As a researcher in the Herschlag lab at Stanford, I am working towards the development of a quantitative and predictive model of RNA folding. For this purpose, I use single-molecule fluorescence, small-angle X-ray scattering, and other experimental tools to dissect the structural and dynamic properties of RNA three-dimensional motifs. These 3D motifs are like LEGOS that build diverse and complex functional RNA machines such as the ribosome. The goal is to develop a general model of RNA folding from the understanding of the energetic properties of small recurring building blocks or motifs. Recently, I joined an ongoing collaboration between the Greenleaf and the Herschlag labs that uses next-generation high-throughput sequencing for the characterization of RNA structural motifs. This powerful high-throughput approach developed in the Greenleaf lab allows dissection of the thermodynamic and kinetic properties of thousands of 3D motifs in parallel.

All Publications

  • The Story of RNA Folding, as Told in Epochs. Cold Spring Harbor perspectives in biology Herschlag, D., Bonilla, S., Bisaria, N. 2018; 10 (10)


    SUMMARYThe past decades have witnessed tremendous developments in our understanding of RNA biology. At the core of these advances have been studies aimed at discerning RNA structure and at understanding the forces that influence the RNA folding process. It is easy to take the present state of understanding for granted, but there is much to be learned by considering the path to our current understanding, which has been tortuous, with the birth and death of models, the adaptation of experimental tools originally developed for characterization of protein structure and catalysis, and the development of novel tools for probing RNA. In this review we tour the stages of RNA folding studies, considering them as "epochs" that can be generalized across scientific disciplines. These epochs span from the discovery of catalytic RNA, through biophysical insights into the putative primordial RNA World, to characterization of structured RNAs, the building and testing of models, and, finally, to the development of models with the potential to yield generalizable predictive and quantitative models for RNA conformational, thermodynamic, and kinetic behavior. We hope that this accounting will aid others as they navigate the many fascinating questions about RNA and its roles in biology, in the past, present, and future.

    View details for DOI 10.1101/cshperspect.a032433

    View details for PubMedID 30275276

  • Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway Journal of the American Chemical Society Bonilla, S., Limouse, C., Bisaria, N., Gebala, M., Mabuchi, H., Herschlag, D. 2017: 18576-18589


    Decades of study of the RNA folding problem have revealed that diverse and complex structured RNAs are built from a common set of recurring structural motifs, leading to the perspective that a generalizable model of RNA folding may be developed from understanding of the folding properties of individual structural motifs. We used single-molecule fluorescence to dissect the kinetic and thermodynamic properties of a set of variants of a common tertiary structural motif, the tetraloop/tetraloop-receptor (TL/TLR). Our results revealed a multistep TL/TLR folding pathway in which preorganization of the ubiquitous AA-platform submotif precedes the formation of the docking transition state and tertiary A-minor hydrogen bond interactions form after the docking transition state. Differences in ion dependences between TL/TLR variants indicated the occurrence of sequence-dependent conformational rearrangements prior to and after the formation of the docking transition state. Nevertheless, varying the junction connecting the TL/TLR produced a common kinetic and ionic effect for all variants, suggesting that the global conformational search and compaction electrostatics are energetically independent from the formation of the tertiary motif contacts. We also found that in vitro-selected variants, despite their similar stability at high Mg2+ concentrations, are considerably less stable than natural variants under near-physiological ionic conditions, and the occurrence of the TL/TLR sequence variants in Nature correlates with their thermodynamic stability in isolation. Overall, our findings are consistent with modular but complex energetic properties of RNA structural motifs and will aid in the eventual quantitative description of RNA folding from its secondary and tertiary structural elements.

    View details for DOI 10.1021/jacs.7b08870

    View details for PubMedCentralID PMC5748328

  • Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere? Journal of the American Chemical Society Gebala, M., Bonilla, S., Bisaria, N., Herschlag, D. 2016; 138 (34): 10925-10934


    Electrostatics are central to all aspects of nucleic acid behavior, including their folding, condensation, and binding to other molecules, and the energetics of these processes are profoundly influenced by the ion atmosphere that surrounds nucleic acids. Given the highly complex and dynamic nature of the ion atmosphere, understanding its properties and effects will require synergy between computational modeling and experiment. Prior computational models and experiments suggest that cation occupancy in the ion atmosphere depends on the size of the cation. However, the computational models have not been independently tested, and the experimentally observed effects were small. Here, we evaluate a computational model of ion size effects by experimentally testing a blind prediction made from that model, and we present additional experimental results that extend our understanding of the ion atmosphere. Giambasu et al. developed and implemented a three-dimensional reference interaction site (3D-RISM) model for monovalent cations surrounding DNA and RNA helices, and this model predicts that Na(+) would outcompete Cs(+) by 1.8-2.1-fold; i.e., with Cs(+) in 2-fold excess of Na(+) the ion atmosphere would contain an equal number of each cation (Nucleic Acids Res. 2015, 43, 8405). However, our ion counting experiments indicate that there is no significant preference for Na(+) over Cs(+). There is an ∼25% preferential occupancy of Li(+) over larger cations in the ion atmosphere but, counter to general expectations from existing models, no size dependence for the other alkali metal ions. Further, we followed the folding of the P4-P6 RNA and showed that differences in folding with different alkali metal ions observed at high concentration arise from cation-anion interactions and not cation size effects. Overall, our results provide a critical test of a computational prediction, fundamental information about ion atmosphere properties, and parameters that will aid in the development of next-generation nucleic acid computational models.

    View details for DOI 10.1021/jacs.6b04289

    View details for PubMedID 27479701

    View details for PubMedCentralID PMC5010015

  • Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting. Journal of the American Chemical Society Gebala, M., Giambasu, G. M., Lipfert, J., Bisaria, N., Bonilla, S., Li, G., York, D. M., Herschlag, D. 2015; 137 (46): 14705-14715

    View details for DOI 10.1021/jacs.5b08395

    View details for PubMedID 26517731

  • Quantifying Nucleic Acid Ensembles with X-ray Scattering Interferometry. Methods in enzymology Shi, X., Bonilla, S., Herschlag, D., Harbury, P. 2015; 558: 75-97


    The conformational ensemble of a macromolecule is the complete description of the macromolecule's solution structures and can reveal important aspects of macromolecular folding, recognition, and function. However, most experimental approaches determine an average or predominant structure, or follow transitions between states that each can only be described by an average structure. Ensembles have been extremely difficult to experimentally characterize. We present the unique advantages and capabilities of a new biophysical technique, X-ray scattering interferometry (XSI), for probing and quantifying structural ensembles. XSI measures the interference of scattered waves from two heavy metal probes attached site specifically to a macromolecule. A Fourier transform of the interference pattern gives the fractional abundance of different probe separations directly representing the multiple conformation states populated by the macromolecule. These probe-probe distance distributions can then be used to define the structural ensemble of the macromolecule. XSI provides accurate, calibrated distance in a model-independent fashion with angstrom scale sensitivity in distances. XSI data can be compared in a straightforward manner to atomic coordinates determined experimentally or predicted by molecular dynamics simulations. We describe the conceptual framework for XSI and provide a detailed protocol for carrying out an XSI experiment.

    View details for DOI 10.1016/bs.mie.2015.02.001

    View details for PubMedID 26068738

  • Roles of Long-Range Tertiary Interactions in Limiting Dynamics of the Tetrahymena Group I Ribozyme JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Shi, X., Bisaria, N., Benz-Moy, T. L., Bonilla, S., Pavlichin, D. S., Herschlag, D. 2014; 136 (18): 6643-6648


    We determined the effects of mutating the long-range tertiary contacts of the Tetrahymena group I ribozyme on the dynamics of its substrate helix (referred to as P1) and on catalytic activity. Dynamics were assayed by fluorescence anisotropy of the fluorescent base analogue, 6-methyl isoxanthopterin, incorporated into the P1 helix, and fluorescence anisotropy and catalytic activity were measured for wild type and mutant ribozymes over a range of conditions. Remarkably, catalytic activity correlated with P1 anisotropy over 5 orders of magnitude of activity, with a correlation coefficient of 0.94. The functional and dynamic effects from simultaneous mutation of the two long-range contacts that weaken P1 docking are cumulative and, based on this RNA's topology, suggest distinct underlying origins for the mutant effects. Tests of mechanistic predictions via single molecule FRET measurements of rate constants for P1 docking and undocking suggest that ablation of the P14 tertiary interaction frees P2 and thereby enhances the conformational space explored by the undocked attached P1 helix. In contrast, mutation of the metal core tertiary interaction disrupts the conserved core into which the P1 helix docks. Thus, despite following a single correlation, the two long-range tertiary contacts facilitate P1 helix docking by distinct mechanisms. These results also demonstrate that a fluorescence anisotropy probe incorporated into a specific helix within a larger RNA can report on changes in local helical motions as well as differences in more global dynamics. This ability will help uncover the physical properties and behaviors that underlie the function of RNAs and RNA/protein complexes.

    View details for DOI 10.1021/ja413033d

    View details for Web of Science ID 000335720200024

    View details for PubMedID 24738560