Synthesis of Benzene-Glycol Nucleic Acids and Their Biophysical and Biological Properties

2016 ◽  
Vol 2016 (14) ◽  
pp. 2435-2443 ◽  
Author(s):  
Nazuki Niwa ◽  
Keisuke Ueda ◽  
Yoshihito Ueno
Keyword(s):  
Nucleic Acids ◽  
Biological Properties

PEGylated Protamine-Based Adsorbing Improves the Biological Properties and Stability of Tetrahedral Framework Nucleic Acids

2019 ◽  
Vol 11 (31) ◽  
pp. 27588-27597 ◽  
Author(s):  
Yichen Ge ◽  
Taoran Tian ◽  
Xiaoru Shao ◽  
Shiyu Lin ◽  
Tao Zhang ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Biological Properties ◽  
Tetrahedral Framework

Hydroxyproline-Based DNA Mimics: A Review on Synthesis and Properties

2006 ◽  
Vol 71 (7) ◽  
pp. 929-955 ◽  
Author(s):  
Vladimir A. Efimov ◽  
Oksana G. Chakhmakhcheva
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Phosphonic Acid ◽  
Peptide Nucleic Acids ◽  
Biological Properties ◽  
High Potential ◽  
Physicochemical And Biological Properties

With the aim to improve physicochemical and biological properties of natural oligonucleotides, many types of DNA analogues and mimics are designed on the basis of hydroxyproline and its derivatives, and their properties are evaluated. Among them, two types of DNA mimics representing hetero-oligomers constructed from alternating monomers of phosphono peptide nucleic acids and monomers on the base of trans-1-acetyl-4-hydroxy-L-proline (HypNA-pPNAs) and oligomers constructed from monomers containing (2S,4R)-1-acetyl-4-hydroxypyrrolidine-2-phosphonic acid backbone (pHypNAs) are of particular interest. In a set of in vitro and in vivo assays, it was shown that HypNA-pPNAs and pHypNAs demonstrated a high potential for the use in nucleic acid based diagnostics, isolation of nucleic acids and antisense experiments. A review with 53 references.

scholarly journals Sticky problems: extraction of nucleic acids from molluscs

2021 ◽  
Vol 376 (1825) ◽  
Author(s):  
Coen M. Adema
Keyword(s):  
Nucleic Acids ◽  
Dna Extraction ◽  
Extraction Methods ◽  
Biological Properties ◽  
Alternative Methods ◽  
28S Rrna ◽  
Future Directions ◽  
Dna And Rna ◽  
Standard Quality ◽  
Dna Extraction Methods

Traditional molecular methods and omics-techniques across molluscan taxonomy increasingly inform biology of Mollusca. Recovery of DNA and RNA for such studies is challenged by common biological properties of the highly diverse molluscs. Molluscan biomineralization, adhesive structures and mucus involve polyphenolic proteins and mucopolysaccharides that hinder DNA extraction or copurify to inhibit enzyme-catalysed molecular procedures. DNA extraction methods that employ the detergent hexadecyltrimethylammoniumbromide (CTAB) to remove these contaminants importantly facilitate molecular-level study of molluscs. Molluscan pigments may stain DNA samples and interfere with spectrophotometry, necessitating gel electrophoresis or fluorometry for accurate quantification. RNA can reliably be extracted but the ‘hidden break’ in 28S rRNA of molluscs (like most protostomes) causes 18S and 28S rRNA fragments to co-migrate electrophoretically. This challenges the standard quality control based on the ratio of 18S and 28S rRNA, developed for deuterostome animals. High-AT content in molluscan rRNA prevents the effective purification of polyadenylated mRNA. Awareness of these matters aids the continuous expansion of molecular malacology, enabling work also with museum specimens and next-generation sequencing, with the latter imposing unprecedented demands on DNA quality. Alternative methods to extract nucleic acids from molluscs are available from literature and, importantly, from communications with others who study the molecular biology of molluscs. This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.

Halogenated Nucleic Acids: Biochemical and Biological Properties of Fluorinated Polynucleotides

1985 ◽  
pp. 125-138 ◽  
Author(s):  
J. L. Alderfer ◽  
R. E. Loomis ◽  
S. D. Soni ◽  
M. Sharma ◽  
R. Bernacki ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Biological Properties

scholarly journals Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes

2020 ◽  
Vol 21 (22) ◽  
pp. 8634
Author(s):  
Zuzana Pös ◽  
Ondrej Pös ◽  
Jakub Styk ◽  
Angelika Mocova ◽  
Lucia Strieskova ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Biomedical Applications ◽  
Clinical Care ◽  
Biological Properties ◽  
Sample Collection ◽  
Bacterial Dna ◽  
Sequence Composition ◽  
Different Types ◽  
Methodological Aspects ◽  
Informational Value

Analyzes of cell-free nucleic acids (cfNAs) have shown huge potential in many biomedical applications, gradually entering several fields of research and everyday clinical care. Many biological properties of cfNAs can be informative to gain deeper insights into the function of the organism, such as their different types (DNA, RNAs) and subtypes (gDNA, mtDNA, bacterial DNA, miRNAs, etc.), forms (naked or vesicle bound NAs), fragmentation profiles, sequence composition, epigenetic modifications, and many others. On the other hand, the workflows of their analyzes comprise many important steps, from sample collection, storage and transportation, through extraction and laboratory analysis, up to bioinformatic analyzes and statistical evaluations, where each of these steps has the potential to affect the outcome and informational value of the performed analyzes. There are, however, no universal or standard protocols on how to exactly proceed when analyzing different cfNAs for different applications, at least according to our best knowledge. We decided therefore to prepare an overview of the available literature and products commercialized for cfNAs processing, in an attempt to summarize the benefits and limitations of the currently available approaches, devices, consumables, and protocols, together with various factors influencing the workflow, its processes, and outcomes.

scholarly journals Biological properties and therapeutic effects of plant-derived nanovesicles

Open Medicine ◽  
2020 ◽  
Vol 15 (1) ◽  
pp. 1096-1122
Author(s):  
Sante Di Gioia ◽  
Md Niamat Hossain ◽  
Massimo Conese
Keyword(s):  
Nucleic Acids ◽  
Mammalian Cells ◽  
Drug Carriers ◽  
Biological Properties ◽  
Oral Route ◽  
Delivery Systems ◽  
Current Evidence ◽  
Therapeutic Effects ◽  
Anticancer Effects ◽  
Effective Delivery

AbstractExosomes-like nanoparticles can be released by a variety of plants and vegetables. The relevance of plant-derived nanovesicles (PDNVs) in interspecies communication is derived from their content in biomolecules (lipids, proteins, and miRNAs), absence of toxicity, easy internalization by mammalian cells, as well as for their anti-inflammatory, immunomodulatory, and regenerative properties. Due to these interesting features, we review here their potential application in the treatment of inflammatory bowel disease (IBD), liver diseases, and cancer as well as their potentiality as drug carriers. Current evidence indicate that PDNVs can improve the disease state at the level of intestine in IBD mouse models by affecting inflammation and promoting prohealing effects. While few reports suggest that anticancer effects can be derived from antiproliferative and immunomodulatory properties of PDNVs, other studies have shown that PDNVs can be used as effective delivery systems for small molecule agents and nucleic acids with therapeutic effects (siRNAs, miRNAs, and DNAs). Finally, since PDNVs are characterized by a proven stability in the gastrointestinal tract, they have been considered as promising delivery systems for natural products contained therein and drugs (including nucleic acids) via the oral route.

scholarly journals fingeRNAt - a novel tool for high-throughput analysis of nucleic acid-ligand interactions

2021 ◽  
Author(s):  
Natalia Anna Szulc ◽  
Zuzanna Mackiewicz ◽  
Janusz M Bujnicki ◽  
Filip Stefaniak
Keyword(s):  
Nucleic Acids ◽  
High Throughput ◽  
Drug Targets ◽  
Software Tool ◽  
Molecular Complexes ◽  
Biological Properties ◽  
Alternative Measure ◽  
High Throughput Analysis ◽  
Molecular Fingerprints ◽  
Throughput Analysis

Computational methods play a pivotal role in drug discovery and are widely applied in virtual screening, structure optimization, and compound activity profiling. Over the last decades, almost all the attention in medicinal chemistry has been directed to protein-ligand binding, and computational tools have been created with this target in mind. With novel discoveries of functional RNAs and their possible applications, RNAs have gained considerable attention as potential drug targets. However, the availability of bioinformatics tools for nucleic acids is limited. Here, we introduce fingeRNAt - a software tool for detecting non-covalent interactions formed in complexes of nucleic acids with ligands. The program detects nine types of interactions: (i) hydrogen and (ii) halogen bonds, (iii) cation-anion, (iv) pi-cation, (v) pi-anion, (vi) pi-stacking, (vii) inorganic ion-mediated, (viii) water-mediated, and (ix) lipophilic interactions. However, the scope of detected interactions can be easily expanded using a simple plugin system. In addition, detected interactions can be visualized using the associated PyMOL plugin, which facilitates the analysis of medium-throughput molecular complexes. Interactions are also encoded and stored as a bioinformatics-friendly Structural Interaction Fingerprint (SIFt) - a binary string where the respective bit in the fingerprint is set to 1 if a particular interaction is present and to 0 otherwise. This output format, in turn, enables high-throughput analysis of interaction data using data analysis techniques. We present applications of fingeRNAt-generated interaction fingerprints for visual and computational analysis of RNA-ligand complexes, including analysis of interactions formed in experimentally determined RNA-small molecule ligand complexes deposited in the Protein Data Bank. We propose interaction-based similarity based on fingerprints as an alternative measure to RMSD to recapitulate complexes with similar interactions but different folding. We present an application of molecular fingerprints for the clustering of molecular complexes. This approach can be used to group ligands that form similar binding networks and thus have similar biological properties.

Electron Microscopy of Nucleic Acids

1974 ◽  
Vol 32 ◽  
pp. 302-303
Author(s):  
Norman Davidson
Keyword(s):  
Electron Microscopy ◽  
Nucleic Acids ◽  
Basic Protein ◽  
Molecular Biologist ◽  
Topological Properties ◽  
Protein Film ◽  
Polynucleotide Chain

The basic protein film technique for mounting nucleic acids for electron microscopy has proven to be a general and powerful tool for the working molecular biologist in characterizing different nucleic acids. It i s possible to measure molecular lengths of duplex and single-stranded DNAs and RNAs. In particular, it is thus possible to as certain whether or not the nucleic acids extracted from a particular source are or are not homogeneous in length. The topological properties of the polynucleotide chain (linear or circular, relaxed or supercoiled circles, interlocked circles, etc. ) can also be as certained.

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