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Joseph E. Wedekind, Ph.D.

Contact Information

Phone Numbers

Office: (585) 273-4516

Fax: (585) 275-6007

Research Labs

The Wedekind lab uses biophysical, biochemical and cell-based techniques to investigate: (i) bacterial riboswitches, and (ii) lab-evolved proteins that target HIV-1 RNA.

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Faculty Appointments



The Wedekind lab investigates the mechanisms of action of non-protein-coding (nc)RNAs. We are interested especially in the elegant, three-dimensional architectures of these RNAs, and how they bind to specific small molecules or peptides, leading to conformations that alter biological function. Model systems include: (i) metabolite-sensing riboswitches that regulate protein translation, and (ii) the application of lab-evolved proteins to target HIV-1 RNA. This work is relevant to the development of new antibiotics and anti-retroviral therapies. This work is funded by NIH/NIGMS grants R01 GM063162 and R01 GM123864.

Our lab employs a variety of biochemical, biophysical, and structural approaches, such as X-ray crystallography. We greatly acknowledge NIH/NCRR award S10 RR026501 for supporting this instrumentation. For access or further information see:



B.Sc. | University of California at Riverside
Biochemistry (Magna Cum Laude)

Ph.D. | University of Wisconsin at Madison
Biochemistry (Structural Enzymology)

Post-doctoral Training & Residency

1995 - 1999
RNA Biophysics, Dept. of Structural Biology, Stanford University School of Medicine. 1995-1999


2018 - 2022
Member, MSFB Study Section
Sponsor: Center for Scientific Review, NIH/PHS

2017 - 2019
Secretary, Medical Faculty Council
Location: University of Rochester SMD

Faculty Teaching Award in Biophysics
Sponsor: University of Rochester SMD
Location: Dept. Biochemistry & Biophysics

2011 - 2016
Editorial Board Member, The Journal of Biological Chemistry
Sponsor: ASBMB

2010 - 2012
Executive Committee Member, CHESS Users' Group
Sponsor: Cornell High Energy Synchrotron Source, Ithaca NY

Faculty Teaching Award in Biophysics
Location: University of Rochester SMD | Dept. Biochemistry & Biophysics

2007 - 2009
Elected Secretary (The Board of Directors)
Sponsor: The Pittsburgh Diffraction Society
Location: Pittsburgh, PA

Faculty Teaching Award in Biophysics
Location: University of Rochester SMD | Dept. Biochemistry & Biophysics

1996 - 1999
Life Sciences Research Foundation Fellow
Sponsor: Burroughs Wellcome Fund
Location: Dept. Structural Biology, Stanford, CA

Individual NRSA Post-doctoral Fellowship (declined)
Sponsor: NIH
Location: Stanford, CA

Leukemia and Lymphoma Society Post-Doctoral Award (declined)
Sponsor: Leukemia and Lymphoma Society
Location: Stanford, CA

1995 - 1996
Dean's Fellow
Location: Stanford University School of Medicine

1992 - 1995
NIH Biophysics Training Grant Recipient
Sponsor: NIH/NIGMS

Elected Member, Phi Beta Kappa
Location: Iota Chapter of California

Edmondson Summer Research Fellow
Sponsor: Dept. of Pathology
Location: University of Southern California

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Title: Anti-HIV Peptides
U.S. Serial #: 15/805,933
Filed: Nov 07, 2017
Invented By: IvanBelashov, DavidCrawford, BrianMcNaughton, JosephWedekind


Journal Articles

Warnasooriya C, Ling C, Belashov IA, Salim M, Wedekind JE, Ermolenko DN. "Observation of preQ-II riboswitch dynamics using single-molecule FRET." RNA biology.. 2018 Oct 17; :1-7. Epub 2018 Oct 17.

Dutta D, Belashov IA, Wedekind JE. "Coupling Green Fluorescent Protein Expression with Chemical Modification to Probe Functionally Relevant Riboswitch Conformations in Live Bacteria." Biochemistry.. 2018 Aug 7; 57(31):4620-4628. Epub 2018 Jun 26.

Belashov IA, Crawford DW, Cavender CE, Dai P, Beardslee PC, Mathews DH, Pentelute BL, McNaughton BR, Wedekind JE. "Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription." Nucleic acids research.. 2018 Jul 27; 46(13):6401-6415.

Books & Chapters

Chapter Title: Tails of Three Knotty Switches: How PreQ1 Riboswitch Structures Control Protein Translation
Book Title: eLifeSciences
Author List: Belashov I.A., Dutta D., Salim M., Wedekind J.E.
Published By: John Wiley & Sons, Inc2015

Chapter Title: Metal Dependence of Ligand Binding and Heavy-Atom Derivatization of Evolutionarily Distinct PreQ1 Riboswitches
Book Title: Chemical Biology of Nucleic Acids
Author List: Joseph E. Wedekind, Joseph A. Liberman, Jermaine L. Jenkins, Mohammad Salim
Published By: Springer2014

Chapter Title: Structural aspects of metal ion binding in small natural and artificial RNA enzymes
Book Title: Metal Ions in Life Sciences: Structural and Catalytic Roles of Metals in RNA
Author List: J.E. Wedekind
Edited By: A. Sigel, S. Sigel, R. Sigel
Published By: Wiley-Blackwell2010