Publications

2024

15. Shin, J. H., Cuevas, L. M., Roy, R., Bonilla, S.L., Al-Hashimi, H., Greenleaf, W. J., Herschlag, D. (2024). RNA. Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs. PMID: 39362695. PDF Supporting Info.

14. Bonilla, S.L., Jones, A. N., Incarnato, D. (2024). Curr. Opin. Struct. Biol. Structural and biophysical dissection of RNA conformational ensembles. PMID: 39146886. PDF

13. Bonilla, S.L., Jang, K. (2024). Curr. Opin. Struct. Biol. Challenges, advances, and opportunities in RNA structural biology by Cryo-EM. PMID: 39121532. PDF

Prior to joining Rockefeller

12. Shin, J.H., Bonilla, S.L., Denny, S.K., Greenleaf, W.J., Herschlag, D. (2023). Proc. Natl. Acad. Sci. U.S.A. Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements. PMID: 36897989. PDF

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

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

9. Bonilla, S. L., Sherlock, M. E., MacFadden, A., & Kieft, J. S. (2021). Science. 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. 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. 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. 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. 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. Does cation size affect occupancy and electrostatic screening of the nucleic acid ion atmosphere? PMCID: PMC5010015. PDF

3. Gebala, M., Giambasu, G., Lipfert, J., Bisaria, N., Bonilla, S., Li, G., York, D., Herschlag, D. (2015) J. Am. Chem. Soc. Cation-anion interactions within the nucleic acid ion atmosphere revealed by ion counting studies. PMCID: PMC4739826. PDF

2. Shi, X.S., Bonilla, S., Herschlag, D., Harbury, P. (2015) Methods in Enzymology. Quantifying Nucleic Acid Ensembles with X-ray Scattering Interferometry. PMID: 26068738. PDF

1. Shi, X.S., Bisaria, N., Benz-Moy, T., Bonilla, S., Pavlichin, D., Herschlag, D. (2014) J. Am. Chem. Soc. Roles of long-range tertiary interactions in limiting dynamics of the tetrahymena group I ribozyme. PMCID: PMC4021564. PDF