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Search for "RNA" in Full Text gives 177 result(s) in Beilstein Journal of Organic Chemistry.
Photocontrolled DNA minor groove interactions of imidazole/pyrrole polyamides
Beilstein J. Org. Chem. 2020, 16, 60–70, doi:10.3762/bjoc.16.8
- suitable as bi-stable switches. Azobenzene and other small photoreactive molecules have been employed as ligands to control DNA or RNA assembly by light [14][15][16][17][18][19][20]. Mascareñas et al. reported the first photoisomerizable transcription factor (Tf) that recognized its target sequences by
Emission and biosynthesis of volatile terpenoids from the plasmodial slime mold Physarum polycephalum
Beilstein J. Org. Chem. 2019, 15, 2872–2880, doi:10.3762/bjoc.15.281
- manufacturer’s manual (https://www.qiagen.com). Total RNA was isolated using Plant RNA Purification Reagent (https://www.thermofisher.com). cDNA was prepared using 1st strand cDNA synthesis kit (https://www.gelifesciences.com). Full length cDNAs of individual PpolyTPS genes were amplified using gene specific
Design, synthesis and investigation of water-soluble hemi-indigo photoswitches for bioapplications
Beilstein J. Org. Chem. 2019, 15, 2822–2829, doi:10.3762/bjoc.15.275
- that allowed to obtain an RNA-binding hemi-indigo derivative with photoswitchable fluorescent properties. Keywords: hemi-indigo; molecular switches; photochromism; photoswitching; visible light; water solubility; Introduction The application of organic photochromes in biological systems is fraught
- provided. Additionally, synthetic peculiarities of the introduction of an RNA-affine alkylamino substituent to the hemi-indigo scaffold are discussed. Results and Discussion Synthesis of hemi-indigo derivatives Z-1a–c The synthesis of hemi-indigo derivatives Z-1a–c with different substitution patterns of
- File 1). Introduction of an alkylamino substituent to the hemi-indigo scaffold Based on the data on photoswitching in water (vide supra), the dimethoxy-substituted hemi-indigo Z-1c was selected as a core structure for the design of RNA binders with photoswitchable properties [12]. To increase the
In search of visible-light photoresponsive peptide nucleic acids (PNAs) for reversible control of DNA hybridization
Beilstein J. Org. Chem. 2019, 15, 2500–2508, doi:10.3762/bjoc.15.243
- targets without causing a permanent knockout. During the last years, the pioneering structural studies of reversible photoregulation of DNA/RNA duplex stability of Asanuma and Komiyama [16][17] have become functional ones, affecting DNA/RNA cleavage [18][19][20], transcription [21][22][23], and
- been employed. In vivo application demands the development of a new generation of artificial agents to target DNA/RNA-associated processes. These compounds must be able to maintain their specificity and effectivity while still being nuclease resistant, nontoxic and susceptible to light of tissue
- -penetrating wavelengths. Peptide nucleic acids (PNAs) [31] are synthetic nucleic acid analogues, in which nucleobases are linked to a repeating N-(2-aminoethyl)glycine polyamide backbone. The lack of phosphate groups provides them with both higher binding affinities to complementary DNA or RNA sequences and
Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye libraries
Beilstein J. Org. Chem. 2019, 15, 1872–1889, doi:10.3762/bjoc.15.183
- cationic dyes was synthesized and investigated with respect to their optical properties, propensity to aggregation in aqueous medium, and capacity to serve as fluorescence “light-up” probes for G-quadruplex (G4) DNA and RNA structures. Among the 61 compounds, 57 dyes showed preferential enhancement of
- fluorescence intensity in the presence of one or another G4-DNA or RNA structure, while no dye displayed preferential response to double-stranded DNA or single-stranded RNA analytes employed at equivalent nucleotide concentration. Thus, preferential fluorimetric response towards G4 structures appears to be a
- ] or its 4-isomer, as optimal fluorescent light-up probes characterized by high fluorimetric response (I/I0 of up to 550-fold), excellent selectivity with respect to double-stranded DNA or single-stranded RNA controls, high quantum yield in the presence of G4 analytes (up to 0.32), large Stokes shift
Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection
Beilstein J. Org. Chem. 2019, 15, 1116–1128, doi:10.3762/bjoc.15.108
- MerMade 6 DNA/RNA synthesizer. The dT-Dmoc-CPG (4) was used as the solid support. Detritylation was carried out under standard conditions suggested by the synthesizer manufacturer for 1 µmol synthesis. The 0.1 M acetonitrile solutions of phosphoramidite monomers 3a–c and the commercially available 5'-DMTr
New terpenoids from the fermentation broth of the edible mushroom Cyclocybe aegerita
Beilstein J. Org. Chem. 2019, 15, 1000–1007, doi:10.3762/bjoc.15.98
- . The biomass and suspended substrates was separated by centrifugation. RNA extraction, cDNA synthesis and qPCR During fermentation, mycelial samples were taken at day 2, 4, 7, 9, 11 and 14 and stored in RNAlater (Qiagen, Venlo, Netherlands) until further use. Fungal mycelium was freeze-dried and ground
- with liquid nitrogen. RNA was extracted from ground mycelium using Ambion TRIzol™ Reagent (life Technologies, Carlsberg, California, USA) according to the manufacturer’s instructions with minor changes according to the method of Chomczynski and Sacchi [21]. RNA concentration was determined
- photometrically by a NanoPhotometer® Pearl (Implen, Munich, Germany). Reverse transcription was performed with the Invitrogen M-MLV Reverse Transcriptase kit (ThermoFisher Scientific, Waltham, Massachusetts, USA) according to the manufacturer’s protocol. 10 µL of extracted RNA and 1 µL of 10 µM oligo-(dT)30
Synthesis and fluorescent properties of N(9)-alkylated 2-amino-6-triazolylpurines and 7-deazapurines
Beilstein J. Org. Chem. 2019, 15, 474–489, doi:10.3762/bjoc.15.41
- for this type of molecules. Traditionally, fluorescent purine nucleoside analogs were recognized as valuable fluorescent probes for DNA and RNA research [17]. This paved a way for development of various adenosine and guanosine analogs which in many cases contained an additional substituent at C(8
Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA
Beilstein J. Org. Chem. 2019, 15, 79–88, doi:10.3762/bjoc.15.9
- oligonucleotides hybridized to complementary DNA or RNA disclosed a significant destabilization of both duplex types (ΔTm/mod = −1.6 to −5.5 °C). However, in the DNA/RNA hybrid the amount of destabilization could be reduced by multiple insertions of the modified unit. In addition, CD spectroscopy of the
- oligonucleotides hybridized to RNA showed a similar structure than the natural DNA/RNA duplex. Furthermore, since the structural investigation on the nucleoside level by X-ray crystallography and ab initio calculations pointed to a furanose conformation in the southern region, a RNase H cleavage assay was
- conducted. This experiment revealed that the oligonucleotide containing five modified units was able to elicit the RNase H-mediated cleavage of the complementary RNA strand. Keywords: DNA/RNA affinity; fluorinated cyclopropanes; fluorinated nucleic acids; RNase H activity; sugar modified nucleosides
6’-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations
Beilstein J. Org. Chem. 2018, 14, 3088–3097, doi:10.3762/bjoc.14.288
- phosphoramidite building blocks into oligonucleotides was achieved with tert-butyl hydroperoxide as oxidation agent. Thermal melting experiments of the modified duplexes disclosed a destabilizing effect versus DNA and RNA complements, but with a lesser degree of destabilization versus complementary DNA (ΔTm/mod
- = −1.5 to −3.7 °C). Molecular dynamics simulation on the nucleoside and oligonucleotide level revealed the preference of the C1’-exo/C2’-endo alignment of the furanose ring. Moreover, the simulation of duplexes with complementary RNA disclosed a DNA/RNA-type duplex structure suggesting that this
- modification might be a substrate for RNase H. Keywords: DNA/RNA affinity; fluorinated cyclopropanes; fluorinated nucleic acids; molecular dynamics simulations; sugar modified nucleosides; Introduction A powerful strategy for the treatment of various disorders like cancer, viral and inherited diseases is the
Repurposing the anticancer drug cisplatin with the aim of developing novel Pseudomonas aeruginosa infection control agents
Beilstein J. Org. Chem. 2018, 14, 3059–3069, doi:10.3762/bjoc.14.284
- 16–18 h. MIC was taken as the lowest concentration where no visual growth (based on OD600) of bacteria was detected. The experiments were performed in triplicate and representative results were shown. RNA preparation Bacterial cells were collected using the method described previously [17] with some
- modifications. Generally, PAO1 cells were cultivated either with (1.5 μM) or without cisplatin. The cells were harvested at the early-stationary phase (after approximately 8 h cultivation). Total RNA was extracted with an RNeasy Protect Bacteria Mini Kit with on-column DNase digestion (Qiagen). A Turbo DNA-free
- vigorous protocol was used for a second round of DNase treatment (Ambion). The 16S, 23S and 5S rRNA was removed using the Ribo-Zero Magnetic Kit (Bacteria) (Epicentre). RNA sequencing and data analysis Gene expression analysis was conducted via Illumina RNA sequencing (RNA-Seq technology). RNA-Seq was
Protein–protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics
Beilstein J. Org. Chem. 2018, 14, 2881–2896, doi:10.3762/bjoc.14.267
- viability is bacterial transcription, a process that is executed by the enzyme RNA polymerase (RNAP) and regulated by several transcription factors. Similarly to the previously described targets, bacterial transcription represents a promising antibacterial drug target for several reasons: it is essential to
Targeting the Pseudomonas quinolone signal quorum sensing system for the discovery of novel anti-infective pathoblockers
Beilstein J. Org. Chem. 2018, 14, 2627–2645, doi:10.3762/bjoc.14.241
- compounds also showed activity against RNA polymerase, a popular target for the development of new antibiotics [52][53]. Hitting such a target would jeopardise the principle of pathoblockers, which should only disarm the bacteria and not kill them. Hence, a follow-up study on PqsD/RNAP selectivity was
- interaction, e.g., protein–protein or protein–DNA/RNA interaction, while the exact molecular mechanism remains unclear. Even though Zender et al. were not able to attenuate PA virulence via blockage of PqsE, important new insights on this target were made. The discovery that pathoblockers targeting PqsE
Impact of Pseudomonas aeruginosa quorum sensing signaling molecules on adhesion and inflammatory markers in endothelial cells
Beilstein J. Org. Chem. 2018, 14, 2580–2588, doi:10.3762/bjoc.14.235
- cellular RNA was isolated using RNeasy Mini kit (Qiagen, Hilden, Germany) and reverse-transcription reaction was performed using M-MLV polymerase (Thermo Fisher Scientific, Massachusetts, USA). The mRNA levels were quantified by amplification of cDNA using a real-time thermocycler (Viia7 Applied Biosystems
Nucleoside macrocycles formed by intramolecular click reaction: efficient cyclization of pyrimidine nucleosides decorated with 5'-azido residues and 5-octadiynyl side chains
Beilstein J. Org. Chem. 2018, 14, 2404–2410, doi:10.3762/bjoc.14.217
- for cyclo-dU 8 and 68% S-type for cyclo-dC 4. The conformation found for the macrocycle 8 is different to that in the solid state (N-type, Figure 4). Apparently, the sugar residue of the macrocycle exhibits sufficient flexibility to adopt the S-conformation of DNA and the N-conformation of RNA
Synthesis and photophysical studies of a multivalent photoreactive RuII-calix[4]arene complex bearing RGD-containing cyclopentapeptides
Beilstein J. Org. Chem. 2018, 14, 1758–1768, doi:10.3762/bjoc.14.150
- activity of enzymes such as RNA polymerase or endonuclease is inhibited in vitro at the level of the photoadduct [23][24]. In order to target a specific DNA sequence, photoreactive RuII complexes have been anchored to specific antisense oligonucleotides to inhibit the expression of the complementary
Glycosylation reactions mediated by hypervalent iodine: application to the synthesis of nucleosides and carbohydrates
Beilstein J. Org. Chem. 2018, 14, 1595–1618, doi:10.3762/bjoc.14.137
- ” (i.e., DNA makes RNA makes proteins). The latter make up the cell walls of microorganisms and also play a role in transmitting information on the cell surface, whose interactions with proteins are a starting point for signal transduction into cells [1]. Since both types of polymers are essential for
Phosphoramidite building blocks with protected nitroxides for the synthesis of spin-labeled DNA and RNA
Beilstein J. Org. Chem. 2018, 14, 1563–1569, doi:10.3762/bjoc.14.133
- could be incorporated by unmodified standard procedures into four different self-complementary DNA and two RNA oligonucleotides. After photochemical removal of the protective group, elimination of formic aldehyde and spontaneous air oxidation, the nitroxide radicals were regenerated in high yield. The
- , for example, nucleophilic displacement by 4-amino-TEMPO has been used to prepare RNA strands containing the cytidine derivative 1 and its adenosine analog 3 [8][25][26] (Figure 1). Alternatively, by adapting the standard synthetic procedures, nitroxides can be directly incorporated into
- therefore developed a third strategy based on photolabile protective groups [41][42][43] finally leading to phosphoramidite 6. This building block behaves in solid-phase RNA synthesis as any normal TOM protected amidite. It is completely stable against the conditions used for strand assembly, RNA
Oligonucleotide analogues with cationic backbone linkages
Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111
- and binds to double-stranded DNA to form a triple helix. The triple helix is not a substrate for the transcription machinery, and hence, RNA biosynthesis (and therefore protein formation) is blocked. In the antisense pathway [3], the ON binds to single-stranded mRNA in the cytoplasm, thus furnishing a
- duplex structure (usually a DNA–RNA heteroduplex) which cannot undergo ribosomal protein biosynthesis. Alternatively, the DNA–RNA heteroduplex can be a substrate for RNAse H-mediated degradation of the mRNA strand. This way, catalytic amounts of the ON can mediate the efficient cleavage of mRNA encoding
- a specific protein, which leads to effective (though reversible) and selective downregulation of the protein's activity. A third option for the biological action of oligonucleotide structures is the triggering of the RNA interference mechanism by double-stranded 'small interfering' RNA (siRNA
An overview of recent advances in duplex DNA recognition by small molecules
Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93
- developed to interrogate its effect on the activity of RNA polymerase II [72]. Lenzmeier et al. provided strong evidence for inhibition of Tax protein–DNA minor groove interaction via synthetic Py/Im polyamides, which is believed to be essential for treating and/or preventing HTLV-I-associated diseases [73
Mechanochemistry of nucleosides, nucleotides and related materials
Beilstein J. Org. Chem. 2018, 14, 955–970, doi:10.3762/bjoc.14.81
- DNA and RNA isolation The lack of free-volume within double-stranded DNA at low hydration levels leads to limited ice formation even under cooling in liquid air [57]. In contrast, cold denaturation of globular proteins at such temperatures is almost ubiquitous [58]. Furthermore, large conformational
- of ribonucleotide-derived material from yeast RNA in 1879 using mechanical disaggregation [68]. Altmann developed a more generalised method for isolating either RNA or DNA from a variety of tissues and organisms during which crude mixtures with protein were ground to a fine powder with 1:1 alcohol/6
- % HCl (aq) and subsequently triturated with pure alcohol and then ether [69]. Typically, RNA depolymerisation (especially when in contact with metal components) would be observed during these operations [70] although isolation of infectious viral RNA from frozen carcinoma tissue following grinding was
Local energy decomposition analysis of hydrogen-bonded dimers within a domain-based pair natural orbital coupled cluster study
Beilstein J. Org. Chem. 2018, 14, 919–929, doi:10.3762/bjoc.14.79
- importance for regulating molecular properties like polarizability [1] and in various biochemical processes, including protein folding [2] and stability [3], replication of DNA and RNA [4], enzyme catalysis [5], proton relay mechanism [6], and drug delivery [7]. Energy decomposition analysis (EDA) schemes
Phosphodiester models for cleavage of nucleic acids
Beilstein J. Org. Chem. 2018, 14, 803–837, doi:10.3762/bjoc.14.68
- studies with small molecular phosphodiesters. Keywords: Cleavage; DNA; kinetics; mechanism; RNA; Introduction Nucleic acids are polymeric diesters of phosphoric acid that store and transfer biological information. In biological systems, the diester linkages bridging 3´-O of one nucleoside to the 5´-O of
- the next one are cleaved by a variety of enzymes [1]. The phosphodiester bonds of DNA are hydrolyzed, depending on the enzyme, either to a 3´- or 5´-phosphate, whereas the bonds in RNA, with few exceptions (above all RNase H-catalyzed cleavages) undergo transesterification to a 2´,3´-cyclic phosphate
- at 25 °C, which means that protein enzymes, nucleases, are able to accelerate the phosphodiester cleavage by a factor of 1017 [2]. The phosphodiester linkages of RNA are much more labile, owing to the presence of neighboring hydroxy function that serves as an intramolecular nucleophile resulting in
Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides
Beilstein J. Org. Chem. 2018, 14, 772–785, doi:10.3762/bjoc.14.65
- stability, ii) altered hydrogen bonding motifs, and iii) altered molecular recognition properties [25][29][37][58]. Because of these changes, C-nucleosides have been useful in the study of RNA and DNA processing enzymes, as well as drug design efforts and novel supramolecular structures [12][29][59
- endothelial cells and RSV with low cytotoxicity towards Huh-7, HEp-2 and MT4 cells. Moreover, the triphosphate of 4 selectively inhibits, HCV RdRp and RSV RdRp over human RNA Pol II and DNA polymerases (α, β, γ) [65]. The 2'-Me compound 7 as its triphosphate (TP) shows anti-HCV activity in replicon assays [77
- ]. However, 7-TP serves as a substrate for mitochondrial RNA polymerase, thereby causing toxicity in rats [63]. The 2'-F and 2'-β-Me compounds 8 and 9 are active against the HCV, but lack activity against EBOV and RSV in cell-based assays [65]. The pharmacokinetic properties of 4 were improved by converting
Enzyme-free genetic copying of DNA and RNA sequences
Beilstein J. Org. Chem. 2018, 14, 603–617, doi:10.3762/bjoc.14.47
- Marilyne Sosson Clemens Richert Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany 10.3762/bjoc.14.47 Abstract The copying of short DNA or RNA sequences in the absence of enzymes is a fascinating reaction that has been studied in the context of prebiotic chemistry
- successful modeling of the reaction, the strength of the template effect, the inhibitory effect of spent monomers, and the rate constants of the chemical steps have to be determined experimentally. While challenges remain for the high fidelity copying of long stretches of DNA or RNA, the available data
- suggest that enzyme-free primer extension is a more powerful reaction than previously thought. Keywords: base pairing; DNA; enzyme-free primer extension; nucleotides; oligonucleotides; replication; RNA; Introduction Replication of genetic information is critical for all living systems. In the cell, this
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