Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The circular dichroism of ribosomal ribonucleic acids.

ABSTRACT: 1. The c.d. (circular dichroism) of Drosophila melanogaster rRNA (42% G+C) and of G+C-rich fragments (78% G+C) obtained by partial hydrolysis of rabbit L-rRNA (the largest RNA species isolated from the large subribosomal particle) were measured and found to differ substantially. 2. To interpret these spectra a relation between c.d. of bihelical RNA and % G+C was derived, namely delta epsilonfG = AFG2+bfG+c, where deltaepsilonfG is the c.d. of RNA characterized by a mole fraction, fG, of guanine nucleotides and a, b and c are constants. 3. A frame of reference was established by studying the c.d. of a range of rRNA species, including S-rRNA (the RNA species isolated from the smaller subribosomal particle) and L-rRNA of Escherichia coli. 4. It was found for the rRNA species studied that 0.60+/-0.05 of residues appear to form bihelical secondary structure. 5. A higher helical content, 0.66+/-0.05, was found for the G+C-rich fragment of L-rRNA. The difference in the c.d. of rabbit L-rRNA and of D. melanogaster rRNA is attributable to the dependence of c.d. of the bihelical parts on %G+C. 6. The minimum in c.d. at 295 nm increases with increasing %G+C. The c.d. of rRNA was compared with that of the parent subparticle in this region of the spectrum, where high precision may be attained.

SUBMITTER: Cox RA

PROVIDER: S-EPMC1172833 | biostudies-other | 1976 May

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Amphibian ribosomal ribonucleic acids.

Project description:1. The larger rRNA molecules of different species of amphibia do not all have the same mobility on polyacrylamide gels, and the difference appears to be one between the Anuran and Urodele amphibia. 2. Alteration of conditions of electrophoresis so as to distinguish between differences of conformation and molecular weight does not affect the results. 3. The mobility on gel electrophoresis of the rRNA precursor in two species of amphibia is similar, although the intermediate processing products differ. 4. It is suggested that the mobility differences observed represent differences of molecular weight, and are an example of the variability of the products of transcription and processing of rRNA genes in two amphibian genera.

| S-EPMC1174325 | biostudies-other

Linear dichroism and circular dichroism in photosynthesis research.

Project description:The efficiency of photosynthetic light energy conversion depends largely on the molecular architecture of the photosynthetic membranes. Linear- and circular-dichroism (LD and CD) studies have contributed significantly to our knowledge of the molecular organization of pigment systems at different levels of complexity, in pigment-protein complexes, supercomplexes, and their macroassemblies, as well as in entire membranes and membrane systems. Many examples show that LD and CD data are in good agreement with structural data; hence, these spectroscopic tools serve as the basis for linking the structure of photosynthetic pigment-protein complexes to steady-state and time-resolved spectroscopy. They are also indispensable for identifying conformations and interactions in native environments, and for monitoring reorganizations during photosynthetic functions, and are important in characterizing reconstituted and artificially constructed systems. This educational review explains, in simple terms, the basic physical principles, and theory and practice of LD and CD spectroscopies and of some related quantities in the areas of differential polarization spectroscopy and microscopy.

| S-EPMC2744782 | biostudies-literature

Circular Dichroism Microscopy Free from Commingling Linear Dichroism via Discretely Modulated Circular Polarization.

Project description:In this work, we developed a circular dichroism (CD) imaging microscope with a device to suppress the commingling of linear birefringence (LB) and linear dichroism (LD) signals. CD signals are, in principle, free from the commingling influence of LD and LB if the sample is illuminated with pure circularly polarized light, with no linear polarization contribution. Based on this idea, we here propose a novel circular polarization modulation method to suppress the contribution of linear polarization, which enables high-sensitivity CD detection (10-4 level in optical density unit or mdeg level in ellipticity) for microscopic imaging at a nearly diffraction limited spatial resolution (sub-?m level). The highly sensitive, diffraction-limited local CD detection will make direct analyses of chiral structures and spatial mappings of optical activity feasible for ?m- to sub-?m-sized materials and may yield a number of applications as a unique optical imaging method.

| S-EPMC5071757 | biostudies-literature

Circular Dichroism of Gold Bipyramid Dimers.

Project description:Chiral nanomaterials attract broad attention, as they offer new possibilities of modulation of optical properties and dissymmetry factors outperforming organic materials. Among various nanoparticles, plasmonic bipyramids present numerous advantages as building blocks of chiral nanomaterials (well-defined modulation of optical properties with the morphology of nanoparticles, narrow optical resonances, and high size and shape uniformity of synthesized particles). We study different possible orientations of gold bipyramids with respect to each other in dimers obtained by wet chemistry methods. For circularly polarized incident light we evaluate linear optical cross sections and plasmonic local field enhancement using COMSOL Multiphysics. We observe coupling of the nanoparticles' local fields and thus changes in extinction spectra, which modulate chiroptical properties of dimers. To assess the chirality of various arrangements, we note differences in cross sections for left- and right-handed polarized light which we further evaluate as the dissymmetry g-factor. Our results provide BPs configurations with dissymmetry factor as high as -0.3.

| S-EPMC8279732 | biostudies-literature

All-dielectric metasurface circular dichroism waveplate.

Project description:We propose and experimentally demonstrate a high efficient circularly polarizing dichroism waveplate (CPDW) using a Si-based all-dielectric 2Dchiral metasurface. We demonstrate that the CPDW exhibits a unique dichroism in that it functions as a transmissive quarter waveplate for one of either left-or right-handed circularly polarized incident lightand a reflective mirror for the opposite polarization. The circular polarization dichroism (CPD = IRCP - ILCP) in transmission at wavelength ~1.5 μm reaches 97% and the extinction ratio (ER = IRCP/ILCP) is as high as 345:1. Experimental fabrications and measurements of the proposed all-dielectric metasurface are implemented and found to be in excellent agreement with the simulations. The proposed all-dielectric chiral metasurface is of advantages of high-dichroism, easy-fabrication and standard semiconductor fabrication techniques compatible, which could lead to enhanced security in fiber and free-space communications, as well as imaging and sensing applications for circularly polarized light with a highly integrated photonic platform.

| S-EPMC5282559 | biostudies-literature

Circular dichroism, magnetic circular dichroism, and variable temperature variable field magnetic circular dichroism studies of biferrous and mixed-valent myo-inositol oxygenase: insights into substrate activation of O2 reactivity.

Project description:myo-Inositol oxygenase (MIOX) catalyzes the 4e(-) oxidation of myo-inositol (MI) to D-glucuronate using a substrate activated Fe(II)Fe(III) site. The biferrous and Fe(II)Fe(III) forms of MIOX were studied with circular dichroism (CD), magnetic circular dichroism (MCD), and variable temperature variable field (VTVH) MCD spectroscopies. The MCD spectrum of biferrous MIOX shows two ligand field (LF) transitions near 10000 cm(-1), split by ~2000 cm(-1), characteristic of six coordinate (6C) Fe(II) sites, indicating that the modest reactivity of the biferrous form toward O2 can be attributed to the saturated coordination of both irons. Upon oxidation to the Fe(II)Fe(III) state, MIOX shows two LF transitions in the ~10000 cm(-1) region, again implying a coordinatively saturated Fe(II) site. Upon MI binding, these split in energy to 5200 and 11200 cm(-1), showing that MI binding causes the Fe(II) to become coordinatively unsaturated. VTVH MCD magnetization curves of unbound and MI-bound Fe(II)Fe(III) forms show that upon substrate binding, the isotherms become more nested, requiring that the exchange coupling and ferrous zero-field splitting (ZFS) both decrease in magnitude. These results imply that MI binds to the ferric site, weakening the Fe(III)-?-OH bond and strengthening the Fe(II)-?-OH bond. This perturbation results in the release of a coordinated water from the Fe(II) that enables its O2 activation.

| S-EPMC3882275 | biostudies-literature

Intranuclear maturation pathways of rat liver ribosomal ribonucleic acids.

Project description:The maturation of pre-rRNA (precursor to rRNA)in liver nuclei is studied by agar/ureagel electrophoresis, kinetics of labelling in vivo with [14C] orotate and electron-microscopic observation of secondary structure of RNA molecules. (1) Processing starts from primary pre-rRNA molecules with average mol. wt. 4.6X10(6)(45S) containing the segments of both 28S and 18S rRNA. These molecules form a heterogeneous peak on electrophoresis. The 28S rRNA segment is homogeneous in its secondary structure. However, the large transcribed spacer segment (presumably at the 5'-end) is heterogeneous in size and secondary structure. A minor early labelled RNA component with mol.wt. about 5.8X10(6) is reproducibly found, but its role as a pre-rRNA species remains to be determined. (2) The following intermediate pre-rRNA species are identified: 3.25X10(6) mol.wt.(41S), a precursor common to both mature rRNA species ; 2.60X10(6)(36S) and 2.15X10(6)(32S) precursors to 28S rRNA; 1.05X10(6) (21S) precursor to 18S rRNA. The pre-rRNA molecules in rat liver are identical in size and secondary structure with those observed in other mammalian cells. These results suggest that the endonuclease-cleavage sites along the pre-rRNA chain are identical in all mammalian cells. (3) Labelling kinetics and the simultaneous existence of both 36S and 21S pre-rRNA reveal that processing of primary pre-rRNA in adult rat liver occurs simultaneously by at least two major pathways: (i) 45S leads to 41S leads to 32S+21S leads to 28S+18S rRNA and (ii) 45S leads to 41S leads to 36S+18S leads to 32S leads to 28S rRNA. The two pathways differ by the temporal sequence of endonuclease attack along the 41 S pre-rRNA chain. A minor fraction (mol.wt.2.9X10(6), 39S) is identified as most likely originating by a direct split of 28S rRNA from 45S pre-rRNA. These results show that in liver considerable flexibility exists in the order of cleavage of pre-rRNA molecules during processing.

| S-EPMC1164266 | biostudies-other

A Comprehensive Analysis Identified the Key Differentially Expressed Circular Ribonucleic Acids and Methylation-Related Function in Pheochromocytomas and Paragangliomas.

Project description:We investigated differentially expressed circular RNAs (circRNAs) and their potential functions in pheochromocytomas and paragangliomas (PCC/PGLs). Expression levels of circRNAs in tumor and adjacent normal tissues from seven PCC/PGL patients were analyzed through RNA sequencing. Real-time PCR was conducted to verify the key candidates identified in the sequencing data. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to predict the functions of these circRNAs. A total of 367 circRNAs were found differentially expressed between tumor and normal samples. The top three histone methylation-related circRNAs (hsa_circ_0000567, hsa_circ_0002897, and hsa_circ_0004473) and their target microRNAs (miRNAs) were identified and validated. We then mapped the circRNA-miRNA-messenger RNA (mRNA) coding-noncoding gene co-expression (CNC) networks to show the potential binding relationships between circRNAs and their targets in PCC/PGLs. The top five mRNAs, 88 miRNAs, and 132 circRNAs related to pathogenesis were utilized to map the CNC network, and we observed that the interactions of these candidates with their target miRNAs regulated histone methylation and further mediated PCC/PGL pathogenesis. This study is the first to provide the whole profile of differentially expressed circRNAs in PCC/PGLs. Our data indicate that altered circRNAs may control the pathogenesis of PCC/PGLs by regulating histone methylation processes, highlighting their role as potential biomarkers.

| S-EPMC7052364 | biostudies-literature

Femtosecond photoelectron circular dichroism of chemical reactions.

Project description:Understanding the chirality of molecular reaction pathways is essential for a broad range of fundamental and applied sciences. However, the current ability to probe chirality on the time scale of primary processes underlying chemical reactions remains very limited. Here, we demonstrate time-resolved photoelectron circular dichroism (TRPECD) with ultrashort circularly polarized vacuum-ultraviolet (VUV) pulses from a tabletop source. We demonstrate the capabilities of VUV-TRPECD by resolving the chirality changes in time during the photodissociation of atomic iodine from two chiral molecules. We identify several general key features of TRPECD, which include the ability to probe dynamical chirality along the complete photochemical reaction path, the sensitivity to the local chirality of the evolving scattering potential, and the influence of electron scattering off dissociating photofragments. Our results are interpreted by comparison with high-level ab-initio calculations of transient PECDs from molecular photoionization calculations. Our experimental and theoretical techniques define a general approach to femtochirality.

| S-EPMC9286499 | biostudies-literature

An electronic circular dichroism spectroscopy method for the quantification of L- and D-amino acids in enantiomeric mixtures.

Project description:Rapid quantitative analysis of single chiral amino acid (aa) was achieved using circular dichroism (CD) with data analysis by standard calibration curve. The absolute concentrations of D- and L-aas in enantiomeric mixtures were determined by CD and achiral liquid chromatography (LC) method. It is worth noting that CD and LC were used independently, not online LC/CD in this study. The errors of the experimental results were less than 10%. The method is also applicable to the quantification of non-aa chiral molecules, such as chiral nucleoside and chiral quinine. With this study, we provide a new method for the chiral quantitative analysis of enantiomeric aas mixtures.

| S-EPMC8074886 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data