scholarly journals Sulfur Modification in Natural RNA and Therapeutic Oligonucleotides

2021 ◽  
Author(s):  
Ya Ying Zheng ◽  
Ying Wu ◽  
Thomas Begley ◽  
Jia Sheng
Keyword(s):  
Nucleic Acid ◽  
Dna And Rna ◽  
Sulfur Modification ◽  
Oxygen Atoms

Sulfur modifications have been discovered on both DNA and RNA. Sulfur substitution of oxygen atoms at nucleobase or backbone locations in the nucleic acid framework led to a wide variety...

High-resolution nucleic acid sequence mapping via in situ hybridization at the Electron Microscope level

1995 ◽  
Vol 53 ◽  
pp. 752-753
Author(s):  
B.A. Hamkalo ◽  
S. Narayanswami ◽  
A.P. Kausch
Keyword(s):  
Nucleic Acid ◽  
Interphase Nucleus ◽  
Genome Mapping ◽  
Precise Location ◽  
Electron Microscope Level ◽  
Rna Sequences ◽  
Fundamental Interest ◽  
Whole Cells ◽  
Dna And Rna

The availability of nonradioactive methods to label nucleic acids an the resultant rapid and greater sensitivity of detection has catapulted the technique of in situ hybridization to become the method of choice to locate of specific DNA and RNA sequences on chromosomes and in whole cells in cytological preparations in many areas of biology. It is being applied to problems of fundamental interest to basic cell and molecular biologists such as the organization of the interphase nucleus in the context of putative functional domains; it is making major contributions to genome mapping efforts; and it is being applied to the analysis of clinical specimens. Although fluorescence detection of nucleic acid hybrids is routinely used, certain questions require greater resolution. For example, very closely linked sequences may not be separable using fluorescence; the precise location of sequences with respect to chromosome structures may be below the resolution of light microscopy(LM); and the relative positions of sequences on very small chromosomes may not be feasible.

scholarly journals Recent developments in nucleic acid based techniques for use in rumen manipulation

2009 ◽  
Vol 38 (spe) ◽  
pp. 341-351 ◽  
Author(s):  
Christopher McSweeney ◽  
Seungha Kang ◽  
Emma Gagen ◽  
Carl Davis ◽  
Mark Morrison ◽  
...  
Keyword(s):  
Microbial Community ◽  
Nucleic Acid ◽  
Microbial Communities ◽  
Marker Gene ◽  
Molecular Ecology ◽  
Functional Gene ◽  
Rumen Microorganisms ◽  
Dna And Rna ◽  
Conventional Culture ◽  
Reference Strains

Nucleic acid-based techniques which can be used to characterise complex microbial communities without incubation are now being employed regularly in ruminant nutrition studies. Conventional culture-based methods for enumerating rumen microorganisms (bacteria, archaea, protozoa, and fungi) have been superseded and are now used mainly to obtain pure isolates of novel organisms and reference strains that are required for the development and validation of the nucleic acid approaches. These reference strains are also essential for physiological studies of the lifestyle of the organisms as well as sources of genomic DNA and RNA that can be analysed for functional gene activity. The foundation of the molecular ecology techniques is 16S/18S rDNA sequence analysis which has provided a phylogenetically based classification scheme for enumeration and identification of microbial community members. The use of this marker gene in assays involving the use of single nucleic acid probes or primer sets is rapidly evolving to high throughput approaches such as microarray analysis and new generation sequencing technologies. While these analyses are very informative for determining the composition of the microbial community and monitoring changes in population size, they can only infer function based on these observations. The focus of nucleic acid research is now shifting to the functional analysis of the ecosystem which involves the measurement of functional genes and their expression in the predominant or specific members of the rumen microbial community. Functional gene studies are less developed than 16S rDNA-based analysis of community structure. Also for gene expression studies there are inherent problems involved in extracting high quality RNA from digesta, and priming cDNA synthesis from bacterial mRNA. This paper reviews nucleic acid based molecular methods which have recently been developed for studying the structure and function of rumen microbial communities.

scholarly journals Cleavage of DNA and RNA by PLD3 and PLD4 limits autoinflammatory triggering by multiple sensors

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Amanda L. Gavin ◽  
Deli Huang ◽  
Tanya R. Blane ◽  
Therese C. Thinnes ◽  
Yusuke Murakami ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Inflammatory Diseases ◽  
Type I ◽  
Multiple Sensors ◽  
Dna And Rna ◽  
Elevated Type ◽  
Minor Contribution ◽  
Ifn Γ ◽  
A Minor ◽  
Rna And Dna

AbstractPhospholipase D3 (PLD3) and PLD4 polymorphisms have been associated with several important inflammatory diseases. Here, we show that PLD3 and PLD4 digest ssRNA in addition to ssDNA as reported previously. Moreover, Pld3−/−Pld4−/− mice accumulate small ssRNAs and develop spontaneous fatal hemophagocytic lymphohistiocytosis (HLH) characterized by inflammatory liver damage and overproduction of Interferon (IFN)-γ. Pathology is rescued in Unc93b13d/3dPld3−/−Pld4−/− mice, which lack all endosomal TLR signaling; genetic codeficiency or antibody blockade of TLR9 or TLR7 ameliorates disease less effectively, suggesting that both RNA and DNA sensing by TLRs contributes to inflammation. IFN-γ made a minor contribution to pathology. Elevated type I IFN and some other remaining perturbations in Unc93b13d/3dPld3−/−Pld4−/− mice requires STING (Tmem173). Our results show that PLD3 and PLD4 regulate both endosomal TLR and cytoplasmic/STING nucleic acid sensing pathways and have implications for the treatment of nucleic acid-driven inflammatory disease.

scholarly journals Skipping and sliding to optimize target search on protein-bound DNA and RNA

2020 ◽  
Author(s):  
Misha Klein ◽  
Tao Ju Cui ◽  
Ian MacRae ◽  
Chirlmin Joo ◽  
Martin Depken
Keyword(s):  
Nucleic Acid ◽  
Single Molecule ◽  
Diffusion Limit ◽  
Optimal Search ◽  
Dna And Rna ◽  
Argonaute Proteins ◽  
Large Pool ◽  
Search Speed ◽  
Crowded Environments ◽  
Acid Substrate

Rapidly finding a specific nucleic-acid sequences in a large pool of competing off-targets is a fundamental challenge overcome by all living systems. To optimize the search and beat the diffusion limit, it is known that searchers should spend time sliding along the nucleic-acid substrate. Still, such sliding generally has to contend with high levels of molecular crowding on the substrate, and it remains unclear what effect this has on optimal search strategies. Using mechanistic modelling informed by single-molecule data, we show how sliding combined with correlated short-ranged skips allow searchers to maintain search speed on densely crowded substrates. We determine the conditions of optimal search, which show that an optimized searchers always spend more than half its time skipping and sliding along the substrate. Applying our theory to single-molecule data, we determine that both human and bacterial Argonaute proteins alternate between sliding 10 nt and skipping 30 nt along the substrate. We show that this combination of skipping and sliding lengths allows the searcher to maintain search speeds largely unaffected by molecular roadblocks covering up to 70% of the substrate. Our novel combination of experimental and theoretical approach could also help elucidate how other systems ensure rapid search in crowded environments.

scholarly journals STUDIES ON NUCLEIC ACID METACHROMASY

1965 ◽  
Vol 27 (2) ◽  
pp. 327-336 ◽  
Author(s):  
Ned Feder ◽  
Merrill K. Wolf
Keyword(s):  
Nucleic Acid ◽  
Ribosomal Rna ◽  
Toluidine Blue ◽  
Color Contrast ◽  
Tissue Sections ◽  
Dna And Rna ◽  
Excellent Preservation ◽  
Structural Preservation ◽  
Intense Color

Acrolein-fixed, polyester wax-embedded tissue sections showed excellent preservation of light microscopic architecture and, when stained with toluidine blue, intense color contrast between DNA, which stained orthochromatically, and RNA, which stained metachromatically. This method has practical value for differentiating DNA from RNA in the same section. The color contrast was impaired by substituting formaldehyde for acrolein or paraffin for polyester wax, and was negligible in tissues fixed in formaldehyde or Carnoy's fluid and embedded in paraffin. Quality of structural preservation paralleled degree of color contrast. Metachromatic staining can be analysed, by the quantitative parameters of Bradley and colleagues, to provide inferences regarding the conformation of biopolymers in tissue sections. Comparison of the nucleic acid color contrasts in toluidine blue-stained sections with titrations of fixative-treated nucleic acids against toluidine blue in solution indicated a greater difference in conformation between DNA- and RNA-protein in acrolein-polyester sections than between acrolein-treated free DNA and RNA in solution. This is supported by recent evidence that the conformation of ribosomal RNA is quite different in whole ribosomes from that assumed by the same RNA free in solution. The acrolein-polyester method may enhance color contrast by providing superior preservation of ordered nucleoprotein conformations.

DNA and RNA enzymes with peroxidase activity — An investigation into the mechanism of action

2006 ◽  
Vol 84 (4) ◽  
pp. 613-619 ◽  
Author(s):  
Paola Travascio ◽  
Dipankar Sen ◽  
Andrew J Bennet
Keyword(s):  
Nucleic Acid ◽  
Hydrophobic Interactions ◽  
Basic Component ◽  
Axial Position ◽  
General Base ◽  
Dna And Rna ◽  
Polar Environment ◽  
Guanine Quadruplex ◽  
Acid Catalyzed ◽  
Catalyzed Reactions

A DNA–hemin complex (PS2.M–hemin), and its RNA counterpart (rPS2.M–hemin), have previously been reported, in the presence of nitrogenous buffers such as HEPES, to show enhanced peroxidative activity relative to both uncomplexed hemin and a control DNA–hemin complex (Chem. Biol. 5, 505, 1998). A kinetic analysis of these two hemin-utilizing nucleic acid enzymes provides key insights into the mechanisms for their catalyzed peroxidation reactions. First, control experiments indicate that charge on the added detergent, required for solubility reasons, has little effect on the efficiency of the nucleic-acid-catalyzed reactions. Second, the key functional impact of the two nucleic acid frameworks, either DNA or RNA, appears to be a reduction in the acidity of a water molecule coordinated to the iron atom of the hemin that is bound to the ribozyme and DNAzyme scaffolds. This effect could result from a polar environment and possibly hydrogen bond(s) at the axial position of the hemin, along with favourable hydrophobic interactions for the periphery of the porphyrin ring. Third, the basic component of the buffer enhances the activities; this likely results from a general-base-catalyzed process. Cumulatively, these data supply important clues as to how biopolymers other than a protein can complex with hemin to form productive peroxidase enzymes.Key words: ribozyme, DNAzyme, hemin, peroxidase, mechanism, guanine quadruplex.

Effect of Cytokinins on the Expansion and Metabolism of Excised Cucumber Cotyledons

1980 ◽  
Vol 7 (3) ◽  
pp. 227
Author(s):  
C Tsui ◽  
Tao Guo-qing ◽  
Chen Hui-ying ◽  
Son Yan-ru ◽  
Lian Han-ping ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Soluble Sugars ◽  
Dry Weight ◽  
Acid Synthesis ◽  
Cell Number ◽  
Cucumis Sativus L ◽  
Biochemical Processes ◽  
Dna And Rna ◽  
Lag Period ◽  
Hydrolysis Of

Expansion of excised cucumber (Cucumis sativus L.) cotyledons was stimulated by treatment with cytokinin, and commenced after a lag period of about 4 h. Expansion induced by benzyladenine (BA) was due mainly to increase of fresh weight, but cell number increased slightly. Hydrolysis of protein and lipid was stimulated by BA, and soluble sugars increased simultaneously. However, there was no significant change in the dry weight of cotyledons during the period of expansion. It is assumed that the transformation of lipid to sugar in the cotyledon is stimulated by BA. The respiration of cotyledons was evidently stimulated by BA and was entirely inhibited by respiratory inhibitors, e.g. NaN,, malonate and dinitrophenol. Inhibitors of protein and nucleic acid synthesis, such as chloramphenicol and actinomycin D, inhibited only the BA-induced expansion. They had no effect on the expansion of controls. These results suggest that different biochemical processes are involved in the expansion of cotyledons induced by BA and in controls. The former is related not only to respiration but also to the synthesis of protein and nucleic acid. BA increased DNA and RNA content per cotyledon. The increase of total RNA is due mainly to the increase of 25 S and 18 S rRNA.

An Investigation of the Anomalous Staining of Chromatin by the Acid Dyes, Methyl Blue and Aniline Blue

1962 ◽  
Vol s3-103 (64) ◽  
pp. 519-530
Author(s):  
R. B. McKAY
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Methyl Blue ◽  
Aniline Blue ◽  
Acid Dyes ◽  
Dna And Rna ◽  
Basic Dyes ◽  
Blue Stain ◽  
High Degree ◽  
Mechanism Of The Reaction

Methyl blue and aniline blue, though acid dyes, stain the chromatin of the spermatogenetic cells of the mouse (especially of the primary spermatocytes) strongly. Extraction of the basiphil nucleic acid constituents from the chromatin causes loss of this property, while destruction of acidophilia in the protein constituents does not. It has been concluded that the dyes interact with the nucleic acids. Further, they appear to react with both DNA and RNA in the chromatin, although they show no affinity for the cytoplasm of the exocrine cells in sections of pancreas, which is rich in RNA. The mechanism of the reaction has not been fully elucidated, although apparently the dyes do not behave as basic dyes towards the nucleic acids, and the interaction is non-ionic. Methyl blue and aniline blue stain strongly other ‘acidic’ substrates, such as cellulose and nitrocellulose, and attempts have been made to relate the staining of nucleic acids to the staining of these substrates, particularly cellulose; for the staining properties of this substrate have been intensively investigated elsewhere. No satisfactory correlation, however, has been obtained, for nitrocellulose has been found to be less strongly stained at pH 3.0 than at pH 7.1, while the reverse is true for cellulose. Further, only one of 3 direct cotton dyes used appears to have any affinity for the chromatin of the spermatogenetic cells. Direct cotton dyes have large flat molecules with a high degree of conjugation. It is suggested that these characteristics are essential for interaction with nucleic acids, and also that the molecule must be reasonably compact. Finally, it has been shown that methyl blue, aniline blue, and 3 direct cotton dyes of the azo type have no ability to stain the glycogen in liver cells, yet glycogen is very closely related to cellulose.

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