Intracellular Delivery of Nucleic Acids: Differences Between Transfection and siFection Reflect Differences Between DNA and RNA, and Between Oligodeoxynucleotides and Oligonucleotides

Natural methylxanthines, caffeine, theophylline and theobromine, are widespread biologically active alkaloids in human nutrition, found mainly in beverages (coffee, tea, cocoa, energy drinks, etc.). Their detection is thus of extreme importance, and many studies are devoted to this topic. During the last decade, graphene oxide (GO) and reduced graphene oxide (RGO) gained popularity as constituents of sensors (chemical, electrochemical and biosensors) for methylxanthines. The main advantages of GO and RGO with respect to graphene are the easiness and cheapness of synthesis, the notable higher solubility in polar solvents (water, among others), and the higher reactivity towards these targets (mainly due to – interactions); one of the main disadvantages is the lower electrical conductivity, especially when using them in electrochemical sensors. Nonetheless, their use in sensors is becoming more and more common, with the obtainment of very good results in terms of selectivity and sensitivity (up to 5.4 × 10−10 mol L−1 and 1.8 × 10−9 mol L−1 for caffeine and theophylline, respectively). Moreover, the ability of GO to protect DNA and RNA from enzymatic digestion renders it one of the best candidates for biosensors based on these nucleic acids. This is an up-to-date review of the use of GO and RGO in sensors.

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Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry

Biomedicines ◽

10.3390/biomedicines9060628 ◽

2021 ◽

Vol 9 (6) ◽

pp. 628

Author(s):

Dagmara Baraniak ◽

Jerzy Boryski

Keyword(s):

Nucleic Acids ◽

State Of The Art ◽

Modified Oligonucleotides ◽

Synthetic Genes ◽

Chemically Modified ◽

Amide Linkage ◽

Dna And Rna ◽

Modified Dna ◽

Modified Nucleic Acids ◽

Non Coding Rnas

This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.

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Characterization of nucleic acids from extracellular vesicle-enriched human sweat

BMC Genomics ◽

10.1186/s12864-021-07733-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Geneviève Bart ◽

Daniel Fischer ◽

Anatoliy Samoylenko ◽

Artem Zhyvolozhnyi ◽

Pavlo Stehantsev ◽

...

Keyword(s):

Nucleic Acids ◽

Human Genome ◽

Body Fluids ◽

Lower Percentage ◽

Rna Seq ◽

Protein Coding ◽

Human Sweat ◽

Dna And Rna ◽

Ribonucleoprotein Complexes ◽

Eccrine Glands

Abstract Background The human sweat is a mixture of secretions from three types of glands: eccrine, apocrine, and sebaceous. Eccrine glands open directly on the skin surface and produce high amounts of water-based fluid in response to heat, emotion, and physical activity, whereas the other glands produce oily fluids and waxy sebum. While most body fluids have been shown to contain nucleic acids, both as ribonucleoprotein complexes and associated with extracellular vesicles (EVs), these have not been investigated in sweat. In this study we aimed to explore and characterize the nucleic acids associated with sweat particles. Results We used next generation sequencing (NGS) to characterize DNA and RNA in pooled and individual samples of EV-enriched sweat collected from volunteers performing rigorous exercise. In all sequenced samples, we identified DNA originating from all human chromosomes, but only the mitochondrial chromosome was highly represented with 100% coverage. Most of the DNA mapped to unannotated regions of the human genome with some regions highly represented in all samples. Approximately 5 % of the reads were found to map to other genomes: including bacteria (83%), archaea (3%), and virus (13%), identified bacteria species were consistent with those commonly colonizing the human upper body and arm skin. Small RNA-seq from EV-enriched pooled sweat RNA resulted in 74% of the trimmed reads mapped to the human genome, with 29% corresponding to unannotated regions. Over 70% of the RNA reads mapping to an annotated region were tRNA, while misc. RNA (18,5%), protein coding RNA (5%) and miRNA (1,85%) were much less represented. RNA-seq from individually processed EV-enriched sweat collection generally resulted in fewer percentage of reads mapping to the human genome (7–45%), with 50–60% of those reads mapping to unannotated region of the genome and 30–55% being tRNAs, and lower percentage of reads being rRNA, LincRNA, misc. RNA, and protein coding RNA. Conclusions Our data demonstrates that sweat, as all other body fluids, contains a wealth of nucleic acids, including DNA and RNA of human and microbial origin, opening a possibility to investigate sweat as a source for biomarkers for specific health parameters.

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Circulating nucleic acids in blood as biomarkers

Norsk Epidemiologi ◽

10.5324/nje.v16i1.204 ◽

2009 ◽

Vol 16 (1) ◽

Author(s):

Reidun Øvstebø ◽

Peter Kierulf ◽

Kari Bente Foss Haug

Keyword(s):

Gene Expression ◽

Nucleic Acids ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Global Gene Expression ◽

Short Review ◽

Drug Susceptibility ◽

Nucleotide Polymorphisms ◽

Cytochrom P450 ◽

Dna And Rna

<p>This short review on a rapidly expanding domain in biomarkers focuses on the value of markers derived from either circulating intracellular DNA and RNA (leukocytes) or from free DNA and RNA in plasma or serum. In circulating intracellular DNA biomarkers, importance has been pointed to reside in the ever increasing number of SNPs directly related to disease such as hemochromatosis or associated with genetic make up that leads to different drug-susceptibility. Quantitative gene expression profiling, increasingly using global expression platforms, is gaining momentum in various disease states such as cancer, inflammation, cardiovascular disease and diabetes. Circulating free nucleic acids in plasma or serum gain in importance as biomarkers particularly in cancer and foeto-maternal understanding. The surprising recent findings of circulating free mRNA carries the potential of examining normal and diseased plasma for global gene expression profiling – opening avenues to new biomarkers. When appropriate, this review gives reference to methodological considerations and refers the readers to important literature in the fields</p><p>I denne korte oversiktsartikkelen redegjøres det for et biomarkørfelt som utvikler seg hurtig. Gjennom en blodprøve kan man få kjennskap til forandringer i sirkulerende leucocytter, intracellulære nukleinsyrer (DNA og RNA) og fritt DNA og RNA fra plasma eller serum. Single Nucleotide Polymorphisms (SNPs) i DNA har allerede bekreftet sine muligheter som biomarkører (f.eks. Hemokromatose, Faktor V Leiden, Cytochrom P450 (CYP’er)). Stadig flere SNP’er vinner innpass i klinisk sammenheng. Siden sirkulerende hvite blodlegemer kan sies kontinuerlig å overvåke kroppens organer og vev, og dette avspeiles i disse blodcellers genekspresjon (RNA), knyttes det i dag forventninger til sykdomsspesifikke genekspresjonsprofiler. Både ved visse kreftformer, betennelsestilstander og hjertekar-sykdom viser hvite blodlegemer mer eller mindre tydelig sykdomsspesifikke genekspresjonsprofiler. Denne type sykdomsspesifikke genekspresjonsmarkører vil bli økende viktig fremover. Ved slike markører vil man kunne ha nytte av kvantitativ måling av enkeltmarkører, og også globale genekspresjonsprofiler på mikroarray-plattformer. Sirkulerende fritt DNA og kanskje særlig RNA i plasma åpner for nye sykdomsmarkører i første rekke ved forskjellige kreftformer og ved foeto-maternelle problemstillinger. Oversikten gir også en henvisning til metodologiske referanser i disse feltene.</p>

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BIOLOGICAL ACTIVITY OF YERSINIA PSEUDOTUBERCULOSIS TOXINS

Journal of microbiology epidemiology immunobiology ◽

10.36233/0372-9311-2016-6-10-19 ◽

2016 ◽

pp. 10-19

Author(s):

N. A. Terentieva ◽

N. F. Timchenko ◽

V. A. Golotin ◽

V. A. Rasskazov

Keyword(s):

Nucleic Acids ◽

Sea Urchin ◽

Yersinia Pseudotuberculosis ◽

Protein Biosynthesis ◽

Sea Urchin Embryos ◽

Dna And Rna ◽

Embryo Cells ◽

Protein Toxins ◽

Rna Biosynthesis ◽

High Concentrations

Aim. Study of effect of heat-labile (HLT) and thermostable (HST) lethal toxins of Yersinia pseudotuberculosis on the development of embryos of sea urchin Strongylocentrotus intermedius, processes of biosynthesis of nucleic acids and protein in embryo cells and activity of nucleoside-kinases of sea urchin. Materials and methods. Y. pseudotuberculosis strains 2517 (pYV-) and 512 (pYV48MD, pYV82MD) were used for isolation of HLT and HST. Gametes and embryos of sea urchin S. intermedius were used to carry out the experiments and isolate nucleoside-kinases. Results. Both of the studied toxins of Y. pseudotuberculosis possessed spermiotoxic effect and reduced fertilizing ability of sea urchin spermies. HLT LD50 was 1 (ig/ml, and HST - 2 pg/ml. Toxins affected the development of embryos of sea urchin resulting in severe morphologic damages, cessation of the development of embryos at early stages of embryogenesis, destruction of cells and death of embryos. Wherein, damaging effect of HLT was observed at lower concentrations compared with HST. HLT inhibited DNA and RNA biosynthesis at concentrations of 1-2 pg/ml. HST did not affect biosynthesis of nucleic acids even at high concentrations, but inhibited protein biosynthesis in sea urchin embryos. HLT did not reduce the level of inclusion of labeled amino acids into embryo cells. HLT had inhibiting effect on the activity of thymidine- and uridine-kinase of sea urchin, whereas HST did not affect these enzymes. Conclusion. Both of Y. pseudotuberculosis protein toxins affect the development of sea urchin embryos, however, mechanisms of action of HLT and HST on embryos and processes occurring in them differ.

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

Journal of Cell Science ◽

10.1242/jcs.s3-103.64.519 ◽

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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Methylation of Guanine in vivo by the Organophosphorus Insecticide Methamidophos*

Zeitschrift für Naturforschung C ◽

10.1515/znc-1987-1-204 ◽

1987 ◽

Vol 42 (1-2) ◽

pp. 17-20 ◽

Cited By ~ 6

Author(s):

Salah M . A . D . Zayed ◽

Fathya M. Mahdi

Keyword(s):

Nucleic Acids ◽

Mouse Liver ◽

Organophosphorus Insecticide ◽

Appreciable Amount ◽

Dna And Rna ◽

Applied Dose

Abstract The methylating capability of methamidophos, assayed by the formation of [7-14C]methylguanine in mouse liver, was investigated using a 14C-insecticide labelled at the O -CH3 group. Following i.p. administration of the toxicant, [7-14C]methylguanine could be isolated from liver nucleic acids of treated mice. The amount of 14C-label reached its maximum 6 h follow ing administration of the insecticide. At maximum 14C-labelling, the amount of 7-methylguanine calculated as fraction of applied dose, was 20-22 × 10-4 and 98 -104 x-4, for DNA and RNA , respectively. The results obtained indicate also, that an appreciable amount of I4C-activity is incorporated via the C-1 pool.

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De Novo Nucleic Acids: A Review of Synthetic Alternatives to DNA and RNA That Could Act as Bio-Information Storage Molecules

Life ◽

10.3390/life10120346 ◽

2020 ◽

Vol 10 (12) ◽

pp. 346

Author(s):

Kevin G Devine ◽

Sohan Jheeta

Keyword(s):

Nucleic Acids ◽

Genetic Information ◽

De Novo ◽

Chemical Properties ◽

Amino Acid Sequences ◽

Information Storage ◽

Heterocyclic Base ◽

Dna And Rna ◽

Phosphate Backbone ◽

Physical And Chemical

Modern terran life uses several essential biopolymers like nucleic acids, proteins and polysaccharides. The nucleic acids, DNA and RNA are arguably life’s most important, acting as the stores and translators of genetic information contained in their base sequences, which ultimately manifest themselves in the amino acid sequences of proteins. But just what is it about their structures; an aromatic heterocyclic base appended to a (five-atom ring) sugar-phosphate backbone that enables them to carry out these functions with such high fidelity? In the past three decades, leading chemists have created in their laboratories synthetic analogues of nucleic acids which differ from their natural counterparts in three key areas as follows: (a) replacement of the phosphate moiety with an uncharged analogue, (b) replacement of the pentose sugars ribose and deoxyribose with alternative acyclic, pentose and hexose derivatives and, finally, (c) replacement of the two heterocyclic base pairs adenine/thymine and guanine/cytosine with non-standard analogues that obey the Watson–Crick pairing rules. This manuscript will examine in detail the physical and chemical properties of these synthetic nucleic acid analogues, in particular on their abilities to serve as conveyors of genetic information. If life exists elsewhere in the universe, will it also use DNA and RNA?

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THE SYNTHESIS OF DNA AND RNA IN HUMAN CARCINOMATOUS ENDOMETRIUM IN SHORT-TERM INCUBATION IN VITRO AND ITS RESPONSE TO OESTRADIOL AND PROGESTERONE

Journal of Endocrinology ◽

10.1677/joe.0.0480029 ◽

1970 ◽

Vol 48 (1) ◽

pp. 29-38 ◽

Cited By ~ 32

Author(s):

S. NORDQVIST

Keyword(s):

Nucleic Acids ◽

Dna Synthesis ◽

High Concentration ◽

Short Term ◽

Younger Women ◽

Dna And Rna ◽

Poorly Differentiated ◽

Endometrial Carcinomas ◽

Dose Dependent

SUMMARY Twenty-five endometrial carcinomas and three non-endometrial carcinomas were studied for the influence of various steroid hormones on the synthesis of DNA and RNA in short-term incubations in vitro. Endometrial carcinomas showed a dose-dependent sensitivity to progesterone in vitro, the response in both nucleic acids sometimes exceeding that of normal endometria. The mean reduction in DNA synthesis was to 46% and in RNA synthesis to 39% of the control values. Poorly differentiated carcinomas showed higher values of DNA synthesis than highly differentiated ones, as did carcinomas from younger women compared with those from older women. The response in vitro to progesterone was not correlated with these factors. Pregnenolone and a synthetic progestogen were less effective in vitro than progesterone. Oestradiol at a high concentration (20 μg/ml) in some cases significantly reduced the synthesis of both nucleic acids, possibly because of a specific 'toxic' action on the cells. No hormonal effects were observed in non-endometrial carcinomas.

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