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Stability and Folding of Secondary Structural Motifs:

Recent studies have begun to provide a general basis for how the cellular environment may affect nucleic acid folding and stability.1-2 However, key questions remain as to how the stability and structure of common secondary structure motifs, characterized by key functional group or base pairing interactions, is affected by interactions with osmolytes or changes in excluded volume due to crowding. Motifs such as non-Watson Crick base pairs, bulged nucleotides, and hairpin loops function as metal binding sites, protein and drug binding sites, and participate in tertiary contacts.3-5 These motifs can distort typical helical conformations and expose a variety of functional groups and surfaces to solvent. Studying these motifs in the presence of cosolutes may reveal unique preferences for osmolyte interactions and differences in the impact of excluded volume on folding.

Base Pair Diagram

Small Functional Nucleic Acids

The stability and folding of functional RNA tertiary structure can be modulated by both osmolytes and macromolecular crowding.6-7 Therefore, these factors could greatly affect folding and function of riboswitches, which bind ligands (aptamer domain) and change conformation to regulate gene expression (expression platform).8-9 It remains to be investigated in detail how osmolytes and macromolecular crowding affect riboswitch folding, ligand binding, and conformational changes of the expression platform. These studies could provide significant insight into how stability and function could be regulated by the cellular environment.


  1. Lambert, D., Draper, D. E. J Mol Biol 2007, 370, 993.

  2. Knowles, D. B., et al. Proc Natl Acad Sci U S A, 108, 12699.

  3. Davidson, A., et al. Proc Natl Acad Sci U S A 2009, 106, 11931.

  4. Wang, W., et al. Nucleos Nucleot Nucl 2009, 28, 424.

  5. Butcher, S. E., Pyle, A. M. Acc Chem Res 2011 (e-pub).

  6. Kilburn, D., et al. J Am Chem Soc, 2010, 132, 8690.

  7. Lambert, D., et al. J Mol Biol, 2010, 404, 138.

  8. Zhang, J., et al. Biochemistry, 2010, 49, 9123.

  9. Breaker, R. R. Mol Cell, 2011, 43, 867.

Last Updated 8/13/18

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