About

Robert Batey is a Professor in the Department of Biochemistry at the University of Colorado Boulder and serves as Associate Chair for Graduate Affairs. He earned his PhD from the Massachusetts Institute of Technology in 1997 and completed postdoctoral work at Yale University from 1997 to 2001. His areas of expertise include bacteriology, gene expression and regulation, genetics and chemical biology, molecular biophysics, nucleic acids, and structural biology. His research focuses on understanding small molecule recognition by biological RNAs, particularly riboswitches, which are non-coding RNA elements that regulate gene expression in bacteria. Batey's group has determined the structures of various aptamers, including purine, SAM-I, SAM-II, lysine, and SAH, using X-ray crystallography to gain insights into RNA-ligand interactions and mechanisms of riboregulation. His work has contributed to understanding how riboswitches recognize diverse ligands and how ligand binding induces conformational changes that regulate gene expression. In addition to structural studies, Batey employs biophysical and biochemical approaches, such as chemical probing techniques like SHAPE, to investigate ligand-induced conformational changes in RNA. His group also develops tools to facilitate RNA structure determination and explores applications of riboswitches in synthetic biology, including engineering RNA-based sensors and regulatory devices. His contributions have advanced the understanding of RNA structure-function relationships and the potential for RNA devices in biotechnology and medicine.

Research topics

• Biology
• Genetics
• Computational biology
• Cell biology
• Chemistry
• Biochemistry
• Physics

Selected publications

• DNA affinity driven chromatin dynamics determine Estrogen Receptor α transcriptional activity independent of RNA binding

  Research Square · 2026-03-10

  preprintOpen accessSenior author
  PublisherOA PDFDOI

• Mechanistically Defined Epoxide- and Aziridine-2-carboxamide Electrophiles Enable Stereoselective Covalent RNA Modulation

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-16

  articleOpen access

  ABSTRACT RNA remains a largely untapped target for covalent small-molecule intervention due to the lack of electrophiles with predictable reactivity and stability in biological settings. Here, a mechanistically defined and tunable class of epoxide- and aziridine-2-carboxamide electrophiles that enable structure-guided covalent targeting of RNA is described. These warheads arise from an unexpected hydrolytic rearrangement of 3-chloropivalamide precursors under physiological conditions and selectively react with guanine N7, with reactivity and stability controlled by substitution pattern, linkage chemistry, and stereochemistry. Application to two distinct RNA targets demonstrates generality: epoxide- and aziridine-based ligands covalently modify pathogenic r(CUG) exp repeat RNA and disrupt RNA–protein interactions in vitro and in cells, while structure-guided placement on a flavin scaffold yields stereoselective covalent modulators of the flavin mononucleotide (FMN) riboswitch with validated reaction site and cellular activity. Together, this work establishes epoxide- and aziridine-2-carboxamides as a versatile platform for covalent RNA targeting and provides a general framework for the rational design of stereochemically controlled RNA-reactive small molecules.

  PublisherOA PDFDOI

• MECP2 MBD-ID Module: A Unified DNA/RNA Binding Interface Disrupted in Rett Syndrome

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-15

  articleOpen access

  Rett syndrome neurodevelopmental disorder is caused by mutations in the gene encoding the epigenetic regulator MECP2. While the MECP2 methyl-CpG binding domain (MBD) is well-characterized, the function of the adjacent intervening domain (ID) remains largely understudied. The ID has been described as a distinct RNA-binding region, yet evidence also suggests RNA competitively displaces MECP2 from DNA. Here, we address these conflicting findings by demonstrating the MBD and ID do not function in isolation but as a synergistic functional unit, establishing a new model for MECP2 function. We show the ID significantly enhances affinity of the MBD for methylated DNA by ∼35-fold. Moreover, together these two subdomains form a high-affinity, promiscuous RNA-binding module, with affinity for structured RNAs increased over 1,000-fold compared to the MBD or ID alone. We find binding to RNA precludes binding to DNA, such that the integrated MBD-ID unit explains the competition phenomenon. Analysis of Rett syndrome-associated ID mutations (R167W, K174Q, and R190H) and a therapeutic MiniGene reveals they do not disrupt methyl-DNA binding but instead selectively weaken RNA and non-methylated DNA binding, thereby disrupting the competitive balance between nucleic acid ligands. Our work establishes the MBD-ID module as MECP2's central nucleic acid interaction hub, whose disruption provides a potential molecular etiology of Rett syndrome due to mutations in the intervening domain.

  PublisherOA PDFDOI

• Mechanistically Defined Epoxide- and Aziridine-2-carboxamide Electrophiles Enable Stereoselective Covalent Ribonucleic Acid Modulation

  Journal of the American Chemical Society · 2026-04-16

  article

  RNA remains a largely untapped target for covalent small-molecule intervention due to the lack of electrophiles with predictable reactivity and stability in biological settings. Here, a mechanistically defined and tunable class of epoxide- and aziridine-2-carboxamide electrophiles that enable structure-guided covalent targeting of RNA is described. These warheads arise from an unexpected hydrolytic rearrangement of 3-chloropivalamide precursors under physiological conditions and selectively react with guanine N7, with reactivity and stability controlled by substitution pattern, linkage chemistry, and stereochemistry. Application to two distinct RNA targets demonstrates generality: epoxide- and aziridine-based ligands covalently modify pathogenic r(CUG)exp repeat RNA and disrupt RNA–protein interactions in vitro and in cells, while structure-guided placement on a flavin scaffold yields stereoselective covalent modulators of the flavin mononucleotide riboswitch with validated reaction site and cellular activity. Together, this work demonstrates epoxide- and aziridine-2-carboxamides as a versatile platform for covalent RNA targeting and provides a general framework for the rational design of stereochemically controlled RNA-reactive small molecules.

  PublisherDOI

• Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer

  Nucleic Acids Research · 2025-06-04 · 1 citations

  articleOpen accessSenior author

  Tagging RNAs with fluorogenic aptamers has enabled imaging of transcripts in living cells, revealing novel aspects of RNA metabolism and dynamics. While a diverse set of fluorogenic aptamers has been developed, a new generation of aptamers uses the ring-opening of spirocyclic rhodamine dyes to achieve robust performance in live mammalian cells. These fluorophores have two chemical states: a cell-permeable spirocyclic state and a fluorescent zwitterionic state. The SpyRho555 dye is mostly non-fluorescent in solution and becomes fluorescent in complex with the RhoBAST aptamer. To understand the basis for RhoBAST-SpyRho555 fluorogenicity, we have determined crystal structures of RhoBAST in complex with 5-carboxytetramethylrhodamine and a SpyRho555 analogue, MaP555. RhoBAST is organized by a perfect four-way junction that positions two loops to form the dye-binding pocket. The core of the ligand resides between a tri-adenine floor and a single guanine base, largely driven by π-stacking interactions. Importantly, the unpaired guanine interacts with the 3-position group of MaP555 to stabilize the open conformation, supported by mutagenesis data, and may play an active role in promoting the open conformation of the dye. This work has implications for the development of new fluorogenic aptamers with improved properties using structure-guided design approaches.

  PublisherOA PDFDOI

• Designing small molecules targeting a cryptic RNA binding site through base displacement

  Nature Chemical Biology · 2025-08-29 · 3 citations

  articleOpen accessSenior author

  Most RNA-binding small molecules have limited solubility, weak affinity and/or lack of specificity, restricting the medicinal chemistry often required for lead compound discovery. We reasoned that conjugation of these unfavorable ligands to a suitable ‘host’ molecule can solubilize the ‘guest’ and deliver it site-specifically to an RNA of interest to resolve these issues. Using this framework, we designed a small-molecule library that was hosted by cobalamin (Cbl) to interact with the Cbl riboswitch through a common base displacement mechanism. Combining in vitro binding, cell-based assays, chemoinformatic modeling and structure-based design, we unmasked a cryptic binding site within the riboswitch that was exploited to discover compounds that have affinity exceeding the native ligand, antagonize riboswitch function or bear no resemblance to Cbl. These data demonstrate how a privileged biphenyl-like scaffold effectively targets RNA by optimizing π-stacking interactions within the binding pocket. This work demonstrates how a biphenyl-like scaffold targets RNA through a common base displacement mechanism by optimizing π-stacking interactions within the binding pocket, helping to inform the design of novel RNA-targeting small molecules.

  PublisherOA PDFDOI

• Enhancement of RNA Imaging Platforms by the Use of Peptide Nucleic Acid-Based Linkers

  BIO-PROTOCOL · 2025-09-09

  articleOpen access
  PublisherDOI

• Structural and functional clues challenge the hypothesis that the <i>yjdF</i> riboswitch is natively regulated through broad recognition of azaaromatic compounds

  Nucleic Acids Research · 2025-11-13 · 1 citations

  articleOpen accessSenior author

  While most riboswitches are highly selective for their cognate ligand, the yjdF riboswitch is distinct in its ability to bind a broad set of aromatic compounds. This observation has led to the hypothesis that this RNA is regulated by toxic azaaromatic compounds, triggering a detoxification mechanism by activating translation of the YjdF protein in response to ligand binding. To understand how these compounds turn on gene expression by the yjdF riboswitch, we determined the crystal structure of the Bacillus subtilis yjdF riboswitch in complex with activating (chelerythrine) and nonactivating (lumichrome) ligands. These structures reveal that the RNA binds these compounds in a near-identical fashion, adopting the same local and global conformation. However, the unexpected extension of the regulatory helix through formation of several base pairs from highly conserved nucleotides suggests that this element plays an important role in ligand-dependent gene expression. Using a reporter assay in B. subtilis, we found that chelerythrine-dependent activation is insensitive to mutation of these conserved nucleotides that are essential for activation of the riboswitch. These data suggest that the yjdF riboswitch is responsive to a yet unknown cellular metabolite and remains an orphan riboswitch.

  PublisherOA PDFDOI

• Structure-Guided Design of a Bioactive Covalent Small Molecule Targeting a Riboswitch

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-02

  preprintOpen access

  Small molecule ligands targeting structured RNA elements hold promise for modulating RNA function, serving as chemical probes and potential therapeutics. In this study, the characterization of phenylglyoxal-based covalent probe designed to target unpaired guanine residues in structured RNAs is reported. A structure-guided design strategy was employed to modify covalently unpaired guanines critical for flavin mononucleotide (FMN) binding to the FMN riboswitch. Covalent modification occurs at the designed site and modulates riboswitch function in a cellular reporter system, highlighting the potential of covalent mechanisms of action for bioactive RNA ligands.

  PublisherOA PDFDOI

• Structure-Guided Design of a Bioactive Covalent Small Molecule Targeting a Riboswitch

  Journal of the American Chemical Society · 2025-10-07 · 4 citations

  articleOpen accessCorresponding

  Small molecule ligands targeting structured RNA elements hold promise for modulating RNA function, serving as chemical probes and potential therapeutics. In this study, the characterization of phenylglyoxal-based covalent probe designed to target unpaired guanine residues in structured RNAs is reported. A structure-guided design strategy was employed to modify covalently unpaired guanines critical for flavin mononucleotide (FMN) binding to the FMN riboswitch. Covalent modification occurs at the designed site and modulates riboswitch function in a cellular reporter system, highlighting the potential of covalent mechanisms of action for bioactive RNA ligands.

  PublisherDOI

Recent grants

• Basis of Gene Regulation by Purine and Cobalamine Riboswitches

  NIH · $4.8M · 2005–2024

• Modular Riboswitch Reporters for Directed Protein Evolution

  NSF · $400k · 2012–2016

• RNA Regulation of Transcription Factor Activity

  NIH · $3.2M · 2016–2026

• Structure and Mechanism of SAM-responsive Riboswitches

  NIH · $2.4M · 2008–2017

• NIH Grant S10RR026516

  NIH · $129k · 2011

Frequent coauthors

• Jennifer A. Doudna

  University of California, Berkeley

  21 shared

• Deborah S. Wuttke

  University of Colorado Boulder

  17 shared

• Andrew D. Garst

  15 shared

• S.D. Gilbert

  Oregon State University

  13 shared

• Jacob T. Polaski

  University of Utah

  13 shared

• F.E. Reyes

  Universidad Peruana Cayetano Heredia

  12 shared

• David J. Nesbitt

  University of Cambridge

  12 shared

• Otto A. Kletzien

  University of Colorado Boulder

  11 shared

Education

• Ph.D.

  Massachusetts Institute of Technology

  1997

• Other

  Yale University

  2001

Awards & honors

• Inventor of the Year, CU Boulder Office of Technology Transf…
• Kavli Frontiers of Science Fellow, National Academy of Scien…
• Distinguished Young Scholars in Medical Research Program, W.…
• National Academies Keck Futures Initiative Grant, W.M. Keck…