Research People Publications

Papers, Reviews, and Book Chapters
  1. Dippel, A. D., Anderson, W. A., Evans, R. S., Deutsch, S., Hammond, M. C. "Chemiluminescent biosensors for detection of second messenger cyclic di-GMP" ACS Chem Bio (2018) in press. Link
    Related Highlights: "Sensors" special issue; Research Highlight in Nat Chem Biol
  2. Truong, J., Hsieh, Y.-F., Truong, L., Jia, G., Hammond, M. C. "Designing fluorescent biosensors using circular permutations of riboswitches" Methods (2018) in press. Link
    Related Highlights: "Designing Synthetic RNAs" special issue
  3. Villa, J. K.*, Su, Y.*, Contreras, L. M., Hammond, M. C. "Synthetic biology of small RNAs and riboswitches" Regulating with RNA in Bacteria and Archaea (2018) Invited contribution - in press.
  4. Yeo, J., Dippel, A. B., Wang, X. C., Hammond, M. C. "In Vivo Biochemistry: Single-cell dynamics of cyclic di-GMP in E. coli in response to zinc overload" Biochemistry (2018) 57, 108-116. Link
    Related Highlights: Future of Biochemistry special issue; College of Chemistry news story
  5. Yeo, J., Wang, X. C., Hammond, M. C. "Live flow cytometry analysis of c-di-GMP levels in single cell populations" Methods Mol Biol (2017) 1657, 111-130. Link to Book
  6. Hallberg, Z. F., Su, Y., Kitto, R. Z., Hammond, M. C. "Engineering and in vivo applications of riboswitches" Annual Rev Biochem (2017) 86, 515-539. Link
  7. Bose, D.*, Su, Y.*, Marcus, A., Raulet, D. H., Hammond, M. C. "An RNA-based fluorescent biosensor for high-throughput analysis of the cGAS-cGAMP-STING pathway" Cell Chem Biol (2016) 23, 1539-1549. Link
  8. Wang, X. C., Wilson, S. C., Hammond, M. C. "Next-generation RNA-based fluorescent biosensors enable anaerobic detection of cyclic di-GMP" Nucleic Acids Res (2016) 44, e139. Link
  9. Su, Y., Hickey, S. F., Keyser, S. G. L., Hammond, M. C. "In vitro and in vivo enzyme activity screening via RNA-based fluorescent biosensors for S-adenosyl-L-homocysteine (SAH)" J Am Chem Soc (2016) 138, 7040-7047. Link
  10. Hallberg, Z. F., Wang, X. C., Wright, T. A., Nan, B., Ad, O., Yeo, J., Hammond, M. C. "Hybrid promiscuous (Hypr) GGDEF enzymes produce cyclic AMP-GMP (3', 3'-cGAMP)" Proc Natl Acad Sci (2016) 113, 1790-1795. Link
    Related Highlights: 2015 NIH High Risk-High Reward Symposium; Berkeley news story
  11. Muller, R. Y., Hammond, M. C., Rio, D. C., Lee, Y. J. "An efficient method for electroporation of small interfering RNAs (siRNAs) into ENCODE Project Tier 1 GM12878 and K562 cell lines" J Biomol Tech (2015) 26, 142-149. Link
  12. Gonzalez, T. L., Liang, Y., Nguyen, B., Staskawicz, B. J., Loque, D., Hammond, M. C. "Tight regulation of plant immune responses by combining promoter and suicide exon elements" Nucleic Acids Res (2015) 43, 7152-7161. Link
  13. Kellenberger, C. A., Sales-Lee, J., Pan, Y., Gassaway, M. M., Herr, A. E., Hammond, M. C. "A minimalist biosensor: quantitation of cyclic di-GMP using the conformational change of a riboswitch aptamer" RNA Biol (2015) 12, 1189-1197. Link
  14. Kellenberger, C. A.*, Chen, C.*, Whiteley, A. T., Portnoy, D. A., Hammond, M. C. "RNA-based fluorescent biosensors for live cell imaging of second messenger cyclic di-AMP" J Am Chem Soc (2015) 137, 6432-6435. Link
  15. Ren, A., Wang, X. C., Kellenberger, C. A., Rajashankar, J. R., Jones, R., Hammond, M. C., Patel, D. J. "Structural basis for molecular discrimination by a 3', 3'-cGAMP sensing riboswitch" Cell Reports (2015), 11, 1-12. Open Access PDF
  16. Kellenberger, C. A.*, Wilson, S. C.*, Hickey, S. F., Gonzalez, T. L., Su, Y., Hallberg, Z. F., Brewer, T. F., Iavarone, A. T., Carlson, H. K., Hsieh, Y. F., Hammond, M. C. "GEMM-I riboswitches from Geobacter sense the bacterial second messenger c-AMP-GMP" Proc Natl Acad Sci (2015) 112, 5383-5388. Link
    Related Highlights: 2015 Signaling Breakthroughs of the Year
  17. Kellenberger, C. A., Hallberg, Z. F., Hammond, M. C. "Live cell imaging using riboswitch-Spinach tRNA fusions as metabolite-sensing fluorescent biosensors" Methods in Mol Biol (2015) 1316, 87-103. Link to Chapter
  18. Kellenberger, C. A., Hammond, M. C. "In vitro analysis of riboswitch-Spinach aptamer fusions as metabolite-sensing fluorescent biosensors" Methods Enz (2015) 550, 147-172. Link to Chapter
  19. Pan, Y., Duncombe, T. A., Kellenberger, C. A., Hammond, M. C., Herr, A. E. "High-throughput electrophoretic mobility shift assays for quantitative analysis of molecular binding reactions" Analytical Chem (2014) 86, 10357-10364. Link
  20. Wilson, S. C., Cohen, D. T., Wang, X. C., Hammond, M. C. "A neutral pH thermal hydrolysis method for quantification of structured RNAs" RNA (2014) 20, 1153-1160. Link
  21. Hickey, S. F., Hammond, M. C. "Structure-guided design of fluorescent S-adenosylmethionine analogs for a high-throughput screen to target SAM-I riboswitch RNAs" Chem Biol (2014) 21, 345-356. Link
  22. Sadhu, M. J., Guan, Q., Li, F., Sales-Lee, J., Iavarone, A. T., Hammond, M. C., Cande, W. Z., Rine, J. "Nutritional control of epigenetic processes in yeast and human cells" Genetics (2013) 195, 831-844. Link
  23. Diner, E. J., Burdette, D. L., Wilson, S. C., Monroe, K. M., Kellenberger, C. A., Hyodo, M., Hayakawa, Y., Hammond, M. C., Vance, R. E. "The innate immune DNA sensor cGAS produces a noncanonical cyclic dinucleotide that activates human STING" Cell Reports (2013), 3, 1355-1361. Link
  24. Leppek, K., Schott, J., Reitter, S., Poetz, F., Hammond, M. C., Stoecklin, G. "Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs" Cell (2013) 153, 869-881. Link
  25. Kellenberger, C. A., Wilson, S. C., Sales-Lee, J., Hammond, M. C. "RNA-based fluorescent biosensors for live cell imaging of second messengers cyclic di-GMP and cyclic AMP-GMP" J Am Chem Soc (2013) 135, 4906-4909. Link
  26. Karns, K., Vogan, J. M., Qin, Q., Hickey, S. F., Wilson, S. C., Hammond, M. C., Herr, A. E. "Microfluidic screening of electrophoretic mobility shifts elucidates riboswitch binding function" J Am Chem Soc (2013), 135, 3136-3143. Link
  27. Hickey, S. F., Sridhar, M., Westermann, A. J., Qin, Q., Vijayendra, P., Liou, G., Hammond, M. C. "Transgene regulation in plants by alternative splicing of a suicide exon" Nucleic Acids Res (2012), 40, 4701-4710. Link
    Selected by NAR editors as a Featured Article
  28. Hammond, M. C. "A tale of two riboswitches" Nat Chem Biol (2011), 7, 342-3. Link

  29. Meyer, M. M., Hammond, M. C., Salinas, Y., Roth, A., Sudarsan, N., Breaker, R. R. "Challenges of ligand identification for riboswitch candidates" RNA Biol (2011), 8, 5-10. Link
  30. Block, K. F., Hammond, M. C., Breaker, R. R. "Evidence for widespread gene control function by the ydaO riboswitch candidate" J Bacter (2010), 192, 3983-9. Link
  31. Hammond, M. C., Wachter, A., Breaker, R. R. "A plant 5S rRNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs" Nat Struct and Mol Biol (2009), 16, 541-9. Link
  32. Weinberg, Z., Regulski, E. E., Hammond, M. C., Barrick, J. E., Yao, Z., Ruzzo, W. L., Breaker, R. R. "The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches" RNA (2008), 14, 822-8. Link
  33. Hammond, M. C., Bartlett, P. A. "Synthesis of amino acid-derived cyclic acyl amidines for use in beta-strand peptidomimetics" J Org Chem (2007), 72, 3104-07. Link
  34. Hammond, M. C., Harris, B. Z.; Lim, W. A., Bartlett, P. A. "Beta-strand peptidomimetics as potent PDZ ligands" Chem Biol (2006), 13, 1247-51. Link
  35. Sudarsan, N.*, Hammond, M. C.*, Block, K. F., Welz, R., Barrick, J. E., Roth, A., Breaker, R. R. "Tandem riboswitch architectures exhibit complex gene control functions" Science (2006), 314, 300-304.
    *co-first authors Link
Patents and Patent Applications
  1. Hammond, M. C., Wright, T. A. "Methods of producing cyclic dinucleotides" U.S. Pat Appl Publ 62/438,126 (2016).
  2. Hammond, M. C., Su, Y., Bose, D. "Fluorescent biosensor for 2', 3'-cGAMP" U.S. Pat Appl Publ 62/349,556 (2016).
  3. Hammond, M. C., Su, Y., Keyser, S. G. L., Hickey, S. F. "A fluorescent biosensor for high throughput screening of methyltransferase activity" U.S. Pat Appl Publ 62/246,953 (2015).
  4. Vance, R. E., Hammond, M. C., Burdette, D., Diner, E. J., Wilson, S. C. "Cyclic di-nucleotide induction of type I interferon" U.S. Pat Appl Publ 14/268,967 (2014).
  5. Hammond, M. C., Westerman, A. J., Qin, Q. "A P5SM suicide exon for regulating gene expression" U.S. Pat Appl Publ 13/747,395 (2013).
  6. Bartlett, P. A., Hammond, M. C. "Peptide beta-strand mimics based on pyridinones, pyrazinones, pyridazinones, and triazinones" U.S. Pat Appl Publ (2005).