Preprints
2026
2. Streit, L. V., Onikubo, T., Astore, M. A., Cioppa, E. A., Olinares, P. D. B., Urnavicius, L., Incarnato, D., Bonilla, S. L. RNA 3D Motif Dynamics Guide Assembly of the Replication Initiation Complex in Flaviviruses.bioRxiv (2026). PDF, Supporting Info.
1. Spear, E., O’Donoghue, Z., Bonilla, S. L., Larsen, K. P., Sherlock, M. E., Kieft, J. S. An A-rich linker between dengue virus tandem xrRNAs facilitates functional coordination.bioRxiv (2026). PMID: 41867834. PDF, Supporting Info.
Publications
2024
3. Shin, J. H., Cuevas, L. M., Roy, R., Bonilla, S.L., Al-Hashimi, H., Greenleaf, W. J., Herschlag, D. Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs.RNA (2024). PMID: 39362695. PDF, Supporting Info.
2. Bonilla, S.L., Jang, K. Challenges, advances, and opportunities in RNA structural biology by Cryo-EM.Curr. Opin. Struct. Biol. (2024). PMID: 39121532. PDF
1. Bonilla, S.L., Jones, A. N., Incarnato, D. Structural and biophysical dissection of RNA conformational ensembles.Curr. Opin. Struct. Biol. (2024). PMID: 39146886. PDF
Prior to joining Rockefeller University
12. Shin, J.H., Bonilla, S.L., Denny, S.K., Greenleaf, W.J., Herschlag, D. Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements.Proc. Natl. Acad. Sci. U.S.A. (2023). PMID: 36897989. PDF
11. Bonilla, S. L., & Kieft, J. S. The promise of cryo-EM to explore RNA structural dynamics.Journal of Molecular Biology (2022). PMID: 36049551. PDF
10. Bonilla, S. L., Vicens, Q., & Kieft, J. S. Cryo-EM reveals an entangled kinetic trap in the folding of a catalytic RNA.Science Advances (2022). PMID: 36026457. PDF, Supporting Info.
9. Bonilla, S. L., Sherlock, M. E., MacFadden, A., & Kieft, J. S. A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure.Science (2021). PMID: 34793227 PDF, Supporting Info.
8. Bonilla, S.L., Denny, S.K., Shin, J.H., Alvarez-Buylla, A., Greenleaf, W., Herschlag, D. High-throughput dissection of the thermodynamic and conformational properties of a ubiquitous class of RNA tertiary contact motifs.Proc. Natl. Acad. Sci. U.S.A. (2021). PMID: 34373334. PDF, Supporting Info.
7. Zettl, T., Shi, X.S., Bonilla, S., Sedlak, S.M., Lipfert, J., Herschlag, D. The structural ensemble of a Holliday junction determined by X-Ray scattering interference.Nucleic Acids Res. (2020). PMID: 32597986. PDF
6. Herschlag, D., Bonilla, S., Bisaria, N. The story of RNA folding, as told in epochs.Cold Spring Harb. Perspect. Biol. (2018). PMID: 30275276. PDF
5. Bonilla, S., Limouse, C., Bisaria, N., Gebala, M., Mabuchi, H., Herschlag, D. Single-molecule fluorescence reveals commonalities and distinctions among natural and in vitro-selected RNA tertiary motifs in a multistep folding pathway.J. Am. Chem. Soc. (2017). PMCID: PMC5748328. PDF, Supporting Info. Part 1, Supporting Info. Part 2
4. Gebala, M., Bonilla, S., Bisaria, N., Herschlag, D. Does cation size affect occupancy and electrostatic screening of the nucleic acid ion atmosphere?J. Am. Chem. Soc. (2016) PMCID: PMC5010015. PDF
3. Gebala, M., Giambasu, G., Lipfert, J., Bisaria, N., Bonilla, S., Li, G., York, D., Herschlag, D. Cation-anion interactions within the nucleic acid ion atmosphere revealed by ion counting studies. J. Am. Chem. Soc. (2015). PMCID: PMC4739826. PDF
2. Shi, X.S., Bonilla, S., Herschlag, D., Harbury, P. Quantifying Nucleic Acid Ensembles with X-ray Scattering Interferometry.Methods in Enzymology (2015). PMID: 26068738. PDF
1. Shi, X.S., Bisaria, N., Benz-Moy, T., Bonilla, S., Pavlichin, D., Herschlag, D. Roles of long-range tertiary interactions in limiting dynamics of the tetrahymena group I ribozyme.J. Am. Chem. Soc. (2014). PMCID: PMC4021564. PDF