Structures of DNA and RNA polymerases and their interactions with nucleic acid substrates

1995 ◽  
Vol 5 (1) ◽  
pp. 27-38 ◽  
Author(s):  
Edward Arnold ◽  
Jianping Ding ◽  
Stephen H. Hughes ◽  
Zdenek Hostomsky
Keyword(s):  
Nucleic Acid ◽  
Rna Polymerases ◽  
Dna And Rna

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 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...

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.

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