. D., Eds., Wiley-VCH: Weinheim, 2003, pp 126-145.
Y. Ye, J. G. Muller, W. Luo, C. L. Mayne, A. J. Shallop, R. A. Jones and C. J. Burrows “Formation of 13C, 15N, and 18O-Labeled Guanidinohydantoin from Guanosine Oxidation with Singlet Oxygen. Implications for Structure and Mechanism,”J. Am. Chem. Soc. 2003, 125, 13926-13927.
O. Kornyushyna and C. J. Burrows, “Effect of the Oxidized Lesions Spiroiminodihydantoin and Guanidinohydantoin on Proofreading by Escherichia coli DNA Polymerase I (Klenow Fragment) in Different Sequence Contexts”Biochemistry, 2003, 42, 13008-13018.
M. Leipold, H. Workman, J. G. Muller, C. J. Burrows, and S. S. David, “Recognition and Removal of Oxidized Guanines in Duplex DNA by the Base Excision Repair Enzymes hOGG1, yOGG1, and yOGG2,”Biochemistry, 2003, 42, 11373-11381.
P. T. Henderson, J. C. Delaney, J. G. Muller, W. L. Neeley, S. R. Tannenbaum, C. J. Burrows, and J. M. Essigmann, “The Hydantoin Lesions Formed from Oxidation of 7,8-Dihydro-8-oxoguanine are Potent Sources of Replication Errors in Vivo,”Biochemistry, 2003, 42, 9257-9262.
J. D. Van Horn, G. Bulaj, D. P. Goldenberg, and C. J. Burrows, “The Cys-Xaa-His Metal-Binding Motif. {N} vs. {S} Coordination and Nickel-Mediated Formation of Cysteinyl Sulfinic Acid,”J. Biol. Inorg. Chem. 2003, 8, 601-610.
O. Kornyushyna, A. M. Berges, J. G. Muller, and C. J. Burrows, “In vitro nucleotide misinsertion opposite the oxidized guanosine lesions spiroiminodihydantoin and guanidinohydantoin and DNA synthesis past the lesions using E. coli polymerase I (Klenow fragment),”Biochemistry, 2002, 41, 15304-15314.
R. A. Jameton, J. G. Muller, and C. J. Burrows, “Oxidative DNA damage from sulfite autoxidation catalyzed by manganese(III),”Comptes Rendus, Chimie, 2002, 5, 461-466.
C. J. Burrows, J. G. Muller, O. Kornyushyna, W. Luo, V. Duarte, M. D. Leipold, and S. S. David, “Structure and Potential Mutagenicity of New Hydantoin Products from Guanosine and 8-Oxo-7,8-dihydroguanosine Oxidation by Transition Metals,”Environ. Health Perspect. 2002, 110 Supp. 5, 713-717.
J. Cai, J. G. Muller, and C. J. Burrows, “Reactivity of bulged bases in duplex DNA with redox-active nickel and cobalt complexes,” Supramol. Chem. 2002, 14, 121-126.
W. Luo, J. G. Muller, and C. J. Burrows, “The pH-dependent role of superoxide in riboflavin-catalyzed photooxidation of 8-oxo-7,8-dihydroguanosine,”Org. Lett. 2001, 3, 2801-2804.
W. Luo, J. G. Muller, E. M. Rachlin, and C. J. Burrows, “Characterization of Hydantoin Products from Oxidation of 8-Oxo-7,8-dihydroguanosine by One-electron Oxidants,”Chem. Res. Toxicol. 2001, 14, 927-938.
T. P. Hazra, J. G. Muller, R. C. Manuel, C. J. Burrows, R. S. Lloyd, and S. Mitra, “Repair of oxidation products of 8-oxoguanine by DNA glycosylases of E. coli,”Nucleic Acids Res. 2001, 29, 1967-1974.
S. E. Rokita and C. J. Burrows, “Nickel- and Cobalt-dependent Oxidation and Cross-linking of Proteins,” in Metal Ions in Biological Systems, Vol. 38, H. Sigel and A. Sigel, Eds., M. Dekker: New York, 2001, 289-311.
A. J. Stemmler and C. J. Burrows, “Guanine vs. deoxyribose damage in DNA oxidation mediated by vanadium(IV) and vanadium(V) complexes,”J. Biol. Inorg. Chem. 2001, 6, 100-106.
1996-2000
M. Pitie, C. J. Burrows, B. Meunier, “Mechanisms of DNA cleavage by copper complexes of 3-Clip-Phen and of its conjugate with a distamycin analog,”Nucleic Acids Res. 2000, 28, 4856-4864.
M. Leipold, J. G. Muller, C. J. Burrows, and S. S. David, “The removal of hydantoin products of 8-oxoguanine oxidation by the E. coli DNA repair enzyme Fpg,”Biochemistry 2000, 39, 14984-14992.
M. Pitie, J. D. Van Horn, D. Brion, C. J. Burrows, and B. Meunier, “Targeting the DNA Cleavage Activity of Copper Phenanthroline and Clip-Phen to AT Tracts via Linkage to a Poly-N-methylpyrrole,”Bioconj. Chem., 2000, 12, 892-900.
W. Luo, J. G. Muller, E. Rachlin, and C. J. Burrows, “Characterization of piroiminodihydantoin as a Product of 7,8-Dihydro-8-oxoguanosine Oxidation,”Org. Lett. 2000, 2, 613-616.
S. E. Rokita and C. J. Burrows, “Probing nucleic acid structure with nickel and cobalt-based reagents,”Current Protocols in Nucleic Acid Chemistry, 2000, 6.4.1-6.4.7.
H.-C. Shih, H. Kassahun, C. J. Burrows, and S. E. Rokita, “Selective Association between a Macrocyclic Nickel Complex and Extrahelical Guanine Residues,”Biochemistry, 1999, 38, 15034-15042.
R. P. Hickerson, C. L. Chepanoske, S. D. Williams, S. S. David, and C. J. Burrows, “Mechanism-based DNA-Protein Cross-linking of MutY via Oxidation of 8-Oxoguanosine,”J. Am. Chem. Soc. 1999, 121, 9901-9902.
R. P. Hickerson, F. Prat, J. G. Muller, C. S. Foote, and C. J. Burrows, “Sequence and Stacking Dependence of 8-Oxoguanine Oxidation: Comparison of One-Electron vs. Singlet Oxygen Mechanisms,”J. Am. Chem. Soc. 1999, 121, 9423-9428.
N. Tang, J. G. Muller, C. J. Burrows, and S. E. Rokita, “Nickel and Cobalt Reagents Promote Selective Oxidation of Z-DNA,”Biochemistry, 1999, 38, 16648-16654.
A. J. Stemmler and C. J. Burrows, “The Sal-XH Motif for Metal-mediated Oxidative DNA-Peptide Cross-linking,”J. Am. Chem. Soc. 1999, 121, 6956-6957.
J. D. Van Horn and C. J. Burrows, “Formation of trans-3-hydroxy-4-phenylbutyrolactone from trans-styrylacetic acid and aqueous KHSO5,”Tetrahedron Lett. 1999, 40, 2069-2070.
J. G. Muller, L. A. Kayser, S. J. Paikoff, V. Duarte, N. Tang, S. E. Rokita, and C. J. Burrows, “Formation of DNA adducts using nickel(II) complexes of redox-active ligands: A comparison of salen and peptide complexes,”Coord. Chem. Rev. 1999, 185-186, 761-774.
V. Lepentsiotis, J. Domagala, I. Grgic, R. van Eldik, J. G. Muller, and C. J. Burrows, “Mechanistic information on the redox cycling of Ni(II/III) complexes in the presence of sulfur oxides and oxygen. Correlation with DNA damage experiments,”Inorg. Chem. 1999, 38, 3500-3505.
V. Duarte, J. G. Muller and C. J. Burrows, “Insertion of dGMP and dAMP during in vitro DNA synthesis opposite an oxidized form of 7,8-dihydro-8-oxoguanine,”Nucleic Acids Res. 1999, 27, 496-502.
R. P. Hickerson, V. Duarte, J. D. Van Horn, R. J. Perez, J. G. Muller, S. E. Rokita, and C. J. Burrows, “DNA cleavage vs. cross-linking using nickel peptides: Mechanistic aspects,” Metals and Genetics, B. Sarkar, Ed., Plenum: New York, 1999, 183-196.
K. Wietzerbin, J. G. Muller, R. A. Jameton, G. Pratviel, J. Bernadou, B. Meunier, and C. J. Burrows, “Hydroxylation, Epoxidation and DNA Cleavage Reactions Mediated by the Biomimetic MnTMPyP/O2/Sulfite Oxidation System,”Inorg. Chem. 1999, 38, 4123-4127.
J. G. Muller, V. Duarte, R. P. Hickerson, and C. J. Burrows, “Gel electrophoretic detection of 7,8-dihydro-8-oxoguanine and 7,8-dihydro-8-oxoadenine via oxidation by Ir(IV),”Nucleic Acids Res. 1998, 26, 2247-2249.
R. P. Hickerson, C. D. Watkins-Sims, C. J. Burrows, J. F. Atkins, R. F. Gesteland, and B. Felden, “A Nickel Complex Cleaves Uridines in Folded RNA Structures: Application to E. coli tmRNA and Related Engineered Molecules,”J. Mol. Biol. 1998, 279, 577-587.
P. Zheng, C. J. Burrows, and S. E. Rokita, “Nickel- and Cobalt-Dependent Reagents Identify Structural Features of RNA that are not Detected by Dimethyl Sulfate or RNase T1,”Biochemistry 1998, 37, 2207-2214.
C. J. Burrows and J. G. Muller, “Oxidative Nucleobase Modifications Leading to Strand Scission,”Chem. Rev. 1998, 98, 1109-1152.
S. A. Ross and C. J. Burrows, “Nickel(II) Complexes of Cysteine- and Cystine-containing Peptides: Spontaneous Formation of Disulfide-Bridged Dimers at Neutral pH,”Inorg. Chem. 1998, 37, 5358-5363.
H.-C. Shih, N. Tang, C. J. Burrows and S. E. Rokita, “Nickel-based Probes of Nucleic Acid Structure Bind to Guanine N7 but do not Perturb the Dynamic Equilibrium of Extrahelical Guanine Residues,”J. Am. Chem. Soc. 1998, 120, 3284-3288.
J. G. Muller and C. J. Burrows, “Metallodrug complexes that mediate DNA and lipid damage via sulfite autoxidation: Copper(II) famotidine and iron(III) bis(salicylglycine),”Inorg. Chim. Acta 1998, 275-276, 314-319.
R. J. Perez, J. G. Muller, S. E. Rokita, and C. J. Burrows, “Oxidative DNA Damage Mediated by Metal-Peptide Complexes,”Pure Appl. Chem. 1998, 70, 275-278.
S. A. Ross and C. J. Burrows, “Bromination of Pyrimidines using Bromide and Monoperoxysulfate: A Competition Study between Cytidine, Thymidine, and Uridine,”Tetrahedron Lett.1997, 38, 2805-2808.
J. G. Muller, R. P. Hickerson, R. J. Perez, and C. J. Burrows, “DNA Damage from Sulfite Autoxidation Catalyzed by a Nickel(II) Peptide,”J. Am. Chem. Soc. 1997, 119, 1501-1506.
G. Gill, A. A. Richter-Rusli, C. J. Burrows, and S. E. Rokita, "Nickel-Dependent Crosslinking of a Protein," Chem. Res. Toxicol. 1997, 10, 302-309.
S. A. Ross and C. J. Burrows, “Cytosine-specific chemical probing of DNA using bromide and monoperoxysulfate,”Nucleic Acids Res. 1996, 24, 5062-5063.
G. A. McLachlan, J. G. Muller, S. E. Rokita, and C. J. Burrows, “Metal-Mediated Oxidation of Guanines in DNA and RNA: A Comparison of Cobalt(II), Nickel(II), and Copper(II) Complexes,”Inorg. Chim. Acta 1996, 251, 193-199.
C.-C. Cheng, J. Gulia, S. E. Rokita, and C. J. Burrows, “Dioxygen Chemistry of Nickel(II) Dioxopentaazamacrocyclic Complexes: Substituent and Medium Effects,”J. Mol. Catal., A 1996, 113, 379-391.
C. J. Burrows, J. G. Muller, G. T. Poulter and S. E. Rokita, “Nickel-Catalyzed Oxidations: From Hydrocarbons to DNA,”Acta Chem. Scand. 1996, 50, 337-344.
W. Nam, S. J. Baek, K. A. Lee, B. T. Ahn, J. G. Muller, C. J. Burrows, and J. S. Valentine, “Nickel Complexes as Antioxidants,” Inorg. Chem. 1996, 35, 6632-6633.
J. G. Muller, P. Zheng, S. E. Rokita, and C. J. Burrows, "DNA and RNA Modification Promoted by [Co(H2O)6]Cl2: Guanine Selectivity, Temperature Dependence and Mechanism,”J. Am. Chem. Soc. 1996, 118, 2320-2325.
J. G. Muller, M. M. P. Ng, and C. J. Burrows, "Hydrophobic vs. Coulombic Interactions in the Binding of Steroidal Polyamines to DNA,"J. Molec. Recognit. 1996, 9, 143-148.
1991-1995
C. J. Burrows and S. E. Rokita, "Nickel Complexes as Probes of Guanine Sites in Nucleic Acid Folding," in Metal Ions in Biological Systems, Vol.33, H. Sigel and A. Sigel, Eds., M. Dekker: New York, 1995, Chap. 18, pp 537-560.
H. P. Hsieh, J. G. Muller, and C. J. Burrows, "Synthesis and DNA Binding Properties of C3-, C12- and C24-Substituted Amino-Steroids Derived from Bile Acids,"Bioorg. Med. Chem. 1995, 3, 823-838.
C. J. Burrows, J. G. Muller, H.-C. Shih, and S. E. Rokita, "Interaction of Metal Complexes with B vs. September 7, 2004 Z DNA," in "Supramolecular Stereochemistry," J. S. Siegel, Ed.; Kluwer: Dordrecht, 1995, pp 57-62.
S. M. Evans, C. J. Burrows, and C. A. Venanzi, "Design of Cholic Acid Macrocycles as Hosts for Molecular Recognition of Monosaccharides,"J. Molec. Struct. 1995, 334, 193-205.
S. E. Rokita, P. Zheng, N. Tang, C.-C. Cheng, R.-H. Yeh, J. G. Muller and C. J. Burrows, "Nickel Complexes in Modification of Nucleic Acids," In Genetic Response to Metals, B. Sarkar, Ed.; M. Dekker: New York, 1995, pp 201-216.
K. J. Fordon, C. G. Crane, and C. J. Burrows, "A Novel Method for the Synthesis of 5-Substituted 6- Membered Cyclic Ureas,"Tetrahedron Lett. 1994, 35, 6215-6216.
H. P. Hsieh, J. G. Muller, and C. J. Burrows, "Structural Effects in Novel Steroidal Polyamine-DNA Binding,"J. Am. Chem. Soc. 1994, 116, 12077-12078.
C. J. Burrows and S. E. Rokita, "Recognition of Guanine Structure in Nucleic Acids by Nickel Complexes,"Acc. Chem. Res. 1994, 27, 295-301.
S. A. Woodson, J. G. Muller, C. J. Burrows and S. E. Rokita, "A Primer Extension Assay for Modification of Guanine N7 by Ni(II) Complexes," Nucl. Acids Res. 1993, 21, 5524-5525.
S. M. Evans, C. A. Venanzi and C. J. Burrows, "Design of Cholic Acid Hosts for Molecular Recognition of Glucose using Systematic Conformational Searching,"J. Molec. Struct.,1994, 308, 159-174.
X. Chen, S. Woodson, C. J. Burrows and S. E. Rokita, "A Highly Sensitive Probe for Guanine N7 in Folded Structures of RNA: Application to tRNAphe and Tetrahymena Group I Intron,"Biochemistry, 1993, 32, 7610-7616.
J. G. Muller, S. J. Paikoff, S. E. Rokita and C. J. Burrows, "DNA Modification Promoted by Water-Soluble Nickel(II) Salen Complexes: A Switch to DNA Alkylation,"J. Inorg. Biochem. 1994, 54, 199-206.
S. J. Wey, K. J. O'Connor, and C. J. Burrows, "Preparation of Primary Vicinal Diamines from Amino Acid Esters and Crystal Structure of a Chiral Nickel Salen Complex,"Tetrahedron Lett. 1993, 34, 1905-1908.
J. G. Muller, X. Chen, A. C. Dadiz, S. E. Rokita, and C. J. Burrows, "Macrocyclic Nickel Complexes in DNA Recognition and Oxidation,"Pure Appl. Chem. 1993, 65, 545-550.
C. C. Cheng, S. E. Rokita, and C. J. Burrows, "Nickel(III)-Promoted DNA Scission using Ambient Dioxygen"Angew. Chem. 1993, 105, 290-292, and Angew. Chem. (Int. Ed. Engl.) 1993, 32, 277-278.
J. G. Muller, X. Chen, A. C. Dadiz, S. E. Rokita, and C. J. Burrows, "Ligand Effects Associated with the Intrinsic Selectivity of DNA Oxidation Promoted by Nickel(II) Macrocyclic Complexes,"J. Am. Chem. Soc. 1992, 114, 6407-6411.
K. J. O'Connor, S. J. Wey and C. J. Burrows, "Alkene Aziridination and Epoxidation Catalyzed by Chiral Metal Salen Complexes,"Tetrahedron Lett. 1992, 33, 1001-1004.
X. Chen, C. J. Burrows, and S. E. Rokita, "Conformation Specific Oxidation of Guanosine in DNA: Ends, Mismatches, Bulges, and Loops,"J. Am. Chem. Soc. 1992, 114, 322-325.
C. A. Salata, M. T. Youinou, and C. J. Burrows, "Preparation and Structural Characterization of Dicopper(II) and Dinickel(II) Imidazolate-Bridged Macrocyclic Schiff Base Complexes,"Inorg. Chem. 1991, 30, 3454-3461.
X. Chen, S. E. Rokita and C. J. Burrows, "DNA Modification: Intrinsic Selectivity of Nickel(II) Complexes,"J. Am. Chem. Soc. 1991, 113, 5884-5886.
K. J. O'Connor and C. J. Burrows, "Catalysis of Aryl Halogen Exchange by Nickel(II) Complexes using NaOCl,"J. Org. Chem. 1991, 56, 1344-1346.
1990 and earlier
H. S. Ham and C. J. Burrows, "Synthesis of a New Molecular Receptor Based on Cholic Acid," Taehan Hwahakhoe Chi 1990, 34, 215-216.
H. Yoon, T. R. Wagler, K. J. O'Connor and C. J. Burrows, "High Turnover Rates in pH-Dependent Alkene Epoxidation using NaOCl and Square Planar Nickel(II) Catalysts,"J. Am. Chem. Soc. 1990, 112, 4568-4570.
C. A. Salata, M. T. Youinou, and C. J. Burrows, "(Template)2 Synthesis of a Dinucleating Macrocyclic Ligand and Crystal Structure of its Dicopper(II) Imidazolate Complex,"J. Am. Chem. Soc. 1989, 111, 9278-9279.
C. J. Burrows, "Catalytic Reactions of Macrocyclic Nickel(II) Complexes," in Inclusion Phenomena and Molecular Recognition, Atwood, J. L., Ed.; Plenum: New York, 1990; 199-207.
T. R. Wagler, Y. Fang and C. J. Burrows, "Optically Active Difunctionalized Dioxocyclam Macrocycles. Ligands for Nickel-Catalyzed Oxidation of Alkenes,"J. Org. Chem. 1989, 54, 1584-1589.
J. F. Marecek, P. A. Fischer and C. J. Burrows, "Complexation of ATP to a Synthetic [15]-N3 Macrocyclic Polyammonium Receptor,"Tetrahedron Lett. 1988, 29, 6231-6234.
T. R. Wagler and C. J. Burrows, "Synthesis of a Chiral Dioxocyclam Derived from L-Phenylalanine and its Application to Olefin Oxidation Chemistry,"Tetrahedron Lett. 1988, 29, 5091-5094.
J. F. Kinneary, T. M. Roy, J. S. Albert, H. Yoon, T. R. Wagler, L. Shen and C. J. Burrows, "Progress Toward Artificial Metalloenzymes: New Ligands for Transition Metal Ions and Neutral Molecules,"J. Inclusion Phenom. 1989, 7, 155-168.
H. Yoon and C. J. Burrows, "Catalysis of Olefin Oxidation by Nickel Salen Complexes Using NaOCl under Phase Transfer Conditions,"J. Am. Chem. Soc., 1988, 110, 4087-4089.
J. F. Kinneary, J. S. Albert and C. J. Burrows, "Mechanistic Studies of Alkene Epoxidation Catalyzed by Nickel(II) Cyclam Complexes. 18O-Labeling and Substituent Effects,"J. Am. Chem. Soc. 1988, 110, 6124-6129.
C. A. Salata, D. Van Engen and C. J. Burrows, "Synthesis and Structure of a Semi-Rigid Dinucleating Macrocycle containing the 2,6-Di(thiomethyl)pyridine Unit and Reactions of its Cu(II) Complex,"J. Chem. Soc., Chem. Commun. 1988, 579-580.
J. F. Kinneary, T. R. Wagler and C. J. Burrows, "Alkene Epoxidation Using Ni(II) Complexes of Chiral Cyclams,"Tetrahedron Lett. 1988, 29, 877-880.
C. J. Burrows and R. Sauter, “Synthesis and Conformational Studies of a New Host System Based on Cholic Acid,"J. Inclusion Phenom. 1987, 5, 117-121.
T. R. Wagler and C. J. Burrows, "Synthesis of an Optically Active C-Functionalized Cyclam, (S)-5-(Hydroxymethyl)-1,4,8,11-tetraazacyclotetradecane and its Ni(II) Complex,"J. Chem. Soc., Chem. Commun. 1987, 277-278.
J. F. Marecek and C. J. Burrows, "Synthesis of an Optically Active Spermine Macrocycle, (S)-6-(Hydroxymethyl)-1,5,10,14-tetraazacyclooctadecane, and its Complexation to ATP"Tetrahedron Lett. 1986, 27, 5943-5946.
J. P. Behr, C. J. Burrows, R. Heng, and J. M. Lehn, "Synthesis of Novel Macrobicyclic Polyfunctional Cryptands,"Tetrahedron Lett. 1985, 26, 215-218.
C. J. Burrows and B. K. Carpenter, "Substituent Effects on the Aliphatic Claisen Rearrangement. 2. Theoretical Analysis"J. Am. Chem. Soc. 1981, 103, 6984-6986.
C. J. Burrows and B. K. Carpenter, "Substituent Effects on the Aliphatic Claisen Rearrangement. 1. Synthesis and Rearrangement of Cyano-Substituted Allyl Vinyl Ethers"J. Am. Chem. Soc. 1981, 103, 6983-6984.