Publications

Prior to joining Rockefeller

(12) Bonilla, S. L., & Kieft, J. S. (2022). Journal of molecular biology. 167802. The promise of cryo-EM to explore RNA structural dynamics. PMID: 36049551. PDF

(11) Bonilla, S. L., Vicens, Q., & Kieft, J. S. (2022). Science Advances. 8(34), eabq4144. Cryo-EM reveals an entangled kinetic trap in the folding of a catalytic RNA. PMID: 36026457. PDF Supporting Info.

(10) Shin, J.H., Bonilla, S.L., Denny, S.K., Greenleaf, W.J., Herschlag, D. (2023) Proc. Natl. Acad. Sci. U.S.A. 11, e2220485120. Dissecting the Energetic Architecture within an RNA Tertiary Structural Motif via High-throughput Thermodynamic Measurements. PMID: 36897989. PDF

(9) Bonilla, S. L., Sherlock, M. E., MacFadden, A., & Kieft, J. S. (2021). Science. 374(6570), 955-960. A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure. PMID: 34793227 PDF Supporting Info.

(8) Bonilla, S.L., Denny, S.K., Shin, J.H., Alvarez-Buylla, A., Greenleaf, W., Herschlag, D. (2021) Proc. Natl. Acad. Sci. U.S.A. 118, e2109085118. High-throughput Dissection of the Thermodynamic and Conformational Properties of a Ubiquitous Class of RNA Tertiary Contact Motifs. PMID: 34373334. PDF Supporting Info.

(7) Zettl, T., Shi, X.S., Bonilla, S., Sedlak, S.M., Lipfert, J., Herschlag, D. (2020) Nucleic Acids Res. 48, 8090-8098. The Structural Ensemble of a Holliday Junction Determined by X-Ray Scattering Interference. PMID: 32597986. PDF

(6) Herschlag, D., Bonilla, S., Bisaria, N. (2018) Cold Spring Harb. Perspect. Biol. 10, pii:a032433. The Story of RNA Folding, as Told in Epochs. PMID: 30275276. PDF

(5) Bonilla, S., Limouse, C., Bisaria, N., Gebala, M., Mabuchi, H., Herschlag, D. (2017) J. Am. Chem. Soc. 139, 18576-18589. Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway. PMCID: PMC5748328. PDF Supporting Info. Part 1 Supporting Info. Part 2

(4) Gebala, M., Bonilla, S., Bisaria, N., Herschlag, D. (2016) J. Am. Chem. Soc.  138, 10925-10934. Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere? PMCID: PMC5010015.

(3) Gebala, M., Giambasu, G., Lipfert, J., Bisaria, N., Bonilla, S., Li, G., York, D., Herschlag, D. (2015) J. Am. Chem. Soc. 137, 14705-14715. Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting Studies. PMCID: PMC4739826.

(2) Shi, X.S., Bonilla, S., Herschlag, D., Harbury, P. (2015) Methods in Enzymology: Structures of Large RNA Molecules and Their Complexes 558, 75-97. Quantifying Nucleic Acid Ensembles with X-ray Scattering Interferometry. PMID: 26068738

(1) Shi, X.S., Bisaria, N., Benz-Moy, T., Bonilla, S., Pavlichin, D., Herschlag, D. (2014) J. Am. Chem. Soc. 136, 6643-6648. Roles of Long-range Tertiary Interactions in Limiting Dynamics of the Tetrahymena Group I Ribozyme. PMCID: PMC4021564.