A new circular dichroic band in nucleic acids and ribosomes

A Conformational Restriction Strategy for the Control of CRISPR/Cas Gene Editing with Photoactivatable Guide RNAs

The CRISPR/Cas system is one of the most powerful tools for gene editing. However, approaches for precise control of genome editing and regulatory events are still desirable. Here, we report the spatiotemporal and efficient control of CRISPR/Cas9- and Cas12a-mediated editing with conformationally restricted guide RNAs (gRNAs). This approach relied on only two or three pre-installed photo-labile substituents followed by an intramolecular cyclization, representing a robust synthetic method in comparison to the heavily modified linear gRNAs that often require extensive screening and time-consuming optimization. This tactic could direct the precise cleavage of the genes encoding green fluorescent protein (GFP) and the vascular endothelial growth factor A (VEGFA) protein within a predefined cutting region without notable editing leakage in live cells. We also achieved light-mediated myostatin (MSTN) gene editing in embryos, wherein a new bow-knot-type gRNA was constructed with excellent OFF/ON switch efficiency. Overall, our work provides a significant new strategy in CRISPR/Cas editing with modified circular gRNAs to precisely manipulate where and when genes are edited.

Visualization of ion-dependent conformational changes in Escherichia coli 23 S rRNA by scanning transmission electron microscopy

Electron micrographs of Escherichia coli 23 S rRNA molecules obtained by scanning transmission electron microscopy, unstained and under nondenaturing conditions, reveal previously unresolved structural patterns. The complexity of the pattern is dependent upon the ambient ionic strength conditions. In water and in very low ionic strength buffer, the conformation of 23 S rRNA is characterized by an extended framework, with short side branches related to the secondary and tertiary structure of the molecule. The total length of this filamentous complex is approximately 2500 A, only about one-fourth of the length of 23 S rRNA when fully stretched under the denaturing conditions used for imaging by conventional electron microscopy. These data, supplemented by the determination of the linear density (M/L), suggest that in low ionic strength the backbone of 23 S rRNA is formed by a structure corresponding, on the average, to the mass of four nucleotide strands (M/L approximately equal to 480 Da/A). With increasing ionic strength, 23 S rRNA coils into more compact forms. Molecules in these states can be characterized by apparent radii of gyration (RG), which can be calculated from the mass distribution within the digitized images of individual RNA molecules. The 23 S rRNA is in its most condensed form (RG = 115 A) in ribosomal reconstitution buffer; however, it still does not attain the compactness of the large subunit (RG = 69 A), nor does it show any resemblance to the native 50 S subunit. The net content of ordered secondary structure, as determined by circular dichroism spectroscopy, is not visibly affected by the changes of ionic strength conditions. These results imply that the observed conformational changes in 23 S rRNA are caused by intramolecular folding of the 23 S rRNA strands induced by the shielding effect of ambient charges.

Structural differences between active and inactive mammalian 60S ribosomal subunits. Circular dichroism and electric birefringence studies

The structure and conformation of different active and inactive forms of the 60S rat liver ribosomal subunits have been analyzed by electric birefringence and circular dichroism. These studies show the following: 1) When a phosphate buffer is used instead of a triethanolamine buffer, there are major changes in RNA stacking, RNA-protein interactions, and particle orientation and conformation with no concomitant loss in ribosome activity. 2) The inactivated subunits by K(+)-depletion exhibit the same electro-optical and near-UV CD behaviour than the active subunits in phosphate buffer. 3) Inactivation by EDTA-treatment leads to drastic changes in RNA structure, RNA-protein interactions and subunit conformation; the 60S particles behave like free RNA, indicating the absence of any stabilization of rRNA by ribosomal proteins. 4) The inactivation of subunits by depletion of either monovalent or divalent cations is accompanied by a net decrease of the alpha-helicity of the ribosomal proteins. 5) The transition from active to inactive form of 60S subunits may involve protein modifications, likely dependent on a specific array of cations. 6) RNA has a certain degree of liberty within the subunits and one can suppose that this property is responsible for the flexible structure of ribosome.

Studies on the negative circular dichroic bands around 297 nm of ribosomes from bacterial cells

The small negative CD bands around 297 nm of isolated 30-S and 50-S ribosomal subunits were precisely measured for three bacteria, Bacillus stearothermophilus, Bacillus subtilis and Escherichia coli Q 13. The intensities of the negative CD bands of 30-S subunits were always much greater than those of 50-S subunits irrespective of the bacterial strains, which may be related to the difference in comformations of rRNAs and proteins in the complexes between these subribosomal particles. The dissociation of 70-S ribosomes into two subunits by lowering Mg2+ concentration caused evident enhancement of intensity of the 297 nm CD band, which was completely reversed by the association of the two subunits into 70-S particles. The melting profiles of CD spectra 3 B. stearothermophilus and E. coli were compared and both subunits of the former were found to be more heat stable than those of the latter. It was found that 5 M urea and 0.5% sodium dodecyl sulfate (SDS) treatment caused considerable reduction of the negative CD intensity around 297 nm of 30-S subunits but no significant change of 50-S subunits, while no significant change was observed for the CD spectra of isolated 16-S and 23-S rRNAs by the same treatment. Effects of EDTA treatment and then addition of Mg2+ on the CD spectra and fluorescence emission spectra of the subunits were also observed and the contribution by the interaction between rRNA s and proteins in ribosomes to the small negative band around 297 nm was discussed.

Use of the 295- to 300-nanometer circular dichroism through of ribonucleic acid to study helix winding: effect of acridine orange

Acridine orange decreases the amplitude of the 295-nm circular dichroism (CD) trough of ribosomal ribonucleic acid (rRNA) where the trough has been related to coil character. Since acridine orange is known from earlier work to intercalate between base pairs of nucleic acids, causing an unwinding of the coil, and our studies show a decrease in the 295-nm CD trough, it appears that CD measurements may be used to observe relative unwinding of rRNA. Under similar solution conditions, melting temperatures with acridine orange indicate no significant change in the stabilization of rRNA structure by acridine orange. Hypochromicity studies show no increase in the percent base pairing in rRNA when 0.1 M tris(hydroxymethyl)aminomethane (pH 7.6) with 1.35 M KCl is used. These results indicate that CD changes in the amplitude of the 295-nm trough of rRNA are related to helix winding in rRNA.

Some observations on the near ultraviolet circular dichroism of tRNA from E. coli

The circular dichroism arising from 4-thiouridine residues in E. coli transfer RNA has been studied under conditions in which the secondary and tertiary structure of the macromolecule is either intact or totally disrupted. Studies on both unfractionated tRNA and on highly purified species of methionine-, valine-, and lysine-specific tRNA suggest that the circular dichroism of the 4-thiouridine residue is highly sensitive to its local environment in the macro-molecule and reveal interesting differences between these purified species. A new chromophore, resembling 4-thiouridine in some respects but showing distinctive chemical and optical properties, has been detected. The implications of these results on model-building studies of tRNA are discussed.