Significance of Knotted Structures for Function of Proteins and Nucleic Acids
Saturday Abstracts
Sedimentation of Macroscopic Rigid Knots and its Relation to Gelelectrophoretic Mobility
of DNA Knots
Giovanni Dietler
.
EPFL, Lausanne, Switzerland.
We address the general question of the extent to which the hydrodynamic behaviour of
microscopic freely fluctuating objects can be reproduced by macrosopic rigid objects. In
particular, we compare the sedimentation speeds of knotted DNA molecules undergoing gel
electrophoresis to the sedimentation speeds of rigid stereolithographic models of ideal knots in
both water and silicon oil. We find that the sedimentation speeds grow roughly linearly with the
average crossing number of the ideal knot configurations, and that the correlation is stronger
within classes of knots. This is consistent with previous observations with DNA knots in gel
electrophoresis.
RNA Pseudoknots in Telomerase and Riboswitches
Juli Feigon
.
University of California, Los Angeles, Los Angeles, USA.
RNA pseudoknots are a common element in structured RNAs, and can play both structural and
functional roles. We have investigated the pseudoknot structures and dynamics in telomerase and
preQ1 class I and II riboswitches. Telomerase is an RNP composed of a unique telomerase
reverse transcriptase, a telomerase RNA (TER), and accessory proteins. While TER varies in
length from ~150 nts in ciliates to >2000 in yeasts, all contain a pseudoknot. We found that
human TER pseudoknot contains a triple helix that is critical for function. Similar triple helices
were predicted for yeasts, and we found that in K. lactis the overall pseudoknot fold is
remarkably similar to human despite differences in sequence. A series of bulge bases, which
were not predicted, allow an extended triple helix to form. Riboswitches are RNA regulatory
elements, often found in the 5’ untranslated region of bacterial genes or operons, that change
conformation upon binding to a ligand, generally a metabolite related to the following genes.
This conformational change affects transcription or translation, depending on the riboswitch, by
exposing or sequestering a transcriptional terminator or the Shine-Delgarno sequence,
respectively. Two classes of riboswitches that bind preQ1, a precursor to the modified nucleotide
queosine almost universally found in the anticodon of some tRNAs, have been identified.
Structures of both classes of riboswitch in complex with preQ1 have been determined by us and
others. Both classes of preQ1 riboswitch form a pseudoknot, but the overall folds, cation
interactions, and mechanism of ligand recognition are different.
This work was supported by grants from the Department of Energy (DOE-DE-
FC0302ER63421), NIH (GM48123), and NSF (MCB1022379)
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