Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• polynucleotide secondary structure. Concurrently, no monomer fluorescence signal at 400 nm changed, except a small increase upon poly dGdC–poly dGdC addition. Negligible thermal stabilization (Table S1, Figures S6–S8, Supporting Information File 1) did not support the classical intercalation of phenanthridine

• and probability of contact, including steric shielding and charge–charge interactions [41]. Circular dichroism (CD) experiments CD spectroscopy was chosen to monitor conformational changes of polynucleotide's secondary structure induced by small molecule binding [42]. Compounds Phen-Py-1 and Phen-Py-2

First series of N-alkylamino peptoid homooligomers: solution phase synthesis and conformational investigation

• Maxime Pypec,
• Laurent Jouffret,
• Claude Taillefumier and
• Olivier Roy

Beilstein J. Org. Chem. 2022, 18, 845–854, doi:10.3762/bjoc.18.85

• form a unique sheet-like secondary structure, whereas molecular modeling showed that N-aryl peptoid oligomers composed of monomers in the same conformation (as observed in the crystal of dimer 2) might adopt right or left-handed helical conformations that resemble the polyproline type II helix. The χ1

Peptide stapling by late-stage Suzuki–Miyaura cross-coupling

• Hendrik Gruß,
• Rebecca C. Feiner,
• Ridhiwan Mseya,
• David C. Schröder,
• Michał Jewgiński,
• Kristian M. Müller,
• Rafał Latajka,
• Antoine Marion and
• Norbert Sewald

Beilstein J. Org. Chem. 2022, 18, 1–12, doi:10.3762/bjoc.18.1

• stapling techniques to stabilise α-helical secondary structure motifs of peptides led to the design of modulators of protein–protein interactions, which had been considered undruggable for a long time. We disclose a novel approach towards peptide stapling utilising macrocyclisation by late-stage Suzuki

• additional ethylene unit in the linker suggested a conformation with the highest similarity to the linear reference peptide P6 (see Supporting Information File 1), thus representing a good compromise between rigidity and preservation of the target secondary structure. Serine in i-position and glutamic acid

• assignment based on other experimental observables, namely, the flexibility of the overall peptide and its propensity to form a helical secondary structure. We then proceed to analyse the effect of the staple and sequence variations on the secondary structure of the peptidic backbone of aAxWt, P5, and P6

Progress and challenges in the synthesis of sequence controlled polysaccharides

• Giulio Fittolani,
• Theodore Tyrikos-Ergas,
• Denisa Vargová,
• Manishkumar A. Chaube and
• Martina Delbianco

Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129

• ]. The replacement of a single Glc unit with a Man unit was sufficient to disrupt this secondary structure and significantly increased the isolated yield of the final compounds. Molecular dynamic (MD) simulations predicted a compact helical conformation for the fully deprotected compound, confirmed by

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

• essentially derived from alanine, leading to the α-helix-dominated protein world as we know it [22]. For this reason, most amino acids in proteins can be exchanged for alanine by point mutations while leaving the secondary structure intact. In molecular biology, the alanine scanning method takes advantage of

• the fact that alanine mimics the secondary structure preferences of most proteinogenic amino acids, allowing the relative importance of each side chain for the biological function to be determined [23]. Classical X-ray crystallography also employs the polyalanine model for backbone chain tracing to

• , which exhibits a distinct conformational profile [24]. These are the general reasons why proline is poorly compatible with regular α-helical and β-sheet structure architectures, which are typical for the polyalanine backbone. Consequently, proline often identifies secondary structure breaks in protein

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

• estrogen receptor (ER) co-activator peptides and enabled the sensitive detection of their protein–peptide interaction inhibition by the ER antagonist tamoxifen [20]. Significantly, different secondary structure conformational preferences were also found among the diastereomers of perfluoro-tert

• ionization and ion mobility), CD spectroscopy and atomic force microscopy, the authors were able to obtain detailed information about the size and secondary structure associated with some of the soluble intermediates. These included: large β-sheet oligomers formed immediately after solubilization (oligomer

• and represent a distinct class of proteins that exhibit no stable 3D structure [72]. It is broadly understood that, unlike folded proteins, IDPs exist as an average combination of interconverting conformers. However, when bound to a substrate, IDPs may acquire a defined secondary structure [73]. The

Supramolecular polymerization of sulfated dendritic peptide amphiphiles into multivalent L-selectin binders

• David Straßburger,
• Svenja Herziger,
• Katharina Huth,
• Moritz Urschbach,
• Rainer Haag and
• Pol Besenius

Beilstein J. Org. Chem. 2021, 17, 97–104, doi:10.3762/bjoc.17.10

• polymerization strongly relies on the formation of secondary structure elements, leading to ordered domains that lead to characteristic CD band spectra. By probing aqueous solutions of I at different concentrations in H2O, a strongly negative CD band at around λ ≈ 220 nm became apparent (Figure 1A). In the past

• by the secondary structure formation (Figure 1). All samples for convential TEM imaging were prepared by placing 5 μL of the aqueous solution on a sample grid for 1 min, followed by the removal of the excess liquid using a filter paper and subsequent negative staining using a 2% uranyl acetate

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• secondary structure, chain B is represented in cartoon and colored by secondary structure. The mucin peptide is represented as licorice. The Tn glycan (N-acetylgalactosamine) is represented as licorice, and the sugar ring is highlighted with the paper chain representation [18][19]. A comparison of root mean

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

• balanced ratio of GC-(48%) and AT-(52%) base pairs, as well as synthetic alternating polynucleotide poly(dAdT)2 with also B-helix structure but with a fully available minor groove for small molecule binding. As alternative we used poly(dGdC)2 differing significantly in the secondary structure as well as in

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

• cations and water molecules from the DNA/RNA grooves [44][45] by side arms interacting with the grooves and thereby supporting the binding. Circular dichroism experiments CD spectroscopy is an ideal method to get insight into the changes of the polynucleotide secondary structure upon binding of small

• longer axes, thus yielding negligible intensity of ICD bands [49][50]. Such different sets of ICD band responses, which varied not only with respect to differences in the dye structure but also depended strongly on the DNA/RNA secondary structure revealed a high sensitivity of the studied NDI

• and secondary structure. Thus, reference 5 with three permanently charged aliphatic sidechains was non-selective, giving virtually the same fluorimetric and CD response for all DNA/RNA. In contrast, the introduction of amino acid side chains in 3a and 3b yielded selective fluorimetric responses

pH- and concentration-dependent supramolecular self-assembly of a naturally occurring octapeptide

• Goutam Ghosh and
• Gustavo Fernández

Beilstein J. Org. Chem. 2020, 16, 2017–2025, doi:10.3762/bjoc.16.168

• development of novel drug nanocarrier assemblies. Keywords: aqueous self-assembly; pH-responsive systems; secondary structure; self-assembled nanostructures; solid-phase peptide synthesis; Introduction The self-assembly of small molecules is a ubiquitous phenomenon in nature [1] and also has key

• of the peptide (Figure S2, Supporting Information File 1). The identity of the peptide was confirmed by MALDI–TOF mass spectrometry (Figure S3, Supporting Information File 1). The yield of the purified PEP-1 was 42%. Self-assembly and secondary-structure formation CD, FTIR spectroscopy, and ThT

• (pH 5.5 and 2.2) and basic (pH 13.0 and 10.3) media. The pH-dependent CD spectra of PEP-1 revealed that the β-sheet secondary structure completely dissociates upon altering the pH from 7.4 to 5.5 (Figure 3a, red spectrum), which can be explained by strong electrostatic repulsions involving Arg

Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines

• Vladimir Kubyshkin

Beilstein J. Org. Chem. 2020, 16, 1837–1852, doi:10.3762/bjoc.16.151

• ambivalent and mainly depends on the underlying secondary structure. The lack of a polar N–H bond in peptidyl-prolyl can decrease the polarity in one case, and increase in another. The first scenario may occur if a free N–H bond would otherwise be exposed to the solvent. Proline lacks an N–H bond, thus the

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

• aptamer module. This solves a problem of secondary structure in hybridization with the target sequence of full-length mRNA. It was shown that within 24 hours the proposed sensor specifically recognized both a synthetic 60-nucleotide RNA fragment (LOD is 1.4 nM of RNA fragment at 37 °C) and a full-sized

• 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

• secondary structure of RNA targets, which complicates the interaction with the biosensor and impedes their widespread use. Another advantage of our sensor is the ability to easily change different oligonucleotide sequences depending on the experimental design. Since the construct is assembled by the

Current understanding and biotechnological application of the bacterial diterpene synthase CotB2

• Ronja Driller,
• Daniel Garbe,
• Norbert Mehlmer,
• Monika Fuchs,
• Keren Raz,
• Dan Thomas Major,
• Thomas Brück and
• Bernhard Loll

Beilstein J. Org. Chem. 2019, 15, 2355–2368, doi:10.3762/bjoc.15.228

• lines. Mg2+ ions are colored in green. Black arrows indicate movement of secondary structure elements from the open to the closed conformation of CotB2. The different C-termini are labeled in all three structures. The C-terminus in the structure of CotB2wt·Mg2+3·F-Dola is colored in purple. View into

Molecular basis for the plasticity of aromatic prenyltransferases in hapalindole biosynthesis

• Takayoshi Awakawa and
• Ikuro Abe

Beilstein J. Org. Chem. 2019, 15, 1545–1551, doi:10.3762/bjoc.15.157

• amino acid sequence alignment of AmbP1, AmbP3, and other ABBA PTases, visualized by ESPript3 [34]. Secondary structure elements: α, α-helices; β, β-strands; η, 310-helices; TT, strict β-turns. The red frames indicate amino acids that anchor pyrophosphate, the blue frames indicate the residues that

Lectins of Mycobacterium tuberculosis – rarely studied proteins

• Katharina Kolbe,
• Sri Kumar Veleti,
• Norbert Reiling and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2019, 15, 1–15, doi:10.3762/bjoc.15.1

• mannose-specific C-type lectins from Caenorhabditis elegans, Mus musculus, and Homo sapiens (see Figure 5 for partial secondary structure prediction and alignment with the human C-type mannose receptor 2) [77][78], and is predicted to be localized to the outer membrane [93]. While Rv2075c orthologues have

• have been found in glycosyltransferases as well as in bacterial hydrolases [95]. The Mtb gene product of Rv1419 shows 41% amino acid sequence similarity to R-type lectins and encodes the Mtb protein sMTL-13 (see Figure 5 for secondary structure prediction and alignment with the ricin B-like lectin from

• Salmonella species [114][115], but lack primary sequence homology and the typical β-sheet secondary structure of curli pili from these latter species [108][116]. The mtp gene is present in all strains of the Mtb complex (MTBC), but absent in non-tuberculosis mycobacteria and other respiratory pathogens [117

Defining the hydrophobic interactions that drive competence stimulating peptide (CSP)-ComD binding in Streptococcus pneumoniae

• Bimal Koirala,
• Robert A. Hillman,
• Erin K. Tiwold,
• Michael A. Bertucci and
• Yftah Tal-Gan

Beilstein J. Org. Chem. 2018, 14, 1769–1777, doi:10.3762/bjoc.14.151

• correction for end effects (2.5) [32]. Secondary structure contents were also calculated using the BeStSel (beta structure selection) method (http://bestsel.elte.hu/) [33]. The competence regulon QS circuitry in S. pneumoniae. ComC is processed and secreted by ComAB as the mature CSP signal. Upon reaching a

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

• initial study for the delivery of the anticancer drug doxorubicin. Results and Discussion Peptide synthesis and analysis of the secondary structure We chose two different nuclear-targeting sequences, on the one hand the N50 peptide, which was derived from the NF-κB/p50 subunit. N50 binds the adaptor

• –S4 (Supporting Information File 1), all peptides could be successfully synthesized in high purities. First, we performed a structural analysis by diluting all peptides to a concentration of 20 μM in phosphate buffer (pH 7.0), with or without the presence of the secondary structure inducing solvent

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

Synthesis and in vitro biochemical evaluation of oxime bond-linked daunorubicin–GnRH-III conjugates developed for targeted drug delivery

• Sabine Schuster,
• Beáta Biri-Kovács,
• Bálint Szeder,
• Viktor Farkas,
• László Buday,
• Zsuzsanna Szabó,
• Gábor Halmos and
• Gábor Mező

Beilstein J. Org. Chem. 2018, 14, 756–771, doi:10.3762/bjoc.14.64

• formaldehyde (e.g., from the softeners of the plastic tubes) not only during the reaction steps (cleavage, ligation) but also under the HPLC purification conditions which has a high impact on the yield [35]. Secondary structure determination by electronic circular dichroism spectroscopy ECD spectra of GnRH-III

• shifted to 235 nm. The Dau has also a negative band at 200 nm. The only difference between the D-Asp derivatives and the original peptides is located near 215 nm. This sign indicates the presence of increased contribution of β-sheet like secondary structure in case of D-Asp derivatives. Because no

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

• due to the conversion of TBANB into TBA. The modulation of the secondary structure transition of an ON in a reduction-responsive manner appears to be beneficial to understand biomolecule behavior and biological phenomena. Esterase-responsive ONs Modifications at the internucleotide linkage: The use of

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 wavelength range where DNA and RNA absorb light (λ = 200–300 nm) and thus possess intrinsic spectra. Changes in the intrinsic spectral properties of DNA or RNA can often be correlated to a specific change in the secondary structure of the polynucleotide (see chapter 2.1.). However, if a ligand’s

• adequately prepared and characterized. For that reason, a short description of the most important issues in sample preparation is summarized in chapters 2.2 and 2.3. 2.1. Relation between DNA or RNA secondary structure and polarization spectroscopy Nucleobases are achiral but nucleoside and nucleotide

• mechanism between the various π→π* transitions of regularly arranged chromophores [14] (Figure 3, top). Chiroptical properties and ECD spectra of particular DNA or RNA sequences are therefore strongly dependent on the polynucleotide secondary structure [15], at variance to the common UV–vis spectra of the

Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion

• Susanne Huhmann,
• Anne-Katrin Stegemann,
• Kristin Folmert,
• Damian Klemczak,
• Johann Moschner,
• Michelle Kube and
• Beate Koksch

Beilstein J. Org. Chem. 2017, 13, 2869–2882, doi:10.3762/bjoc.13.279

• fluorinated GLP-1 analogues displayed higher proteolytic stability against this enzyme [27]. Usually, the enhanced proteolytic stability of fluorinated peptides is explained by their greater hydrophobicity and altered secondary structure compared to the parent, non-fluorinated peptide. A further reason is the

Recent progress in the racemic and enantioselective synthesis of monofluoroalkene-based dipeptide isosteres

• Myriam Drouin and
• Jean-François Paquin

Beilstein J. Org. Chem. 2017, 13, 2637–2658, doi:10.3762/bjoc.13.262

• important for the activity (Table 6). Conformational studies of the fluorinated peptide using circular dichroism also showed that the incorporation of the monofluoroalkene did not perturb the formation of the secondary structure of the peptide, which was a α-helix. Dory and co-workers wanted to study the

Homologated amino acids with three vicinal fluorines positioned along the backbone: development of a stereoselective synthesis

• Raju Cheerlavancha,
• Ahmed Ahmed,
• Yun Cheuk Leung,
• Aggie Lawer,
• Qing-Quan Liu,
• Marina Cagnes,
• Hee-Chan Jang,
• Xiang-Guo Hu and
• Luke Hunter

Beilstein J. Org. Chem. 2017, 13, 2316–2325, doi:10.3762/bjoc.13.228

• affect the secondary structure of peptides within which they are contained, with consequent implications for the peptides’ biological potency and selectivity [1]. A more subtle example of this concept is provided by the amino acid β-methylphenylalanine (2), which exerts conformational bias through