Non-Watson–Crick base pairs in crystal structures of studied SRD motifs

<p><b>Copyright information:</b></p><p>Taken from "Molecular dynamics simulations of sarcin–ricin rRNA motif"</p><p>Nucleic Acids Research 2006;34(2):697-708.</p><p>Published online 2 Feb 2006</p><p>PMCID:PMC1360246.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> Tetraloop region, () SE/H G/A base pair; G-bulged region, () G/U/A triplet of SE/H G/U and WC/H U/A base pairs; flexible region, () H water-mediated A/C base pair; () SE/H water-mediated U/C base pair, () H A/A base pair and () SE/H C/C base pair. (a–d) are based on the crystal structure of ECOLI system (PDB, 1Q9A), (e and f) are based on the crystal structure of mutated RAT system (PDB, 1Q96). () Stereo view of the flexible region of the RAT crystal structure (PDB, 430D) with unpaired bases in A/A and C/C base pairs (highlighted)

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

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)

Comparison of the bond distances and angles characterizing the steric conditions for the in-line attack of O3’ at the next phosphate in the crystal structure of 3’,5’ cGMP and 3’,5’ cAMP [10,11].

<p>Comparison of the bond distances and angles characterizing the steric conditions for the in-line attack of O3’ at the next phosphate in the crystal structure of 3’,5’ cGMP and 3’,5’ cAMP [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165723#pone.0165723.ref010" target="_blank">10</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165723#pone.0165723.ref011" target="_blank">11</a>].</p

Non-Enzymatic Oligomerization of 3’, 5’ Cyclic AMP

<div><p>Recent studies illustrate that short oligonucleotide sequences can be easily produced from nucleotide precursors in a template-free non-enzymatic way under dehydrating conditions, i.e. using essentially dry materials. Here we report that 3’,5’ cyclic AMP may also serve as a substrate of the reaction, which proceeds under moderate conditions yet with a lower efficiency than the previously reported oligomerization of 3’,5’ cyclic GMP. Optimally the oligomerization requires (i) a temperature of 80°C, (ii) a neutral to alkaline environment and (iii) a time on the order of weeks. Differences in the yield and required reaction conditions of the oligomerizations utilizing 3’,5’ cGMP and cAMP are discussed in terms of the crystal structures of the compounds. Polymerization of 3’,5’ cyclic nucleotides, whose paramount relevance in a prebiotic chemistry context has been widely accepted for decades, supports the possibility that the origin of extant genetic materials might have followed a direct uninterrupted path since its very beginning, starting from non-elaborately pre-activated monomer compounds and simple reactions.</p></div

MALDI analysis of the reaction products obtained by reacting 3’,5’ cAMP for 60 days, pH 7.0, 80°C.

<p>Panel A: the overall pattern recorded for the reacted 3’,5’ cAMP sample. Panel B: spectrum of the unreacted sample. Panels C and D show the blow-ups of the relevant areas from panels A and B, respectively.</p

3’, 5’ cAMP oligomerization as a function of temperature and of pH.

<p>Panel A: 3’,5’ cAMP oligomerization as a function of temperature, from 25 to 85°C (lanes 2 to 10, respectively), pH 7.0, 24 hrs. Panel B: 3’,5’ cAMP oligomerization as a function of pH, from 2.7 to 10.6 (lanes 2 to 9, respectively). The dry buffered material (for preparation see the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165723#sec004" target="_blank">Methods</a> section), was reacted at 80°Cfor 6 hrs, purposely in sub-optimal time conditions. U = untreated.</p

PAGE-analysis of the 3’, 5’ cAMP oligomerization products as a function of time at pH 10.6.

<p>Panel A. The material obtained by drying the initial 3’,5’ cAMP solution (pH 10.6) was reacted at 80°C for the indicated times (between 1 and 312 hours, see lanes 3 to 6). U = untreated (see lane 2). Panel B shows a blow-up analysis of the time periods encompassed between 1 and 1440 minutes (lanes from 2 to 9). The plot shows that the reaction rate slows down after 5 hours. Markers (M): formamide-digested 5’-labelled A₂₄. For the attribution of the molecular species involved, see the text. Gels with few samples were routinely preferred in order to avoid “gel smiling” effects due to the relatively large concentrations of materials loaded, present in the oligomerization assays. Therefore, the analysis was usually split in small-number groups. Acrylamide = 20%. The salts migration front, below which no attribution is possible, is indicated. The interpolating line in the plot is drawn as a guide to the eye here and in the following figures.</p

Packing of the cyclic nucleotides in the crystal structure of 3’,5’ cGMP provides with better steric conditions for the transphophorylation leading to oligonucleotides than that of 3’,5’ cAMP [10,11].

<p>Packing of the cyclic nucleotides in the crystal structure of 3’,5’ cGMP provides with better steric conditions for the transphophorylation leading to oligonucleotides than that of 3’,5’ cAMP [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165723#pone.0165723.ref010" target="_blank">10</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165723#pone.0165723.ref011" target="_blank">11</a>].</p