Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

Synthesis of dibenzosuberenone-based novel polycyclic π-conjugated dihydropyridazines, pyridazines and pyrroles

• Ramazan Koçak and
• Arif Daştan

Beilstein J. Org. Chem. 2021, 17, 719–729, doi:10.3762/bjoc.17.61

• , antihypertensive, anti-Parkinson, anti-inflammatory, anticonvulsant, vasodilatory, antidiabetic, antitubercular, antifungal, and antibacterial activities [32][33][34][35][36][37][38], pH-sensing [39], OLEDs [40], chemiluminescent materials [41][42], metal complexes (Figure 1) [43][44][45][46], liquid crystal [47

• tautomerization A with a [1,7]-H shift 13 would be formed. Alternatively, in the second mechanism, 13 is thought to occur by tautomerization B and a [1,5]-H shift (Scheme 9). Photophysical properties In our previous work, we examined the photophysical and fluoride sensing properties of dihydropyridazine

Synthesis, crystal structures and properties of carbazole-based [6]helicenes fused with an azine ring

• Daria I. Tonkoglazova,
• Anna V. Gulevskaya,
• Konstantin A. Chistyakov and
• Olga I. Askalepova

Beilstein J. Org. Chem. 2021, 17, 11–21, doi:10.3762/bjoc.17.2

• have led to promising applications of helicenes. The latter have been studied with respect to conductivity [12][13][14][15], nonlinear optics [16][17], circularly polarized luminescence [18][19][20][21][22][23][24], organocatalysis [25][26][27][28][29], conformational analysis [30], chirality sensing

Naphthalonitriles featuring efficient emission in solution and in the solid state

• Sidharth Thulaseedharan Nair Sailaja,
• Iván Maisuls,
• Jutta Kösters,
• Alexander Hepp,
• Andreas Faust,
• Jens Voskuhl and
• Cristian A. Strassert

Beilstein J. Org. Chem. 2020, 16, 2960–2970, doi:10.3762/bjoc.16.246

• substitution and environment is reported with potential applications in sensing, bioimaging and optoelectronics. Keywords: aggregation caused quenching (ACQ); aggregation-induced emission enhancement (AIEE); naphthalonitriles (NCNs); solution and solid state emitters (SSSE); solvent quenching (SQ

Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response

• Rakesh Biswas,
• Surya Ghosh,
• Shubhra Kanti Bhaumik and
• Supratim Banerjee

Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223

• sensing is an active area of research which has developed tremendously in the last few decades [1][2][3][4]. The importance of anion sensing stems from its importance in various practical applications which range from identifying and detecting environmentally toxic anions to medical diagnostics. In recent

• general challenging to design high-affinity synthetic probes for anion sensing under such competitive conditions [7]. One of the strategies that has proven to be quite successful in this regard, not only for bio-anions, rather for a variety of several other analytes also, is multivalency [8][9][10][11

• adenosine phosphates (ADP and AMP) and pyrophosphate (PPi). The detection of ATP was also possible in the presence of 150 mM NaCl. The modular nature of the sensing platform provided by the multivalent nano-assemblies of the bisimidazolium amphiphiles can in principle be extended for the detection of other

Optical detection of di- and triphosphate anions with mixed monolayer-protected gold nanoparticles containing zinc(II)–dipicolylamine complexes

• Lena Reinke,
• Julia Bartl,
• Marcus Koch and
• Stefan Kubik

Beilstein J. Org. Chem. 2020, 16, 2687–2700, doi:10.3762/bjoc.16.219

• water/methanol 1:2 (v/v). These anions caused the bright red solutions of the nanoparticles to change their color because of nanoparticle aggregation followed by precipitation, whereas halides or oxoanions such as sulfate, nitrate, or carbonate produced no effect. The sensitivity of phosphate sensing

• depended on the nature of the anion, with diphosphate and triphosphate inducing visual changes at significantly lower concentrations than hydrogenphosphate. In addition, the sensing sensitivity was also affected by the ratio of the ligands on the nanoparticle surface, decreasing as the number of

• introducing a method to assess whether certain biologically relevant anions are present in an aqueous solution within a specific concentration range. Keywords: chemosensor; diphosphate; gold nanoparticles; optical sensing; triphosphate; Introduction Gold nanoparticles (AuNPs) are versatile platforms for the

Thermodynamic and electrochemical study of tailor-made crown ethers for redox-switchable (pseudo)rotaxanes

• Henrik Hupatz,
• Marius Gaedke,
• Hendrik V. Schröder,
• Julia Beerhues,
• Arto Valkonen,
• Fabian Klautzsch,
• Sebastian Müller,
• Felix Witte,
• Kari Rissanen,
• Biprajit Sarkar and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2020, 16, 2576–2588, doi:10.3762/bjoc.16.209

• intramolecular folding which was observed in the solid-state structure and is likely also present in solution, as indicated by a charge-transfer band. Nevertheless, it might be applicable for redox-controlled metal-sensing [60][61][62]. On the contrary, NDIC8 forms pseudo[2]rotaxanes and facilitates the

Styryl-based new organic chromophores bearing free amino and azomethine groups: synthesis, photophysical, NLO, and thermal properties

• Anka Utama Putra,
• Deniz Çakmaz,
• Nurgül Seferoğlu,
• Alberto Barsella and
• Zeynel Seferoğlu

Beilstein J. Org. Chem. 2020, 16, 2282–2296, doi:10.3762/bjoc.16.189

• anticancer activity, to name a few. Moreover, Schiff bases bearing a salicylidene moiety are also used as chemosensors for sensing of specific ions. In addition, some derivatives also show NLO activity [25][34][35][36][37]. Herein, we report on the synthesis and full photophysical characterization of a

• amines led to the increase in the Stokes shift and a significant red shift between the absorption and the emission maxima. This was due to the varying electronic contributions to the host structure induced by the heterocyclic amino constituents [50][51][52] (Figure 4). Hydroxide anion sensing properties

• The dyes 8–12 could have the ability to detect hydroxide anions due to the presence of an OH substituent at the salicylidene moiety. Therefore, the OH− sensing activity of compounds 8–12 was investigated by the addition of hydroxide anions in the form of the corresponding tetrabutylammonium (TBA) salt

The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY

• Patrizia Andreozzi,
• Lorenza Tamberi,
• Elisamaria Tasca,
• Gina Elena Giacomazzo,
• Marta Martinez,
• Mirko Severi,
• Marco Marradi,
• Stefano Cicchi,
• Sergio Moya,
• Giacomo Biagiotti and
• Barbara Richichi

Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188

• exploited in many applications including the selective sensing of saccharides, the separation and purification of glycoproteins, and the immobilization of antibodies in microarrays [17][18][19][20][21]. However, the synthesis of boronic esters is sometimes problematic, as it often requires a fine tuning of

Synthetic approaches to bowl-shaped π-conjugated sumanene and its congeners

• Shakeel Alvi and
• Rashid Ali

Beilstein J. Org. Chem. 2020, 16, 2212–2259, doi:10.3762/bjoc.16.186

• ][22][23]. On the other hands, further extension of these molecules leads to homochiral carbon nanotubes which can produce innovative perception in chiral sensing, chiral catalysis, separation techniques and chiral ligands for organocatalysis [24]. Additionally, control on the bowl-to-bowl inversion

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• major groove; in that way allowing two GCP units different recognition environment and therefore eventually better sensing of ds-polynucleotide secondary structures. However, if for some particular ds-DNA or ds-RNA threading intercalation is hampered, such novel NDI-(GCP)2 conjugate (4; Scheme 1) will

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

• the type of polynucleotide, thus the studied NDI dyes act as dual fluorimetric/ICD probes for sensing the difference between here used GC-DNA, AT-DNA and AU-RNA. Keywords: amino acid–fluorophore conjugate; circular dichroism; DNA/RNA recognition; fluorescence; intercalation; naphthalene diimide

• ; 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

• [9]). One of the approaches relies on amino acids conjugated with various DNA/RNA-binding chromophores, thereby yielding effective spectrometric sensing systems due to their interactions with DNA. In this approach, chromophores can be combined with peptide sequences in various ways, thus giving

Design, synthesis and application of carbazole macrocycles in anion sensors

• Alo Rüütel,
• Ville Yrjänä,
• Sandip A. Kadam,
• Indrek Saar,
• Mihkel Ilisson,
• Astrid Darnell,
• Kristjan Haav,
• Tõiv Haljasorg,
• Lauri Toom,
• Johan Bobacka and
• Ivo Leito

Beilstein J. Org. Chem. 2020, 16, 1901–1914, doi:10.3762/bjoc.16.157

• , Laboratory of Molecular Science and Engineering, Åbo Akademi University, Biskopsgatan 8, FI-20500 Turku/Åbo, Finland 10.3762/bjoc.16.157 Abstract Carboxylate sensing solid-contact ion-selective electrodes (ISEs) were created to provide a proof-of-concept ISE development process covering all aspects from in

• directed our efforts towards sensing carboxylates. The detection of these analytes is important in a number of areas and there is an obvious lack of easy-to-use sensing methods. Carboxylates are challenging analytes for two reasons. Firstly, binding is mainly achieved through either ion–ion interactions or

• -life sensing, also influences binding [4]. Within an ion-selective electrode (ISE), lipophilicity is mostly contributed by the low polarity membrane, which is commonly based on plasticized PVC [5]. One possible receptor family for carboxylates is based on the biscarbazolylurea moiety (Figure 1). This

Clickable azide-functionalized bromoarylaldehydes – synthesis and photophysical characterization

• Dominik Göbel,
• Marius Friedrich,
• Enno Lork and
• Boris J. Nachtsheim

Beilstein J. Org. Chem. 2020, 16, 1683–1692, doi:10.3762/bjoc.16.139

• ][8], biological imaging [9][10][11][12] and chemical sensing [13][14][15]. Referring to the Jablonski diagram (see Scheme 1a) [16][17], upon excitation from the singlet ground state (S0) to higher singlet states (Sn), followed by internal conversion (IC), either non-radiative or radiative decay to S0

4-Hydroxy-3-methyl-2(1H)-quinolone, originally discovered from a Brassicaceae plant, produced by a soil bacterium of the genus Burkholderia sp.: determination of a preferred tautomer and antioxidant activity

• Dandan Li,
• Naoya Oku,
• Yukiko Shinozaki,
• Yoichi Kurokawa and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1489–1494, doi:10.3762/bjoc.16.124

• rutaceous plants [9]. Examples from microbes include chymase inhibitors SF2809-I to VI from an actinomycete of the genus Dactylosporangium [10], a quorum sensing signaling molecule 2,4-dihydroxyquinoline (DHQ, 4) from Gram-negative bacteria Pseudomonas aeruginosa and Burkholderia thailandensis, [7], and 4-O

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

• 4 °C for 24 h. These results were consistent with our hypothesis on facilitating the ease of access to target 60-AR_RNA by cutting a short 27-nt fragment from the full target sequence by deoxyribozymes, thus increasing the local concentration of this fragment near to the sensing part of SDFS (Figure

Synthesis of triphenylene-fused phosphole oxides via C–H functionalizations

• Md. Shafiqur Rahman and
• Naohiko Yoshikai

Beilstein J. Org. Chem. 2020, 16, 524–529, doi:10.3762/bjoc.16.48

• extended π-system. These included, in particular, those fused with polycyclic aromatic hydrocarbons (PAHs) for possible applications in organic electronics, bioimaging and sensing, and asymmetric catalysis (Figure 1). To name a few examples, Yamaguchi et al. described synthetic routes to novel phosphorus

The reaction of arylmethyl isocyanides and arylmethylamines with xanthate esters: a facile and unexpected synthesis of carbamothioates

• Narasimhamurthy Rajeev,
• Toreshettahally R. Swaroop,
• Ahmad I. Alrawashdeh,
• Shofiur Rahman,
• Abdullah Alodhayb,
• Seegehalli M. Anil,
• Kuppalli R. Kiran,
• Chandra,
• Paris E. Georghiou,
• Kanchugarakoppal S. Rangappa and
• Maralinganadoddi P. Sadashiva

Beilstein J. Org. Chem. 2020, 16, 159–167, doi:10.3762/bjoc.16.18

• , Manasagangothri, Mysuru, Karnataka 570 006, India Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador A1B3X7, Canada Aramco Laboratory for Applied Sensing Research, King Abdullah Institute for Nanotechnology, King Saudi University, Riyadh, Saudi Arabia Surface, and

Automated glycan assembly of arabinomannan oligosaccharides from Mycobacterium tuberculosis

• Alonso Pardo-Vargas,
• Priya Bharate,
• Martina Delbianco and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2019, 15, 2936–2940, doi:10.3762/bjoc.15.288

• Mai Hoang for the proofreading of the manuscript. This work used Dr. Bharate’s thesis “Automated Glycan Assembly of Oligomannose Glycans for Sensing Applications” as a source.

A chiral self-sorting photoresponsive coordination cage based on overcrowded alkenes

• Constantin Stuckhardt,
• Diederik Roke,
• Wojciech Danowski,
• Edwin Otten,
• Sander J. Wezenberg and
• Ben L. Feringa

Beilstein J. Org. Chem. 2019, 15, 2767–2773, doi:10.3762/bjoc.15.268

• is essential for the application of SCCs towards chiral recognition and sensing [34][35][36][37]. To the best of our knowledge no self-sorted responsive SCCs have been reported so far. Molecular motors based on overcrowded alkenes are unique photoswitches that are able to undergo unidirectional

Arylisoquinoline-derived organoboron dyes with a triaryl skeleton show dual fluorescence

• Vânia F. Pais,
• Tristan Neumann,
• Ignacio Vayá,
• M. Consuelo Jiménez,
• Abel Ros and
• Uwe Pischel

Beilstein J. Org. Chem. 2019, 15, 2612–2622, doi:10.3762/bjoc.15.254

• ], BASHY dyes [10][11] or Boranils [12][13]) often feature quite rigid structures which contribute to high fluorescence quantum yields. These dyes have been applied for example in optoelectronics [14][15][16], sensing [17][18][19][20], and bioimaging [6][20][21][22][23][24][25][26]. On the other hand

Synthesis of novel sulfide-based cyclic peptidomimetic analogues to solonamides

• José Brango-Vanegas,
• Luan A. Martinho,
• Lucinda J. Bessa,
• Andreanne G. Vasconcelos,
• Alexandra Plácido,
• Alex L. Pereira,
• José R. S. A. Leite and
• Angelo H. L. Machado

Beilstein J. Org. Chem. 2019, 15, 2544–2551, doi:10.3762/bjoc.15.247

• analogues were prepared in moderate overall yields and did not show toxic effects on Staphylococcus aureus growth and were not toxic to human fibroblasts. Two of them inhibited the hemolytic activity of S. aureus, suggesting an interfering action in the bacterial quorum sensing similar to the one already

• , methicillin-resistant S. aureus (MRSA) is considered an endemic cause of nosocomial infections and has spread into the community and livestock animals as well [8]. Expression of many S. aureus virulence factors is controlled by a sophisticated intercellular chemical signalling pathway named quorum-sensing (QS

• exert an effect on S. aureus quorum sensing. To evaluate this hypothesis, we are now rationally designing new solonamide analogues, based on the SN2’ strategy reported here, to be tested for AgrC-inhibitory activity. Chemical structure of solonamides and autoinducing peptides (AIP). Effect of compounds

Formation of alkyne-bridged ferrocenophanes using ring-closing alkyne metathesis on 1,1’-diacetylenic ferrocenes

• Celine Bittner,
• Dirk Bockfeld and
• Matthias Tamm

Beilstein J. Org. Chem. 2019, 15, 2534–2543, doi:10.3762/bjoc.15.246

• sensing. ORTEP diagram of 1a with thermal displacement parameters drawn at 50% probability; hydrogen atoms are omitted for clarity; occupation Fe 74%, Fe’ 26%. Selected bond lengths [Å] and angles [°]: Fe–Ct1 1.6947(12), Fe-Ct11 1.6695(12), Ct1-Fe-Ct11 176.96(8), C9–C10 1.186(11), C8–C9–C10 177.2(9), C19

Targeted photoswitchable imaging of intracellular glutathione by a photochromic glycosheet sensor

• Xianzhi Chai,
• Hai-Hao Han,
• Yi Zang,
• Jia Li,
• Xiao-Peng He,
• Junji Zhang and
• He Tian

Beilstein J. Org. Chem. 2019, 15, 2380–2389, doi:10.3762/bjoc.15.230

• signals has been developed, aiming at reducing interferences and improving sensing precision in complex physiological environments [9][10][11][12][13][14][15][16][17]. This photoresponsive design presents several advantages over conventional probes: 1) The light-activation mode endows the probe with light

• precise outputs can be obtained for targeted analytes even at low concentrations. Though promising, common “photochromophore–fluorophore”-type sensors require elaborate designs to integrate multifunctionality (e.g., photoswitching, fluorescence sensing, targetability, water solubility, etc.) into one

• , indicating the successful coating of MnO2 nanosheets with the Glyco-DTE reporter [25]. An increasing Zeta potential was also observed after the assembly, confirming again the successful fabrication of Glyco-DTE@MnO2 glycosheet (Figure 2D) [26]. GSH sensing and fluorescence photoswitching of Glyco-DTE@MnO2

1,2,3-Triazolium macrocycles in supramolecular chemistry

• Mastaneh Safarnejad Shad,
• Pulikkal Veettil Santhini and
• Wim Dehaen

Beilstein J. Org. Chem. 2019, 15, 2142–2155, doi:10.3762/bjoc.15.211

• have led to applications in molecular recognition, sensing, molecular machines and devices, supramolecular polymers, stimuli-responsive materials, supramolecular catalysis and drug-delivery systems [4][5][6][7]. Inspired by the attractive role of various N-heterocyclic building blocks such as

• results in the sensing of anions. In fact, strictly speaking this interaction is not a hydrogen bonding interaction seen as there is no X···H–Y unit (X, Y = O, N, F) but these interactions are often referred to as such in the literature. The anion binding can be enhanced by the alkylation of 1,2,3

• selectivity of this receptor for chloride anion is due to the cavity size (see Figure 3) [37]. 2.2. Optical anion sensing by 1,2,3-triazolium macrocycles within porphyrin cages Various porphyrin-based host supramolecules containing hydrogen-bond donor groups such as integrated amide, urea, pyrrole, ammonium