How does RNA fold?
We are now developing a quantitative and predictive framework for RNA folding kinetics and thermodynamics. We have developed a “Reconstitution Model” toward this goal and we have evidence that we can describe the folding of complex RNA based on the physical properties of their component helices, junctions, and tertiary motifs. Achieving this goal now requires combining high-throughput quantitative dissection of those RNA components, which is being carried out via new technology developed in the Greenleaf lab (Genetics). Implementation of this model will require translating these and additional high-throughput experiments into quantitative, testable computational models. We are also fascinated with the question of how RNAs assemble active sites and the factors that affect and limit RNA pre-organization and we would like to apply ultra-high-throughput mechanistic approaches to answer these questions.
1. Herschlag, D., Allred, B.E., Gowrishankar, S. (2015) Curr. Opin. Struct. Biol. 30, 125-133. From Static to Dynamic: The Need for Structural Ensembles and a Predictive Model of RNA Folding and Function. PMID: 25744941. (Medline) (PDF File) (Supporting Info)
2. Lipfert, J., Doniach, S., Das, R., Herschlag, D. (2014) Annu. Rev. Biochem. 83, 19.1-19.29. Understanding Nucleic Acid-Ion Interactions. PMCID: PMC4384882. (Medline) (PDF File)
3. Chu, V.B., Lipfert, J., Bai, Y., Pande, V.S., Doniach, S., Herschlag, D. (2009) RNA 15, 2195-2205. Do Conformational Biases of Simple Helical Junctions Influence RNA Folding Stability and Specificity? PMCID: PMC2779674. (Medline) (PDF File) (Supporting Info)
4. Chu, V.B., Herschlag, D. (2008) Curr. Opin. Struc. Biol. 18, 305-314. Unwinding RNA's Secrets: Advances in the Biology, Physics, and Modeling of Complex RNAs. PMCID: PMC2574980. (Medline) (PDF File)
5. Chu, V.B., Bai, Y., Lipfert, Y., Doniach, S., Herschlag, D. (2008) Curr. Opin. Chem. Biol. 12, 619-625. A Repulsive Field: Advances in the Electrostatics of the Ion Atmosphere. PMCID: PMC2976615. (Medline) (PDF File)
6. Herschlag, D. (1995) J. Biol. Chem. 270, 20871-20874. RNA Chaperones and the RNA Folding Problem. PMID: 754662. (Medline) (PDF File)
More on RNA Folding
The repertoire of biological functions of RNA goes well beyond that of a messenger between transcription and translation. RNA-based molecular machines carry out important biological processes such as protein synthesis by the ribosome and pre-mRNA splicing by the splicesome. RNAs also play essential roles in gene regulation via riboswitches, microRNAs and lncRNAs. The functional capability of RNA relies on its ability to fold into stable structures and undergo conformational changes. Indeed, studies of RNA folding have contributed to our understanding of how RNA functions in the cell.
The capability of RNA to act as a functional molecule in addition to its coding capacity led to the ‘RNA World’ hypothesis –that RNA was a key functional molecule in early evolution. Understanding RNA’s evolutionary history is necessary to fully understand its roles in modern day biology.
Observations that RNA can form highly-stable alternative structures led to our proposition that RNA chaperones must exist in vivo –i.e., proteins that help RNA unfold, explore its conformational space, and fold into its active conformation.
In the Herschlag lab, we study RNA folding at all levels, from complex functional RNAs to simple model systems that allow us to interrogate the energetics that underlie the folding of RNA molecules and build toward quantitative and predictive models.
Through our efforts to understand the fundamental forces that govern RNA folding, we aim to develop a quantitative and predictive model for RNA structure and function.
RNA is known to fold hierarchically, with the formation of secondary structure typically preceding tertiary structure. Secondary structure consists of quasi-rigid helices linked by junctions (i.e., regions that are not Watson-Crick base paired). We are exploring the dynamics of helices and conformational preferences of junctions and how they bias the positioning of the attached helices and thereby affect the folding stability and specificity. Distant elements of secondary structure are “glued” together in three-dimensional space by tertiary contacts, RNA structural units that are often conserved. We are investigating the structural and energetic properties of tertiary contacts and their role in the overall folding process. RNA is a highly charged polyelectrolyte and therefore its structure and function depends strongly on the presence of ions. In collaboration with theoretical and computational groups, we are dissecting the properties of the ‘ion-atmosphere,’ the dynamic sheath of ions that surrounds all polyelectrolytes, and the properties of specific metal ion binding sites.
To accomplish our goals in RNA folding, we have developed and continue to develop novel methods to get deeper insights into RNA folding. The range of techniques we employ includes single molecule fluorescence (smFRET), small angle X-ray scattering (SAXS), atomic emission spectroscopy (AES) and NMR. We are particularly excited about opportunities from novel high-throughput methods developed by W. Greenleaf (Stanford).
Some leading papers from the lab:
1. Bisaria, N., Greenfeld, M., Limouse, C., Pavlichin, D., Mabuchi, H., Herschlag, D. (2016) Proc. Natl. Acad. Sci. U.S.A. In Press. A Kinetic and Thermodynamic Framework for P4-P6 RNA Reveals Tertiary Motif Modularity and Modulation of the Folding Preferred Pathway.
2. Shi, X.S., Huang, L., Lilley, D.M.J., Harbury, P.A.B., Herschlag, D. (2016) Nat. Chem. Biol. 12, 146-152. The Solution Structural Ensembles of RNA Kink-turn Motifs and Their Protein Complexes. PMID: 26727239. (Medline) (PDF File) (Supporting Info)
See also: RNA Conformation - Lightening up invisible states, March 2016
3. Solomatin, S.V., Greenfeld, M., Chu, S., Herschlag, D. (2010) Nature 463, 681-684. Multiple Native States of an RNA Enzyme Reveal Persistent Ruggedness of an RNA Folding Landscape. PMCID: PMC2818749. (Medline) (PDF File) (Supporting Info)
4. Shi, X.S., Mollova, E., Pljevaljcic, G., Millar, D., Herschlag, D. (2009) J. Am. Chem. Soc. 131, 9571-9578. Probing the Dynamics of the P1 Helix within the Tetrahymena Group I Intron. PMICD: PMC2758093. (Medline) (PDF File) (Supporting Info)
5. Sattin, B.D., Zhao, W., Travers, K., Chu, S., Herschlag, D. (2008) J. Am. Chem. Soc. 130, 6085-6087. Direct Measurement of Tertiary Contact Cooperativity in RNA Folding. PMCID: PMC2835547. (Medline) (PDF File) (Supporting Info)
See also: Navigating the RNA Folding Landscape. Nat. Chem. Biol. 4, 451-452. (2008)
6. Bai, Y., Greenfeld, M., Travers, K., Chu, V.B., Lipfert, J., Doniach, S., Herschlag, D. (2007) J. Am. Chem. Soc. 129, 14981-14988. Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids. PMCID: PMC3167487. (Medline) (PDF File) (Supporting Info)
7. Woodside, M.T., Behnke-Parks, W.M., Larizadeh, K., Travers, K., Herschlag, D., Block, S.M. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 6190-6195. Nanomechanical Measurements of the Sequence-dependent Folding Landscapes of Single Nucleic Acid Hairpins. PMCID: PMC1458853. (Medline) (PDF File) (Supporting Info)
8. Bai, Y., Das, R., Millet, I.S., Herschlag, D., Doniach, S. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 1035-1040. Probing Counterion Modulated Repulsion and Attraction Between Nucleic Acid Duplexes in Solution. PMCID: PMC545826. (Medline) (PDF File) (Supporting Info)
9. Das, R., Travers, K., Bai, Y., Herschlag, D. (2005) J. Am. Chem. Soc. 127, 8272-8273. Determining the Mg2+ Stoichiometry for Folding an RNA Metal Ion Core. PMCID: PMC2538950. (Medline) (PDF File) (Supporting Info)
See also: Faculty of 1000, June 2005
10. Russell, R., Zhaung, X., Babcock, H.P., Millett, I.S., Doniach, S., Chu, S., Herschlag, D. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 155-160. Exploring the Folding Landscape of a Structured RNA. PMCID: PMC117531. (Medline) (PDF File) (Supporting Info)
11. Zhuang, X., Bartley, L.E., Babcock, H.P., Russell, R., Ha, T., Herschlag, D., Chu, S. (2000) Science 288, 2048-2051. A Single Molecule Study of RNA Catalysis and Folding. PMID: 10856219. (Medline) (PDF File)