We are interested in the chemical mechanisms by which components of the cellular environment
affect the structural stability and folding of nucleic acids such as DNA and RNA.
Biomolecules are often studied under dilute solution conditions, which are in contrast
to actual cellular conditions, where macromolecules occupy a significant fraction
of the cellular volume and other small molecules (osmolytes) accumulate in response
to environmental stress. By utilizing a variety of spectroscopic techniques including
UV-Vis, CD, fluorescence, and small-angle X-ray scattering (SAXS), we can observe
the effects of potential nucleic acid effectors, both large and small, on the stability
and folding of key secondary structural motifs (Specific Aim I) and on small functional
nucleic acids (Specific Aim II). Results from these studies will contribute to the
understanding of how nucleic acids function in vivo.
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.
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.
- Lambert, D., Draper, D. E. J Mol Biol 2007, 370, 993.
- Knowles, D. B., et al. Proc Natl Acad Sci U S A, 108, 12699.
- Davidson, A., et al. Proc Natl Acad Sci U S A 2009, 106, 11931.
- Wang, W., et al. Nucleos Nucleot Nucl 2009, 28, 424.
- Butcher, S. E., Pyle, A. M. Acc Chem Res 2011 (e-pub).
- Kilburn, D., et al. J Am Chem Soc, 2010, 132, 8690.
- Lambert, D., et al. J Mol Biol, 2010, 404, 138.
- Zhang, J., et al. Biochemistry, 2010, 49, 9123.
- Breaker, R. R. Mol Cell, 2011, 43, 867.