About

Professor Amy E. Palmer leads the Palmer Lab at the University of Colorado Boulder, where her research is situated at the interface of chemistry and biology. Her work leverages chemical and physical principles to gain a deeper understanding of the fundamental biochemistry of living cells. The lab focuses on the complexity and dynamic nature of living cells, which must integrate both internal and external signals to coordinate a wide range of functions. A central challenge addressed by the lab is deciphering the molecular details that define healthy and diseased cellular states, as well as understanding how cellular dynamics propagate to the organismal level. The Palmer Lab is committed to fostering diversity, equity, and inclusion, welcoming individuals regardless of race, ethnicity, color, country of origin, religion, gender, sexual orientation, gender identity and expression, or disability status. This commitment is rooted in the belief that diversity enhances excellence, innovation, creativity, and the ability to challenge conventional norms. Professor Palmer is affiliated with several departments and programs at the University of Colorado Boulder, including the BioFrontiers Institute, the CU Graduate School, and the Department of Biochemistry, as well as training programs in biophysics, signaling, and cell regulation.

Research topics

• Biology
• Chemistry
• Cell biology
• Computational biology
• Physics
• Genetics
• Quantum mechanics
• Biophysics
• Nanotechnology
• Optics
• Materials science
• Biochemistry
• Atomic physics

Selected publications

• Measuring alignment between the ADRC UDS data elements, FDA, and EHR data standards

  Alzheimer s & Dementia · 2025-09-01 · 1 citations

  articleOpen access

  INTRODUCTION: We compared and measured alignment between the Health Level Seven (HL7) Fast Healthcare Interoperability Resources (FHIR) standard used by electronic health records (EHRs), the Clinical Data Interchange Standards Consortium (CDISC) standards used by industry, and the Uniform Data Set (UDS) used by the Alzheimer's Disease Research Centers (ADRCs). METHODS: The ADRC UDS, consisting of 5959 data elements across eleven packets, was mapped to FHIR and CDISC standards by two independent mappers, with discrepancies adjudicated by experts. RESULTS: Forty-five percent of the 5959 UDS data elements mapped to the FHIR standard, indicating possible electronic obtainment from EHRs. Ninety-four percent mapped to the CDISC standards, demonstrating high compatibility with industry standards. DISCUSSION: The study highlights the feasibility of harmonizing ADRC data with industry and clinical standards. CDISC demonstrated superior alignment with ADRC UDS data, whereas FHIR showed potential for improvement through resource maturation and enhanced standardization. HIGHLIGHTS: Forty-five percent of Alzheimer's Disease Research Center Uniform Data Set (ADRC UDS) data elements could be mapped to Fast Healthcare Interoperability Resources (FHIR), indicating potential electronic health records (EHRs) extraction. Ninety-four percent of ADRC UDS data elements could be mapped to Clinical Data Interchange Standards Consortium (CDISC) Study Data Tabulation Model (SDTM), showing high industry compatibility. Identified areas for improving data standards harmonization in Alzheimer's disease and related dementias (ADRD) research. Systematic mapping method aligns ADRC UDS with Health Level Seven (HL7) FHIR and CDISC SDTM standards. Results support feasibility of data sharing across ADRC research, EHRs, and industry.

  PublisherOA PDFDOI

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

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

  articleOpen access

  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

• Zn2+ transients and signaling in mammalian systems

  Trends in Biochemical Sciences · 2025-10-05 · 3 citations

  reviewSenior author
  PublisherDOI

• Systematic characterization of zinc in a series of breast cancer cell lines reveals significant changes in zinc homeostasis

  Journal of Biological Chemistry · 2025-07-02 · 2 citations

  articleOpen accessSenior author

  <h2>Abstract</h2> An optimal amount of zinc (Zn²⁺) is essential for proliferation of human cells; Zn²⁺ levels that are too high or too low cause cell cycle exit. Tumors of the breast have been characterized by high levels of total Zn²⁺. Given the role of Zn²⁺ in proliferation of human cells and elevation of zinc in breast cancer tumors, we examined the concentration of total and labile Zn²⁺ across a panel of 5 breast cancer cell lines, compared to the normal MCF10A cell line. We found that three cell lines (MDA-MB-231, MDA-MB-157, and SK-Br-3) showed elevated labile Zn²⁺ in the cytosol, while T-47D showed significantly lower Zn²⁺, and MCF7 showed no change compared to MCF10A cells. There was no change in total Zn²⁺ across the cell lines, as measured by ICP-MS, but we did observe a difference in the cells ability to accumulate Zn²⁺ when Zn²⁺ in the media was elevated. Therefore, we examined how proliferation of each cell line was affected by increases and decreases in the media. We found striking differences, where three cancer cell lines (MDA-MB-231, MDA-MB-157, and MCF7) showed robust proliferation in high Zn²⁺ at concentrations that killed MCF10A, T-47D, and SK-Br-3 cells. We also discovered that 4 of the 5 cancer cell lines demonstrate compromised proliferation and increased cell death in low Zn²⁺, suggesting these cells may be addicted to Zn²⁺. Overall, our study suggests significant differences in Zn²⁺ homeostasis and regulation in different types of breast cancer cells, with consequences for both proliferation and cell viability.

  PublisherOA PDFDOI

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

  BIO-PROTOCOL · 2025-09-09

  articleOpen accessSenior author
  PublisherDOI

• Systematic characterization of zinc in a series of breast cancer cell lines reveals significant changes in zinc homeostasis

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-13

  preprintOpen accessSenior authorCorresponding

  Abstract An optimal amount of labile zinc (Zn 2+ ) is essential for proliferation of human cells, where Zn 2+ levels that are too high or too low cause cell cycle exit. Tumors of the breast have been characterized by high levels of total Zn 2+ . Given the role of Zn 2+ in proliferation of human cells and elevation of zinc in breast cancer tumors, we examined the concentration of total and labile Zn 2+ across a panel of 5 breast cancer cell lines, compared to the normal MCF10A cell line. We found that three cell lines (MDA-MB-231, MDA-MB-157, and SK-Br-3) showed elevated labile Zn 2+ in the cytosol, while T-47D showed significantly lower Zn 2+ , and MCF7 showed no change compared to MCF10A cells. There was no change in total Zn 2+ across the cell lines, as measured by ICP-MS, but we did observe a difference in the cells ability to accumulate Zn 2+ when Zn 2+ in the media was elevated. Therefore, we examined how proliferation of each cell line was affected by increases and decreases in the media. We found striking differences, where three cancer cell lines (MDA-MB-231, MDA-MB-157, and MCF7) showed robust proliferation in high Zn 2+ at concentrations that killed MCF10A, T-47D, and SK-Br-3 cells. We also discovered that 4 of the 5 cancer cell lines demonstrate compromised proliferation and increased cell death in low Zn 2+ , suggesting these cells may be addicted to Zn 2+ . Overall, our study suggests significant differences in Zn 2+ homeostasis and regulation in different types of breast cancer cells, with consequences for both proliferation and cell viability.

  PublisherOA PDFDOI

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

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-12-30

  preprintOpen access

  Tagging RNAs with fluorogenic aptamers has enabled imaging of transcripts in living cells, thereby revealing novel aspects of RNA metabolism and dynamics. While a diverse set of fluorogenic aptamers has been developed, a new generation of aptamers are beginning to exploit the ring-opening of spirocyclic rhodamine dyes to achieve robust performance in live mammalian cells. These fluorophores have two chemical states: a colorless, cell-permeable spirocyclic state and a fluorescent zwitterionic state. Recently, the developed dye SpyRho555 almost exclusively adopts the closed state 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.

  PublisherOA PDFDOI

• Unveiling the promise of peptide nucleic acids as functional linkers for an RNA imaging platform

  RSC Chemical Biology · 2024-12-19 · 3 citations

  articleOpen accessSenior authorCorresponding

  and in live cells, enhancing visualization of RNA in stress granules and U-bodies at low concentrations. The modular nature of the Riboglow platform allows for flexible modifications of the PNA linker, fluorophore, and RNA tag, while maintaining high specificity and affinity. This work establishes a new approach for enhancing RNA imaging platforms through the use of PNA linkers, highlighting the potential of combining short oligonucleotides with small molecules to improve the affinity and specificity of RNA-targeting probes. Furthermore, this dual-binding approach presents a promising strategy for driving advancements in RNA-targeted drug development.

  PublisherOA PDFDOI

• Cellular zinc status alters chromatin accessibility and binding of p53 to DNA

  Life Science Alliance · 2024-07-05 · 8 citations

  articleOpen accessSenior authorCorresponding

  Zn 2+ is an essential metal required by approximately 850 human transcription factors. How these proteins acquire their essential Zn 2+ cofactor and whether they are sensitive to changes in the labile Zn 2+ pool in cells remain open questions. Using ATAC-seq to profile regions of accessible chromatin coupled with transcription factor enrichment analysis, we examined how increases and decreases in the labile zinc pool affect chromatin accessibility and transcription factor enrichment. We found 685 transcription factor motifs were differentially enriched, corresponding to 507 unique transcription factors. The pattern of perturbation and the types of transcription factors were notably different at promoters versus intergenic regions, with zinc-finger transcription factors strongly enriched in intergenic regions in elevated Zn 2+ . To test whether ATAC-seq and transcription factor enrichment analysis predictions correlate with changes in transcription factor binding, we used ChIP-qPCR to profile six p53 binding sites. We found that for five of the six targets, p53 binding correlates with the local accessibility determined by ATAC-seq. These results demonstrate that changes in labile zinc alter chromatin accessibility and transcription factor binding to DNA.

  PublisherOA PDFDOI

• Transient Zn ²⁺ deficiency induces replication stress and compromises daughter cell proliferation

  Proceedings of the National Academy of Sciences · 2024-04-30 · 11 citations

  articleOpen accessSenior authorCorresponding

  Cells must replicate their genome quickly and accurately, and they require metabolites and cofactors to do so. Ionic zinc (Zn 2+ ) is an essential micronutrient that is required for hundreds of cellular processes, including DNA synthesis and adequate proliferation. Deficiency in this micronutrient impairs DNA synthesis and inhibits proliferation, but the mechanism is unknown. Using fluorescent reporters to track single cells via long-term live-cell imaging, we find that Zn 2+ is required at the G1/S transition and during S phase for timely completion of S phase. A short pulse of Zn 2+ deficiency impairs DNA synthesis and increases markers of replication stress. These markers of replication stress are reversed upon resupply of Zn 2+ . Finally, we find that if Zn 2+ is chelated during the mother cell’s S phase, daughter cells enter a transient quiescent state, maintained by sustained expression of p21, which disappears upon reentry into the cell cycle. In summary, short pulses of mild Zn 2+ deficiency in S phase specifically induce replication stress, which causes downstream proliferation impairments in daughter cells.

  PublisherOA PDFDOI

Recent grants

• Genetically Encoded Sensors Shed Light on Zinc Homeostasis

  NIH · $2.6M · 2008–2018

• Technologies to Define and Map Novel Interorganelle Macromolecular Interactions

  NIH · $1.6M · 2013–2018

• NIH Grant R01GM083849

  NIH · $1.5M · 2013

• Riboglow: a robust multi-color riboswitch-based platform for imaging RNA in living cells

  NIH · $1.2M · 2019–2024

• NIH Grant F32GM06748801

  NIH · $42k · 2005

Frequent coauthors

• Ralph Jimenez

  52 shared

• Edward I. Solomon

  SLAC National Accelerator Laboratory

  33 shared

• Jennifer L. Lubbeck

  University of Colorado Boulder

  18 shared

• Liliana Quintanar

  17 shared

• Kevin M. Dean

  The University of Texas Southwestern Medical Center

  16 shared

• Roger Y. Tsien

  Howard Hughes Medical Institute

  15 shared

• Premashis Manna

  Massachusetts Institute of Technology

  15 shared

• Pia Friis

  University of Colorado System

  13 shared

Labs

• The Palmer Lab at University of Colorado BoulderPI

  Our research lies at the interface of chemistry and biology, where the application of chemical and physical principles provides a unique opportunity to better understand the fundamental biochemistry of living cells.

Education

• PhD, Chemistry

  Stanford University

  2001

• A.B., Chemistry

  Dartmouth College

  1994