Publications

27. O’Flaherty D. K.^‡*; Zhou, L.^‡; Szostak, J. W.* “Nonenzymatic RNA-templated synthesis of N3′→P5′ phosphoramidate DNA”, Bio-protocol, 2020, 10, e3734.

26. Kim S. C.; Zhou L.; Zhang W.; O’Flaherty D. K.; Rondo-Brovettoc V.; Szostak J. W.* “A model for the emergence of RNA from a prebiotically plausible mixture of ribonucleotides, arabinonucleotides and 2′-deoxynucleotides”, J. Am. Chem. Soc., 2020, 142, 2317-2326.

25. O’Flaherty D. K.^‡; Zhou L.^‡; Szostak J. W.* “Nonenzymatic template-directed synthesis of mixed-sequence 3′-NP-DNA up to 25 nucleotides long inside model protocells”, J. Am. Chem. Soc., 2019, 141, 10481-10488.

24. Zhou L.; Kim S. C.; Ho K. H.; O’Flaherty D. K.; Giurgiu C.; Wright T. W.; Szostak J. W.* “Non-enzymatic primer extension with strand displacement”, eLife, 2019, 8, e51888.

23. Lelyveld V. S.; O’Flaherty D. K.; Zhou L.; Izgu E. C.; Szostak J. W.* “DNA polymerase activity on synthetic N3′–P5′ phosphoramidate DNA templates”, Nucleic Acid Res., 2019, 47, 8941-8949.

22. Wright T. W.^‡; Giurgiu C.^‡; Zhang W.; Radakovic A.; O’Flaherty D. K.; Zhou L.; Szostak J. W.* “Prebiotically plausible ‘patching’ of RNA backbone cleavage through a 3′-5′ pyrophosphate linkage”. J. Am. Chem. Soc., 2019, 141, 18104-18112.

21. O’Flaherty D. K.^‡; Kamat N. P.^‡*; Mirza F. N.; Li L.; Prywes N.; Szostak J. W.* “Copying of mixed-sequence RNA templates inside model protocells”, J. Am. Chem. Soc., 2018, 140, 5171-5178.

20. Copp W.; O’Flaherty D. K.; Wilds C. J.* “Covalent capture of OGT’s active site using engineered human-E.coli chimera and intrastrand DNA cross-links”, Org. Biomol. Chem., 2018, 16, 9053-9058.

19. Sacre L.; O’Flaherty D. K.; Archambault P.; Copp W.; Peslherbe G. H.; Muchall H. M.; Wilds C. J.*; “O4-alkylated-2- deoxyuridine repair by O6-alkylguanine DNA alkyltransferase is augmented by a C5-fluorine modification. Chembiochem, 2018, 19, 575 – 582.

18. Giurgiu C.; Wright T. H.; O’Flaherty D. K.; Szostak J. W.* “A fluorescent G-quadruplex sensor for chemical RNA copying”, Angew. Chem. Int. Ed., 2018 57, 9844-9848.

17. Kim S. C.; O’Flaherty D. K; Zhou L.; Lelyveld V. S.; Szostak J. W.* “Inosine, but none of the 8-oxo-purines, is a plausible component of a primordial version of RNA”, Proc. Natl. Acad. Sci. U.S.A., 2018, 115, 13318-13323.

16. O’Flaherty D. K.; Wilds C. J.* “AGT activity towards intrstrand crosslinked DNA is modulated by the alkylene linker”, ChemBioChem, 2017, 18, 2351-2357.

15. Denisov A. Y.^‡: McManus F. M.^‡; O’Flaherty D. K.; Noronha A. M.; Wilds C. J.* “Structural basis of interstrand cross-link repair by O6-alkylguanine DNA alkyltransferase”, Org. Biomol. Chem., 2017, 15, 8361-8370.

14. Giurgiu C.; Li L.; O’Flaherty D. K.; Tam C. P.; Szostak J. W.* “A mechanistic explanation for the regioselectivity of nonenzymatic RNA primer extension”, J. Am. Chem. Soc., 2017, 139, 16741-16747.

13. Schoonhoven N. M.^‡; O’Flaherty D. K.^‡; McManus F. P.^‡; Sacre L.; Noronha A. M.; Kornblatt M. J.*; Wilds C. J.* “Altering residue 134 confers an increased substrate range of alkylated nucleosides to the E. coli OGT protein” Molecules, 2017, 22, 1948.

12. O’Flaherty D. K.; Wilds C. J.* “Site-specific covalent capture of human O6-alkylguanine-DNAalkyltransferase using single-stranded intrastrand cross-linked DNA”. Org. Biomol. Chem., 2017, 15, 189-196.

11. Li L.; Prywes N.; Tam C. P; O’Flaherty D. K.; Lelyveld V. S.; Izgu E. C.; Pal A.; Szostak J. W.* “Enhanced nonenzymatic RNA copying with 2-aminoimidazole activated nucleotides”, J. Am. Chem. Soc., 2017, 139, 1810-1813.

10. Xu W.; Kool D.; O’Flaherty D. K.; Keating A. M.; Sacre L.; Egli M.; Noronha A. M.; Wilds C. J.; Zhao L.* “O6-2′-Deoxyguanosine-butylene-O6-2′-deoxyguanosine DNA interstrand cross-links are replication-blocking and mutagenic DNA lesions” Chem. Res. Toxicol. 2016, 29, 1872-1882.

9. O’Flaherty D. K.; Wilds C. J.* “Preparation of intrastrand {G}O6-alkylene-O6{G} cross-linked oligonucleotides”, Curr. Protoc. Nucleic Acid Chem., 2016, 66, 5.17.1-5.17.24

8. O’Flaherty D. K.; Wilds C. J.* “O6-Alkylguanine DNA alkyltransferase activity towards intrastrand crosslinked DNA is influenced by the internucleotide linkage”, Chem Asian J, 2016, 11, 576-583.

7. O’Flaherty D. K.; Patra A.; Su Y.; Guengerich F. P.; Egli M.*; Wilds C. J.* “Lesion orientation of O4-alkylthymidine influences replication by human DNA polymerase η“, Chemical Science, 2016, 7, 4896-4904.

6. O’Flaherty D. K.; Wilds C. J.* “Synthesis, characterization and repair of a flexible O6-2′-deoxyguanosinealkylene-O6-2′-deoxyguanosine intrastrand cross-link”, Chem. Eur. J., 2015, 21, 10522-10529.

5. O’Flaherty D. K.; Guengerich F. P.; Egli M.*; Wilds C. J.* “Backbone flexibility influences nucleotide incorporation by human translesion DNA polymerase eta opposite intrastrand cross-linked DNA”, Biochemistry, 2015, 54, 7449-7456.

4. O’Flaherty D. K.^‡; Denisov A. Y.^‡; Noronha A. M.; Wilds C. J.* “NMR structure of an ethylene interstrand crosslinked DNA which mimics the lesion formed by 1,3-bis(2-chloroethyl)-1-nitrosourea”, ChemMedChem, 2014, 9
2099-2103.

3. O’Flaherty D. K.; Guengerich F. P.* “Steady-state kinetic analysis of DNA polymerase single-nucleotide incorporation products”, Curr. Protoc. Nucleic Acid Chem., 2014, 59, 7.21.1-7.21.13.

2. O’Flaherty D. K.; McManus F. P.; Noronha A. M.; Wilds C. J.* “Synthesis of Building Blocks and Oligonucleotides Containing {T}O4-Alkylene-O4{T} Interstrand Cross-Links”, Curr. Protoc. Nucleic Acid Chem., 2013, 55, 5.13.1-5.13.19.

1. McManus F. P.; O’Flaherty D. K.; Noronha A. M.; Wilds C. J.* “O4-Alkyl-2′-deoxythymidine cross-linked DNA to probe recognition and repair by O6-alkylguanine DNA alkyltransferases” Org. Biomol. Chem., 2012, 10, 7078-7090.

Published abstracts

1. Schoonhoven N. M.; Murphy S. P.; O’Flaherty D. K.; Noronha A. M.; Kornblatt M. J.; Wilds C. J.* “Synthesis, Biophysical and Repair Studies of O6-2′-deoxyguanosine Adducts by Escherichia coli OGT”, Nucleic Acids Symposium Series, 2008, 52, 449-450