Valorisation of plastic waste via metal-catalysed depolymerisation

• Francesca Liguori,
• Carmen Moreno-Marrodán and
• Pierluigi Barbaro

Beilstein J. Org. Chem. 2021, 17, 589–621, doi:10.3762/bjoc.17.53

• oxidation, cross-linkage, bond cleavage). The term “biodegradation” indicates a “degradation caused by enzymatic processes resulting from the action of cells”. Although commonly used, also for artificial polymers, the term “biodegradable” specifically refers to biorelated polymers (i.e., proteins, nucleic

• acids, polysaccharides), which are "susceptible to degradation by biological activity by lowering of the molar masses of macromolecules". Therefore, in this situation, “chain cleavage” and “degradation” are used interchangeably. To avoid confusion, instead of “(bio)degradation”, in the present review

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

• fluorinated probes and their incorporation into macromolecules, the application of 19F NMR to monitor protein–protein interactions, protein–ligand interactions, physiologically relevant ions and in the structural analysis of proteins and nucleic acids. The continued relevance of the technique to investigate

• labelling 19F NMR offers an attractive option for investigating the interactions between proteins and other biomolecules such as nucleic acids. Many of the advantages of 19F NMR have already been discussed but it is worth highlighting that it is a particularly useful technique to study large proteins that

• nucleic acids [89]. Following early advances by Micura and co-workers in the late 2000s that investigated the suitability of 19F NMR for the conformational analysis of single and double helix RNA strands [90][91][92][93] 19F NMR has found a particularly rich niche of applications in the conformational

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• can only be fully exploited via interactions, either in the form of PPIs or with other metabolites and biomolecules, such as nucleic acids. Thus, the identification of the molecular binding partners that proteins interact with is an interesting avenue to facilitate the discovery of the protein

• initial capsid formation is limited due to the time required for an intermediate steady state for the consequent assembly. These mathematical calculations and generalisations, however, do not take into consideration biological scaffolds, such as nucleic acids, which can facilitate or disrupt the capsid

• more complicated systems, such as in cowpea chlorotic mottle virus (CCMV), the viral capsid is made up of different assembly units. In vivo, viral nucleic acids may serve as biological scaffold to attract free assembly units [84] and organise on the surface [85]. Assembly with viral RNA present can be

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• to perform FRET in vitro and in vivo, particularly in living cells [30]. FRET-based peptide probes are heavily used for ratiometric fluorescence detection of biomolecules. Pyrene-functionalized oligonucleotides and locked nucleic acids (LNAs) are considerably used for targeting nucleic acids [31

• detection The genetic information carrier nucleic acids are present in nearly all living organisms. Fluorescence monitoring of nucleic acids has become increasingly important in medical diagnosis, drug discovery, environmental monitoring, food safety etc. [40][41]. Schmuck et al. reported several

• fluorescent probes for nucleic acids detection. The first probe 2 is a pyrene-based peptide beacon containing two Trp–Thr–Lys tripeptide arms attached to a central lysine spacer (Figure 3A) [34]. Unbound peptide beacon 2 in folded form exhibits typical pyrene excimer emission at 490 nm. Peptide beacon 2

Regioselective synthesis of heterocyclic N-sulfonyl amidines from heteroaromatic thioamides and sulfonyl azides

• Vladimir Ilkin,
• Vera Berseneva,
• Tetyana Beryozkina,
• Tatiana Glukhareva,
• Lidia Dianova,
• Wim Dehaen,
• Eugenia Seliverstova and
• Vasiliy Bakulev

Beilstein J. Org. Chem. 2020, 16, 2937–2947, doi:10.3762/bjoc.16.243

• , rich chemistry and technically useful properties of heterocyclic compounds have made them a focal point of science and industry over the years. Heterocyclic compounds including azoles and azines have been found in natural products, and they are included in the structures of nucleic acids, vitamins

Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function

• Marius H. Heddinga and
• Jens Müller

Beilstein J. Org. Chem. 2020, 16, 2870–2879, doi:10.3762/bjoc.16.236

• mostly unstructured in solution, aptamers typically fold into their three-dimensional structure upon binding the respective target molecule [2]. Aptamers are normally identified by the in vitro selection from combinatorial libraries of nucleic acids [3]. In the past decades, interest in aptamers has

• risen significantly, as they can be applied in a variety of disciplines, e.g., as therapeutics or as sensors [4][5][6][7]. Another topical area of research in the field of nucleic acids involves the development of nucleic acids whose structure (and therefore function) can be regulated by the addition

Changed reactivity of secondary hydroxy groups in C8-modified adenosine – lessons learned from silylation

• Jennifer Frommer and
• Sabine Müller

Beilstein J. Org. Chem. 2020, 16, 2854–2861, doi:10.3762/bjoc.16.234

• nucleic acids via Förster Resonance Energy Transfer (FRET) [20]. More recently, we started an effort to develop an efficient strategy for the preparation of a linker-modified adenosine building block, which in a future project is to be used for post synthetic conjugation of reporters or functional

• structure and function studies of nucleic acids. Often, the effort to synthesize a specifically modified oligonucleotide is underestimated, since a wide spectrum of precursors and standard methodology is available. However, dependent on the specific synthetic aim, standard methods can fail or lead to

Synthesis and investigation of quadruplex-DNA-binding, 9-O-substituted berberine derivatives

• Jonas Becher,
• Daria V. Berdnikova,
• Heiko Ihmels and
• Christopher Stremmel

Beilstein J. Org. Chem. 2020, 16, 2795–2806, doi:10.3762/bjoc.16.230

• ; DNA recognition; G4-DNA; nucleic acids; Introduction In nucleic acids chemistry, quadruplex DNA (G4-DNA) has been established as an attractive target [1][2][3]. This noncanonical DNA form is assembled through stacking of at least two guanine quartets and has been observed with highly diverse

• -inflammatory [25], antibacterial [26][27], and anticancer reagents [28][29]. The latter property is mainly based on the binding interaction of berberine with nucleic acids and the resulting inhibition of topoisomerase and telomerase [2][30]. Most notably, berberine (1a) induces a strong growth inhibition in

• additional hydrophobic effect is the main contribution of the different substituents of 4a–e to the overall binding affinity. It is well known that the emission of the parent berberine increases strongly upon the accommodation in sterically constrained binding sites in, e.g., nucleic acids, cucurbiturils

Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

• Annike Weißenstein,
• Myroslav O. Vysotsky,
• Ivo Piantanida and
• Frank Würthner

Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170

• ; Introduction The interplay of non-covalent interactions between nucleic acids and proteins or peptides is the basis of life and is also often used for the design of artificial small molecules, aiming for sensing or control of biorelevant processes. Many naturally occurring bioactive molecules contain a short

Synthesis of new dihydroberberine and tetrahydroberberine analogues and evaluation of their antiproliferative activity on NCI-H1975 cells

• Giacomo Mari,
• Lucia De Crescentini,
• Serena Benedetti,
• Francesco Palma,
• Stefania Santeusanio and
• Fabio Mantellini

Beilstein J. Org. Chem. 2020, 16, 1606–1616, doi:10.3762/bjoc.16.133

• to position 13 of the BER skeleton, usually causes a geometric propensity for additional stacking-type, noncovalent aromatic interactions with cellular targets forming stronger complexes with nucleic acids than BER [9][10][11][12]. In fact, the so obtained functionalized BER shows better anticancer

A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA

• Ekaterina A. Bryushkova,
• Erik R. Gandalipov and
• Julia V. Nuzhina

Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100

• technique is more frequently used in diagnostic laboratories than the direct sequencing method [6]. A serious problem for the detection of full-sized nucleic acids is the secondary structure, which interrupts the access of sensors to the binding site. For single-stranded RNA this problem may be partially

• and cheap, but today it is not too often applied for the detection of nucleic acids. We showed that SDFS can be used to efficiently detect at least 60 nt AR mRNA fragments both at 37 °C and at room temperature (25 °C) with different sensitivity and incubation times. Thus, by varying the test setup

Reversible photoswitching of the DNA-binding properties of styrylquinolizinium derivatives through photochromic [2 + 2] cycloaddition and cycloreversion

• Sarah Kölsch,
• Heiko Ihmels,
• Jochen Mattay,
• Norbert Sewald and
• Brian O. Patrick

Beilstein J. Org. Chem. 2020, 16, 111–124, doi:10.3762/bjoc.16.13

• ; photodimerization; photoswitches; Introduction The association of DNA-targeting drugs with nucleic acids [1][2][3][4][5][6][7][8] is considered one of the essential properties that determine their biological activity [9]. Specifically, a ligand may occupy particular binding sites of DNA or induce significant

In search of visible-light photoresponsive peptide nucleic acids (PNAs) for reversible control of DNA hybridization

• Lei Zhang,
• Greta Linden and
• Olalla Vázquez

Beilstein J. Org. Chem. 2019, 15, 2500–2508, doi:10.3762/bjoc.15.243

• , artificial probes activated by visible-light irradiation are highly desired in biological applications. Here, we report two novel types of visible-light photoswitchable peptide nucleic acids (PNAs) based on the molecular transducers: hemithioindigo and tetra-ortho-fluoroazobenzene. Our study reveals that the

• hybridization has demonstrated an enormous potential to regulate on-demand biological responses such as gene expression [1]. There are indeed a number of successful examples based on photocaged strategies [2][3][4][5], in which modified nucleic acids interfere irreversibly with gene expression in vitro [6][7

• -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

• Xiao Xie,
• Michela Zuffo,
• Marie-Paule Teulade-Fichou and
• Anton Granzhan

Beilstein J. Org. Chem. 2019, 15, 1872–1889, doi:10.3762/bjoc.15.183

• rapid topological classification of G4-DNA structures. Keywords: fluorescent probes; G-quadruplex DNA; G-quadruplex RNA; nucleic acids; styryl dyes; Introduction Development of fluorescent probes for G-quadruplex (G4) DNA and RNA is an active research area. In fact, these non-canonical nucleic acid

• , validating the potential of this molecular scaffold (Figure 1) [22][33][60][61][62][63]. Nevertheless, the structural determinants for the desired properties of the probes (i.e., high selectivity for G4-DNA or G4-RNA with respect to double-stranded or single-stranded nucleic acids, high fluorimetric response

• ; antiparallel G4: TBA, HRAS), two G4-RNA structures (TERRA and NRAS), as well as genomic double-stranded DNA (calf thymus DNA, ct DNA) and RNA from calf liver (cl RNA). Screened samples contained fixed concentrations of dyes (2.5 µM) and nucleic acids (5 µM). Corrections to the concentration of nucleic acids

Convergent synthesis of the pentasaccharide repeating unit of the biofilms produced by Klebsiella pneumoniae

• Arin Gucchait,
• Angana Ghosh and
• Anup Kumar Misra

Beilstein J. Org. Chem. 2019, 15, 431–436, doi:10.3762/bjoc.15.37

• nucleic acids and (c) loss of homogeneity of the polysaccharide fragments to name a few. It has already been established that in many cases the oligosaccharide repeating units resemble similar antigenic potential to those of the native polysaccharides [8][9][10]. Therefore, the best alternative way to get

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

• 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

• ’-fluorinated hexitol nucleic acids FHNA and Ara-FHNA (Figure 1) with the fluorine in axial or equatorial orientation, respectively. Both modifications preferentially adopt a chair conformation with the nucleobase in axial orientation which mimics the C3’-endo conformation of the furanose ring. Thermal

• fluorinated nucleic acids such as 2’-fluorocyclohexenyl nucleic acid (F-CeNA, Figure 1) [27] and other modifications [28][29][30][31] have been analyzed on their antisense properties. In our own work we already investigated the effect of the fluorine substituent at various positions of the [3.3.0]bicyclo-DNA

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

• 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

• bridges [12]. Prominent members of this class of conformationally restricted nucleic acids are locked nucleic acids (LNAs) [13][14][15], hexitol nucleic acids (HNAs) [16][17], cyclohexenyl nucleic acids (CeNAs) [18][19], tricyclo-DNAs (tc-DNAs, Figure 1) [20][21][22], and [4.3.0]bicyclo-DNAs (bc4,3-DNAs

• ’-deoxy-2’-fluoroarabino nucleic acid (F-ANA) [32][33][34], 3’-hexitol nucleic acids (FHNA and Ara-FHNA) [35], 2’-fluorocyclohexenyl nucleic acid (F-CeNA) [36], and other modifications [37][38][39][40][41] were evaluated for their antisense properties. In this context, our research group has

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

• connectivity and gave an insight to the conformation. The sugar conformation (N vs S) in solution was different to that in the solid state. The macrocycles display free accessible Watson–Crick recognition sites valuable for base pairing with nucleic acids or proteins. Since the compact nucleoside macrocycles

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

• ; nucleoside; oligosaccharide; Introduction Nucleic acids and oligosaccharides are both mandatory polymers for the maintenance of life and cell growth. The former exists in nuclei and codes genetic information, which is transformed into proteins through a transcription process known as the “central dogma

• quite important, and informs the development of new drugs for diseases including cancers and infectious diseases caused by viruses [4][5][6][7]. Indeed, many drugs related to nucleic acids and oligosaccharides have been developed and used in clinical fields. Synthetic chemists have contributed to the

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

• ; Introduction EPR spectroscopy is well established to study the structure and dynamics of nucleic acids [1][2][3][4][5][6][7][8]. Although the information attainable by EPR is less detailed when compared to NMR, it is often complementary. While local conformations are normally obtained from NMR data, EPR can

• measure long distances that are hardly accessible by NMR [9][10]. Furthermore, spin labeling of biopolymers can support NMR studies by paramagnetic relaxation enhancement [11][12]. For nucleic acids, spin labeling is most often achieved by covalent attachment of nitroxides. Unfortunately, the conditions

Steric “attraction”: not by dispersion alone

• Ganna Gryn’ova and
• Clémence Corminboeuf

Beilstein J. Org. Chem. 2018, 14, 1482–1490, doi:10.3762/bjoc.14.125

• of the other is greater than the electron–electron and nuclei–nuclei repulsion. The crucial role of charge penetration has been demonstrated for a diverse range of chemical systems, including the saturated [9][28] and unsaturated hydrocarbons [30], nucleic acids [31], metal ions interacting with

Design and biological characterization of novel cell-penetrating peptides preferentially targeting cell nuclei and subnuclear regions

• Anja Gronewold,
• Mareike Horn and
• Ines Neundorf

Beilstein J. Org. Chem. 2018, 14, 1378–1388, doi:10.3762/bjoc.14.116

• or basic character. During the last 25–30 years, many different CPPs have been described and used for manifold applications like the delivery of nucleic acids, proteins, peptides, nanoparticles, small organic drugs, and others [10]. CPP conjugates can be generated by covalent conjugation between

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

• endogenous nucleic acids in a selective and sequence-specific manner. They can therefore modulate biological functions via different mechanisms [1]. Single-stranded oligonucleotides (ONs) can act in cellulo mainly via two different pathways (Figure 1). In the antigene pathway [2], the ON enters the nucleus

• chemically modify ON structures in order to make them suitable drug candidates or chemical probes, e.g., for diagnostic purposes [6][7]. The relevance of the polyanionic phosphate diester-linked backbone to the overall function of nucleic acids has been discussed by Westheimer [8], Benner [9][10], and others

• linkages, with the nucleic acid mimic 'peptide nucleic acid' (PNA) [11][12][13] representing a striking example. Although the achiral PNA backbone is pronouncedly different from native nucleic acid structures, PNAs are capable of sequence-specific hybridization to native nucleic acids. However, their

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

• binding agents [16][17][18][19][20][21][22][23]. A few others have covered nucleic acids binders in general [20] as well as an emerging therapeutic DNA target: the DNA G-quadruplex [24]. In this review, we provide a detailed overview of discoveries made in the search of duplex DNA recognition agents