Sequence and structure of the -acting genomic HDV ribozyme used in this study

<p><b>Copyright information:</b></p><p>Taken from "The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis"</p><p></p><p>Nucleic Acids Research 2007;35(6):1933-1946.</p><p>Published online 2 Mar 2007</p><p>PMCID:PMC1874588.</p><p>© 2007 The Author(s)</p> () Secondary structure of the genomic HDV ribozyme with the set of 5′-sequences (green) immediately upstream of the cleavage site (open arrow) as employed in our cleavage and footprinting experiments. Nucleotides in color correspond to important structural elements in the catalytic core. Red dashed lines, functionally relevant tertiary interactions. () Secondary structure of the truncated sequence used in our MD simulations, color coded as in (A). () Backbone ribbon representation of the precursor crystal structure (), color-coded as in (A and B)

Top, Watson–Crick G/U (wobble) basepair with water molecules (W) in its SGP and DGP

<p><b>Copyright information:</b></p><p>Taken from "Structural and evolutionary classification of G/U wobble basepairs in the ribosome"</p><p>Nucleic Acids Research 2006;34(5):1326-1341.</p><p>Published online 6 Mar 2006</p><p>PMCID:PMC1390688.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> The angles formed between the C1′–C1′ axis and the glycosidic bonds show the asymmetry of this basepair compared with the classical WC basepairs. Bottom, the isosteric A/C basepair. Produced by ChemDraw (CambridgeSoft Corporation)

Terbium(III)-mediated footprinting of the four 3′-P-labeled -acting genomic HDV ribozyme variants

<p><b>Copyright information:</b></p><p>Taken from "The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis"</p><p></p><p>Nucleic Acids Research 2007;35(6):1933-1946.</p><p>Published online 2 Mar 2007</p><p>PMCID:PMC1874588.</p><p>© 2007 The Author(s)</p> () Control experiment of background cleavage in the presence of Tb. The HDV ribozyme N − 1 variants were incubated for 30 min at 22°C under the indicated ionic conditions (see also Materials and methods section). We then separated the 88-nt reaction precursor from the 85-nt, faster migrating 3′-product, as identified by comparison with purified 3′-product from self-cleavage of the U − 1, A − 1 and G − 1 variants (3′P-N − 1). ‘Fresh’ indicates that the material was not incubated before loading onto the gel. () Terbium(III)-mediated footprinting of genomic HDV ribozyme variants. As in (A), the HDV ribozyme N − 1 variants were incubated for 30 min at 22°C under the indicated ionic conditions and then analyzed on a sequencing gel alongside alkaline hydrolysis (OH) and G-specific RNase T1 ladders for sequence identification (see also Materials and methods section). ‘Fresh’ indicates that the material was not incubated before loading onto the gel