Publications

Research Publications

(note: * indicates undergraduate collaborator)

Stein EM, Wang S*, Dailey K*, Gravel CM*, Wang S*, Olejniczak M, Berry KE. 2023. Biochemical and genetic dissection of the RNA-binding surface of the FinO domain of Escherichia coli ProQ. RNA, 29, 1772–1791. Link. (open access).

Stockert OM*, Gravel CM* & Berry KE. 2022. A bacterial three-hybrid assay for forward and reverse genetic analysis of RNA–protein interactions. Nature Protocols, 17, 941-961. https://doi.org/10.1038/s41596-021-00657-4. https://rdcu.be/cHCl7 (Free view-only)

Wang CD*, Mansky R*, LeBlanc H*, Gravel CM*, Berry KE. 2021. Optimization of a bacterial three-hybrid assay through in vivo titration of an RNA-DNA adapter-protein. RNA, 27, 513-526. Link. (open access).

Stein, E.M.., Kwiatkowska, J., Basczok, M.M., Gravel, C.M.*, Berry, K.E., & Olejniczak, M. (2020) Determinants of RNA recognition by the FinO domain of the Escherichia coli ProQ protein. Nucleic Acids Res., gkaa497, Link. (open access).

Pandey S*, Gravel CM*, Stockert OM*, Wang CD*, Hegner CL*, LeBlanc H*, Berry KE. (2020) Genetic identification of the functional surface for RNA binding by Escherichia coli ProQ. Nucleic Acids Res. gkaa144, https://doi.org/10.1093/nar/gkaa144. Link. (open access).

Berry KE‡, Hochschild A‡. (2018) A bacterial three-hyrbid assay detects E. coli Hfq-sRNA interactions. Nucleic Acids Res. gkx1086, https://doi.org/10.1093/nar/gkx1086 (‡co-corresponding authors). Link. (open access).

Berry KE, Waghray S*, Mortimer SA, Bai Y, Doudna JA. (2011) Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning. Structure, 19, 1456-66. Link. PDF (open access).

Berry KE, Peng B, Koditek D, Beeman D, Pagratis N, Perry JK, Parrish J, Zhong W, Doudna JA, Shih I-h. (2011) Optimized high-throughput screen for Hepatitis C virus translation inhibitors. J Biomol Screen, 16, 211-20. Link. PDF (PMC manuscript).

Berry KE, Waghray S*, Doudna JA. (2010) The HCV IRES pseudoknot positions the initiation codon on the 40S ribosomal subunit. RNA, 16, 1559-69. Link. PDF (open access).

Paley RS, Berry KE, Liu JM, Sanan TT. (2009) Diastereoselective intramolecular pinacol couplings of sulfinyl iron(0) diene complexes. J Org Chem, 74, 1611-20. Link.

Kovaks EW, Hooker JM, Romanini DW, Holder PG, Berry KE, Francis MB. (2007) Dual-surface-modified bacteriophage MS2 as an ideal scaffold for a viral capsid-based drug delivery system. Bioconj Chem, 18, 1140-7. Link.

Fraser CS, Berry KE, Hershey JW, Doudna JA. (2007) eIF3j is located in the decoding center of the human 40S ribosomal subunit. Mol Cell, 26, 811-9. Link. PDF (open access).

General Audience Publications

(note: * indicates undergraduate collaborator)

Click HERE for information and citations of Children's books in the LyonCub Biochemist series, written by Prof. Berry and students in her RNA World seminar.

Berry KE. (2009) Battle of the bugs: The evolution of bacterial immunity. Berkeley Science Review, 16, 10-11. Link. PDF.

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