Aminoglycoside−Nucleic Acid Interactions:  Remarkable Stabilization of DNA and RNA Triple Helices by Neomycin

2001 ◽  
Vol 123 (23) ◽  
pp. 5385-5395 ◽  
Author(s):  
Dev P. Arya ◽  
R. Lane Coffee ◽  
Bert Willis ◽  
Anna I. Abramovitch
Keyword(s):  
Nucleic Acid ◽  
Dna And Rna ◽  
Triple Helices ◽  
Nucleic Acid Interactions

ChemInform Abstract: Aminoglycoside-Nucleic Acid Interactions: Remarkable Stabilization of DNA and RNA Triple Helices by Neomycin.

ChemInform ◽  
2010 ◽  
Vol 32 (38) ◽  
pp. no-no
Author(s):  
Dev P. Arya ◽  
R. Lane Coffee Jr. ◽  
Bert Willis ◽  
Anna I. Abramovitch
Keyword(s):  
Nucleic Acid ◽  
Dna And Rna ◽  
Triple Helices ◽  
Nucleic Acid Interactions

scholarly journals Convolutional models of RNA energetics

2018 ◽  
Author(s):  
Michelle J. Wu
Keyword(s):  
Nucleic Acid ◽  
Network Architecture ◽  
Nearest Neighbor ◽  
Current Model ◽  
Mrna Translation ◽  
Large Space ◽  
Dna And Rna ◽  
Nucleic Acid Interactions

AbstractNucleic acid molecular biology and synthetic biology are undergoing rapid advances with the emergence of designer riboswitches controlling living cells, CRISPR/Cas9-based genome editing, high-throughput RNA-based silencing, and reengineering of mRNA translation. Many of these efforts require the design of nucleic acid interactions, which relies on accurate models for DNA and RNA energetics. Existing models utilize nearest neighbor rules, which were parameterized through careful optical melting measurements. However, these relatively simple rules often fail to quantitatively account for the biophysical behavior of molecules even in vitro, let alone in vivo. This is due to the limited experimental throughput of optical melting experiments and the infinitely large space of possible motifs that can be formed. Here, we present a convolutional neural network architecture to model the energies of nucleic acid motifs, allowing for learning of representations of physical interactions that generalize to arbitrary unmeasured motifs. First, we used existing parameterizations of motif energies to train the model and demonstrate that our model is expressive enough to recapitulate the current model. Then, through training on optical melting datasets from the literature, we have shown that the model can accurately predict the thermodynamics of hairpins containing unmeasured motifs. This work demonstrates the utility of convolutional models for capturing the thermodynamic parameters that underlie nucleic acid interactions.

Model studies of the effects of intracellular crowding on nucleic acid interactions

2017 ◽  
Vol 13 (1) ◽  
pp. 32-41 ◽  
Author(s):  
Shu-ichi Nakano ◽  
Naoki Sugimoto
Keyword(s):  
Nucleic Acid ◽  
Experimental Model ◽  
Model Systems ◽  
Model Studies ◽  
Intracellular Environment ◽  
Dna And Rna ◽  
Experimental Model Systems ◽  
Nucleic Acid Interactions

Studies using experimental model systems have revealed significant effects of the intracellular environment on the interactions of DNA and RNA.

Snapshot blotting: The transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to EM grids

1992 ◽  
Vol 50 (1) ◽  
pp. 762-763
Author(s):  
Stephen D. Jett
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Nucleic Acid Binding ◽  
Mobility Shift ◽  
Carbon Coated ◽  
Nucleoprotein Complexes ◽  
Mobility Shift Assay ◽  
Protein Nucleic Acid ◽  
Gel Mobility Shift ◽  
Nucleic Acid Interactions

The electrophoresis gel mobility shift assay is a popular method for the study of protein-nucleic acid interactions. The binding of proteins to DNA is characterized by a reduction in the electrophoretic mobility of the nucleic acid. Binding affinity, stoichiometry, and kinetics can be obtained from such assays; however, it is often desirable to image the various species in the gel bands using TEM. Present methods for isolation of nucleoproteins from gel bands are inefficient and often destroy the native structure of the complexes. We have developed a technique, called “snapshot blotting,” by which nucleic acids and nucleoprotein complexes in electrophoresis gels can be electrophoretically transferred directly onto carbon-coated grids for TEM imaging.

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...

Visualization of drug-nucleic acid interactions at atomic resolution

1977 ◽  
Vol 114 (3) ◽  
pp. 333-365 ◽  
Author(s):  
Henry M. Sobell ◽  
Chun-Che Tsai ◽  
Shri C. Jain ◽  
Steven G. Gilbert
Keyword(s):  
Nucleic Acid ◽  
Atomic Resolution ◽  
Nucleic Acid Interactions

Implications and concepts of polyamine-nucleic acid interactions

1991 ◽  
Vol 46 (1) ◽  
pp. 37-47 ◽  
Author(s):  
Burt G. Feuerstein ◽  
Loren D. Williams ◽  
Hirak S. Basu ◽  
Laurence J. Marton
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acid Interactions

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.

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