Synthesis and fluorescent properties of N(9)-alkylated 2-amino-6-triazolylpurines and 7-deazapurines

• Andrejs Šišuļins,
• Jonas Bucevičius,
• Yu-Ting Tseng,
• Irina Novosjolova,
• Kaspars Traskovskis,
• Ērika Bizdēna,
• Huan-Tsung Chang,
• Sigitas Tumkevičius and
• Māris Turks

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

• Sibylle Frei,
• Adam K. Katolik and
• Christian J. Leumann

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

• Sibylle Frei,
• Andrei Istrate and
• Christian J. Leumann

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

• Mingjun Yuan,
• Song Lin Chua,
• Yang Liu,
• Daniela I. Drautz-Moses,
• Joey Kuok Hoong Yam,
• Thet Tun Aung,
• Roger W. Beuerman,
• May Margarette Santillan Salido,
• Stephan C. Schuster,
• Choon-Hong Tan,
• Michael Givskov,
• Liang Yang and
• Thomas E. Nielsen

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

• Laura Carro

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

• Christian Schütz and
• Martin Empting

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

• Carmen Curutiu,
• Florin Iordache,
• Veronica Lazar,
• Aurelia Magdalena Pisoschi,
• Aneta Pop,
• Mariana Carmen Chifiriuc and
• Alina Maria Hoban

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

• Jiang Liu,
• Peter Leonard,
• Sebastian L. Müller,
• Constantin Daniliuc and
• Frank Seela

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 Ru^II-calix[4]arene complex bearing RGD-containing cyclopentapeptides

• Sofia Kajouj,
• Lionel Marcelis,
• Alice Mattiuzzi,
• Adrien Grassin,
• Damien Dufour,
• Pierre Van Antwerpen,
• Didier Boturyn,
• Eric Defrancq,
• Mathieu Surin,
• Julien De Winter,
• Pascal Gerbaux,
• Ivan Jabin and
• Cécile Moucheron

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

• Yuichi Yoshimura,
• Hideaki Wakamatsu,
• Yoshihiro Natori,
• Yukako Saito and
• Noriaki Minakawa

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

• Timo Weinrich,
• Eva A. Jaumann,
• Ute M. Scheffer,
• Thomas F. Prisner and
• Michael W. Göbel

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

• Melissa Meng and
• Christian Ducho

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

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

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

• Olga Eguaogie,
• Joseph S. Vyle,
• Patrick F. Conlon,
• Manuela A. Gîlea and
• Yipei Liang

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

• Ahmet Altun,
• Frank Neese and
• Giovanni Bistoni

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

• Satu Mikkola,
• Tuomas Lönnberg and
• Harri Lönnberg

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

• Kartik Temburnikar and
• Katherine L. Seley-Radtke

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

• Marilyne Sosson and
• Clemens Richert

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

Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing

• Françoise Debart,
• Christelle Dupouy and
• Jean-Jacques Vasseur

Beilstein J. Org. Chem. 2018, 14, 436–469, doi:10.3762/bjoc.14.32

• bind to mRNA targets through Watson–Crick base pairing and form a RNA/DNA duplex [4]. This can result in either mRNA cleavage mediated by RNase H or mRNA translational arrest through steric blocking. Another strategy for gene inhibition involves ribozymes [5] and DNAzymes [6], which are nucleic acid

• molecules with enzymatic activity. These catalytic RNAs and DNAs trigger the cleavage of RNA substrates at a specific position. Additionally, ribozymes can catalyze the ligation of target mRNA, extending their therapeutic potential to RNA repair applications. Finally, another promising ON-based therapy

• , more potent than AONs or ribozymes for gene knockdown, is centered on the RNA interference (RNAi) mechanism, which uses two natural pathways for gene silencing. One is guided by double-stranded siRNAs of 19–23 nucleotides in length that are fully complementary to the mRNA targets, and the other is

Synthesis and biological evaluation of RGD and isoDGR peptidomimetic-α-amanitin conjugates for tumor-targeting

• Lizeth Bodero,
• Paula López Rivas,
• Barbara Korsak,
• Torsten Hechler,
• Andreas Pahl,
• Christoph Müller,
• Daniela Arosio,
• Luca Pignataro,
• Cesare Gennari and
• Umberto Piarulli

Beilstein J. Org. Chem. 2018, 14, 407–415, doi:10.3762/bjoc.14.29

• bicyclic octapeptide toxin belonging to the amatoxin family, found in Amanita Phalloides (death cap mushroom), see Figure 1 [1]. Its mechanism of action consists in the inhibition of cellular transcription by an effective blocking of RNA polymerase II, which is present in the nuclei of eukaryotic cells and

Preparation of trinucleotide phosphoramidites as synthons for the synthesis of gene libraries

• Ruth Suchsland,
• Bettina Appel and
• Sabine Müller

Beilstein J. Org. Chem. 2018, 14, 397–406, doi:10.3762/bjoc.14.28

• polystyrene support decorated with a photolabile linker and its potential use for the synthesis of siRNA duplexes under mild and neutral conditions [36]. A similar strategy was used for the synthesis of partially 2'/3'-O-acetylated RNA oligonucleotides [37]. A photo-cleavable linker would also have potential

Fluorogenic PNA probes

• Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17

• the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years. Keywords: DNA; fluorescence; molecular beacons; molecular probes; oligonucelotides; RNA; Review Introduction The development of molecular probes that

• (aeg) backbone that can recognize its target DNA and RNA was reported [21]. Considering the enormous difference between the two backbones, it is quite surprising that PNA can still retain the ability to recognize natural oligonucleotides having a complementary sequence with high affinity and

• unique properties not observed in other classes of oligonucleotide analogues with negatively charged phosphate groups. These include the relative insensitivity of the PNA–DNA or PNA–RNA hybrids to the ionic strength of the solvent [23], and the complete stability towards nucleases as well as proteases

5-Aminopyrazole as precursor in design and synthesis of fused pyrazoloazines

• Ranjana Aggarwal and
• Suresh Kumar

Beilstein J. Org. Chem. 2018, 14, 203–242, doi:10.3762/bjoc.14.15

• are currently used in several marketed drugs like cartazolate (1), zaleplon (2), sildenafil (3), allopurinol (4), indiplon (5), etazolate (6) etc. (Figure 1). Fused pyrazole derivatives, especially pyrazoloazines have been reported to mimic purine bases, present in DNA and RNA, due to close structural

Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

• Mattias Bood,
• Sangamesh Sarangamath,
• Moa S. Wranne,
• Morten Grøtli and
• L. Marcus Wilhelmsson

Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7

• FBAs (see Figure 2 for chemical structures) include C8 to S8 thio-RNA analogue thA [23], the C8-naphtalene substituted adenines cnA and dnA [24], as well as our own quadracyclic qAN1 [25]. A handful of fluorescent guanine analogues has been synthesized and characterized and includes the recent turn-on

• probe BFdG, 3-MI, 2PyG, as well as the emissive RNA analogue thG [23][26][27][28]. Some notable pyrimidine analogues include our tricyclic analogues tC and tCO [29][30][31], pyrrolo-dC [32] and its derivatives [33] as well as thU, thC [23] and DMAC [34]. Apart from tC, tCO, qAN1 and thG, FBAs have not

• made it impractical to handle. Instead, KF was used in combination with 18-crown-6 in anhydrous diglyme which furnished compounds 24a–e in modest 3–24% yields after isolation (Scheme 5) [47]. Recently, our group gained interest in RNA chemistry and therefore revisited the synthesis of tCO containing a

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• the most commonly used method for the characterization of the helical structure of DNA and RNA and their complexes with ligands. Less common but complementary to ECD, is flow-oriented linear dichroism (LD). Other methods such as vibrational CD (VCD) and emission-based methods (FDCD, CPL), can also be

• used for suitable samples. Despite the popularity of polarization spectroscopy in biophysics, aside several highly focused reviews on the application of these methods to DNA/RNA research, there is no systematic tutorial covering all mentioned methods as a tool for the characterization of adducts

• of these methods are found in structural studies of biomacromolecules [3]. For instance electronic circular dichroism (ECD), the most commonly used method, is indispensable in the structural studies of proteins and also intensively used in the characterization of the helical structure of DNA and RNA