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Search for "PNA" in Full Text gives 34 result(s) in Beilstein Journal of Organic Chemistry.
Dipeptide analogues of fluorinated aminophosphonic acid sodium salts as moderate competitive inhibitors of cathepsin C
Beilstein J. Org. Chem. 2023, 19, 434–439, doi:10.3762/bjoc.19.33
- of more effective fluorinated inhibitors of cathepsin C in our laboratory. Dixon plot for the hydrolysis of Gly-Phe-pNA substrate catalyzed by bovine cathepsin C in the presence of 9b (T = 37 °C, pH 5.0). Synthetic strategy towards 5 and 7. Synthesis of 9 and 11. (a) R = -CH3; (b) R = -CH(CH3)2; (c
Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications
Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116
- /bjoc.17.116 Abstract Peptide nucleic acid (PNA) is arguably one of the most successful DNA mimics, despite a most dramatic departure from the native structure of DNA. The present review summarizes 30 years of research on PNA’s chemistry, optimization of structure and function, applications as probes
- and diagnostics, and attempts to develop new PNA therapeutics. The discussion starts with a brief review of PNA’s binding modes and structural features, followed by the most impactful chemical modifications, PNA enabled assays and diagnostics, and discussion of the current state of development of PNA
- therapeutics. While many modifications have improved on PNA’s binding affinity and specificity, solubility and other biophysical properties, the original PNA is still most frequently used in diagnostic and other in vitro applications. Development of therapeutics and other in vivo applications of PNA has
A recent overview on the synthesis of 1,4,5-trisubstituted 1,2,3-triazoles
Beilstein J. Org. Chem. 2021, 17, 1600–1628, doi:10.3762/bjoc.17.114
- via intramolecular cyclization reaction of ketones 31, p-nitrophenyl azide (PNA, 32) and amino esters 33 has been described by Dehaen et al. The products were often obtained in good yield and in all cases with the retention of the configuration of the stereocenter. The reaction was carried out by
Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications
Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76
- arguably the most radical alternative nucleic acid pairing system, peptide nucleic acid (PNA), the sugar-phosphate backbone is replaced by an amide-based, neutral and achiral scaffold that allows cross-pairing with both DNA and RNA as well as formation of double- and triple-stranded species [57]. Despite
DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies
Beilstein J. Org. Chem. 2021, 17, 749–761, doi:10.3762/bjoc.17.65
- of natural ONs, such as peptide nucleic acids (PNA) [20], locked nucleic acids [21] (LNA, also known as bridged nucleic acids (BNA) [22]) and phosphorothioate (PS) ONs [23][24] have been evaluated for antigene/antisense applications, however, each of the analogues did not meet all the requirements
- . For example, both PNA and modified PNAs have excellent chemical stability, are resistant to enzymatic degradation, and have high binding affinity towards complementary DNA and RNA, but have a tendency to aggregate, require high salt conditions, and have low solubility in water [1][25][26]. LNA (BNA
- charged backbone also improved the binding of PNA to DNA or RNA strands. It has been shown that positively charged PNA bind more strongly to DNA and RNA than negatively charged PNA at low salt concentrations (0–100 mM Na+) whereas at medium to high salt concentrations (250–1000 mM Na+) the trend is
Photocontrolled DNA minor groove interactions of imidazole/pyrrole polyamides
Beilstein J. Org. Chem. 2020, 16, 60–70, doi:10.3762/bjoc.16.8
- major groove recognition [21][22]. Woolley et al. reported other photoisomerizable Tf mimetics that interacted through the major groove [23][24]. Hybridization of DNA [25][26][27] or PNA/DNA [28] can be light-controlled by azobenzene-modified DNA. While DNA covalently modified with azobenzene moieties
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
- tetra-ortho-fluoroazobenzene–PNA conjugates have promising properties (fast reversible isomerization, exceptional thermal stability, high isomer conversions and sensitivity to visible-light irradiation) as reversible modulators to control oligonucleotide hybridization in biological contexts. Furthermore
- , we verified that this switchable modification delivers a slightly different hybridization behavior in the PNA. Thus, both melting experiments and strand-displacement assays showed that in all the cases the trans-isomer is the one with superior binding affinities. Alternative versions, inspired by our
- first compounds here reported, may find applications in different fields such as chemical biology, nanotechnology and materials science. Keywords: azobenzene; hemithioindigo; peptide nucleic acid (PNA); photoswitch; visible-light irradiation; Introduction Light-driven control of oligonucleotide
Targeted photoswitchable imaging of intracellular glutathione by a photochromic glycosheet sensor
Beilstein J. Org. Chem. 2019, 15, 2380–2389, doi:10.3762/bjoc.15.230
- cell lines, endowing our hybrid sensor with specific cell target ability [35]. The cytoselectivity of the Glyco-DTE reporter was firstly checked in PBS buffer through lectin binding experiments. The lectin used here, peanut agglutinin (PNA), can selectively bind with β-ᴅ-galactoside that mimics the
- role of ASGPr on HepG2 cell membranes [36][37]. As shown in Figure S4 (Supporting Information File 1), the addition of PNA to the solution of Glyco-DTE resulted in a fluorescence enhancement with an obvious spectral blue-shift, while the addition of another lectin, conconavalin A (Con A), did not cause
- a substantial variation of the fluorescence spectra. For control reporter 8o, either the addition of PNA or Con A led to minute changes in the emission spectra. The phenomena described above solidly proved the cell target ability of the β-ᴅ-galactoside moiety of the Glyco-DTE reporter. In the next
Selectivity in multiple multicomponent reactions: types and synthetic applications
Beilstein J. Org. Chem. 2019, 15, 521–534, doi:10.3762/bjoc.15.46
- illustrate a repetitive Ugi 4CR-deprotection-Ugi 4CR protocol to obtain peptide nucleic acid (PNA) oligomers (Scheme 13A) [49], peptidic tetrazoles and hydantoinimides (Scheme 13B) [50], respectively. Incidentally, the later processes take place in solid phase, which enhances their synthetic suitability. The
- sequence. High order MMCRs. A) Ugi/Ugi–Smiles 7C combination; B) imidazoline-N-cyanomethylamide-Ugi union leading to an 8CR. Consecutive Ugi 4CR-deprotection–Ugi 4CR strategy towards A) PNA oligomers and B) peptidic tetrazoles and hydantionimides. Sequential Ugi 4CR-deprotection access to cyclopeptoids
Synthesis of new p-tert-butylcalix[4]arene-based polyammonium triazolyl amphiphiles and their binding with nucleoside phosphates
Beilstein J. Org. Chem. 2018, 14, 1980–1993, doi:10.3762/bjoc.14.173
- or DMSO-d6) as internal standard. MALDI mass spectra were measured on an UltraFlex III TOF/TOF with PNA matrix, laser Nd:YAG, λ = 355 nm. The IR spectra were recorded on a Bruker Vector-22 spectrometer. Samples were prepared as suspension in mineral oil or as thin films, obtained from chloroform
Oligonucleotide analogues with cationic backbone linkages
Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111
- 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
Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing
Beilstein J. Org. Chem. 2018, 14, 436–469, doi:10.3762/bjoc.14.32
- nucleic acids (PNAs), a lipophilic triphenylphosphonium (TPP) cation was attached to the N-terminal extremity of a PNA through a biodegradable carbamate linker containing a disulfide bridge (Scheme 4B) [20]. It was shown that such PNA conjugates entered cells rapidly and efficiently. Furthermore, a 16-mer
Fluorogenic PNA probes
Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17
- attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical
- and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce
- 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
Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications
Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7
- ]. The tricyclic core was synthesized as reported by Roth et al., and subsequently functionalized with a carboxylic acid handle for PNA labeling [39]. In 2003, tC [35] was synthesized bearing a 2´-deoxyribose functionality and thoroughly photophysically characterized (vide infra). tC was later
Halogen-containing thiazole orange analogues – new fluorogenic DNA stains
Beilstein J. Org. Chem. 2017, 13, 2902–2914, doi:10.3762/bjoc.13.283
- been conjugated to a variety of molecules, including peptides [29], proteins [30], DNA [17], and DNA analogues such as peptide nucleic acid (PNA) [16][31]. TO-based chromophores assembled as a structural scaffold inside nucleic acids (TO-tethered nucleic acids) have attracted considerable attention [32
- ]. Hybridization-sensitive fluorescent probes in which TO is tethered to a nucleic acid: DNA [22][23][33][34][35][36], RNA [20][36] or PNA [18][19][21][31]) strands have been constructed by several research groups (the Krull, Kubista, Seitz and Wagenknecht groups). The continued scientific and commercial interest
Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies
Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249
- [4], pyrene-modified peptide nucleic acids (PNA) [5], locked nucleic acids (LNA) [6][7], invader LNA [8], and twisted intercalating nucleic acids (TINA) [9]. Furthermore pyrene-modified nucleotides have been used for the construction of DNA-based multichromophore systems [10][11][12][13], as cancer
Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models
Beilstein J. Org. Chem. 2017, 13, 2442–2457, doi:10.3762/bjoc.13.241
- measurements can be used to study ligand–protein [12] and protein–protein interactions [13]; membrane proteins [14][15][16] and membrane-associated peptides [17][18]; equilibria among conformations of RNA [19], DNA [20], and peptide nucleic acids (PNA) [21]; and many others. Particularly recent is the
Glyco-gold nanoparticles: synthesis and applications
Beilstein J. Org. Chem. 2017, 13, 1008–1021, doi:10.3762/bjoc.13.100
- and purify proteins by covalent crosslinking (Figure 5). GAuNPs were synthesized by coating the metal surface via thio-chemistry with a β-D-lactose residue (recognized by a series of lectins, i.e., PNA or Ricinus communis agglutinin) and a benzophenone moiety as photoreactive group. GAuNPs were
- treated with PNA which cross-linked with the photoreactive group, affording a PNA-AuNPs complex. The latter was easily purified by the non-interacting protein via centrifugation and, eventually, the protein was quantified after an appropriate cleavage with 2-mercaptoethanol. A very recent and interesting
- showed that GAuNPs were still able to recognize specific lectin (peanut agglutinin, PNA) and human galectin-3 (Gal-3), exploiting multiple lactose residues displayed on gold surface. Moreover, due to the presence of the β-cyclodextrin cavity, these nanostructures worked as site-specific delivery systems
Synthesis of multi-lactose-appended β-cyclodextrin and its cholesterol-lowering effects in Niemann–Pick type C disease-like HepG2 cells
Beilstein J. Org. Chem. 2017, 13, 10–18, doi:10.3762/bjoc.13.2
- -Lac-β-CD (DSL5.6) for 24 h. Interaction between multi-Lac-β-CD (DSL5.6) and peanut agglutinin We initially attempted to clarify the role of the lactose moieties in multi-Lac-β-CD for binding to ASGPR by determining the dissociation constant of multi-Lac-β-CD (DSL5.6) with peanut agglutinin (PNA), a
- response in the frequency of detection unit of QCM, thus indicating a negligible interaction with PNA (Figure 4B). Hence, the data indicated specific galactose-binding ability of multi-Lac-β-CD (DSL5.6). Intracellular distribution of TRITC-multi-Lac-β-CD (DSL5.6) Next, to investigate whether multi-Lac-β-CD
- [15][16]. Therefore, the binding affinity of multi-Lac-β-CD (DSL5.6) to ASGPR is likely to be much higher than that of mono-Lac-β-CD. In fact, multi-Lac-β-CD (DSL5.6) has a quite low dissociation constant (2.6 × 10−8 M) with PNA, probably a result of its clustering effect in ASGPR recognition. The
DNA functionalization by dynamic chemistry
Beilstein J. Org. Chem. 2016, 12, 2136–2144, doi:10.3762/bjoc.12.203
- analogue with a peptide backbone carrying nucleobases on its amino acid side chains [42] while Bradley et al. used the backbone of a peptide nucleic acid (PNA) with abasic sites which gives a reactive secondary amine for reversible attachment of aldehyde modified nucleobases [43]. Moreover, the DNA
Synthesis and NMR studies of malonyl-linked glycoconjugates of N-(2-aminoethyl)glycine. Building blocks for the construction of combinatorial glycopeptide libraries
Beilstein J. Org. Chem. 2016, 12, 1939–1948, doi:10.3762/bjoc.12.183
- Markus Norrlinger Sven Hafner Thomas Ziegler Institute of Organic Chemistry, University of Tuebingen, Auf der Morgenstelle 18, 72076 Tuebingen, Germany 10.3762/bjoc.12.183 Abstract Four glycoconjugate building blocks for the construction of combinatorial PNA like glycopeptide libraries were
- ligand are highly desirable [10][11][12][13]. In our previous work we introduced various trifunctional glycopeptide building blocks derived from aspartic acid, 3-aminomethyl-5-aminobenzoic acid [14] and from the PNA-like N-(2-aminoethyl)glycine (AEG) backbone to which sugar moieties were linked through
- these studies, we now describe the preparation of PNA-based glycoconjugate building blocks 1–3 as well as a dimeric glycoconjugate 4 in which the sugar moieties are attached through a malonyl linker (Figures 1–3). For these compounds we studied the cis/trans-rotameric structures via temperature
DNA display of glycoconjugates to emulate oligomeric interactions of glycans
Beilstein J. Org. Chem. 2015, 11, 707–719, doi:10.3762/bjoc.11.81
- sequence dependent and not uniquely due to the high glycosylation of the DNAs. The tertiary structure of the glycan conjugates predisposed the ligands productively thus resulting in a high affinity. A variation of this strategy using mRNA also yielded peptidoglycans with high affinity to 2G12 [33]. DNA–PNA
- glycosylated hybrids As an alternative to DNA, peptide nucleic acid (PNA) [34] has also been used to tag glycans and to program their assembly based on the rules of hybridization. From an assembly standpoint, stable PNA–DNA duplexes can be achieved with shorter sequences than the corresponding DNA homoduplex
- (10–14mer PNA typically provides sufficient duplex stability) [35]. From a chemistry standpoint, the fact that PNA synthesis involves peptide coupling reactions with a broad arsenal of protecting group combinations facilitates the introduction of functionalities for the conjugation of glycans [36
Sequence-specific RNA cleavage by PNA conjugates of the metal-free artificial ribonuclease tris(2-aminobenzimidazole)
Beilstein J. Org. Chem. 2015, 11, 493–498, doi:10.3762/bjoc.11.55
- acids (PNA). RNA degradation occurs with similar rates and substrate specificities as in experiments with DNA conjugates we performed earlier. Although aggregation phenomena are observed in some cases, proper substrate recognition is not compromised. While our previous synthesis of 2-aminobenzimidazoles
- of RNA cleavers to oligonucleotide analogues such as peptide nucleic acids (PNA) [4]. The benefits of oligonucleotide analogues are higher affinity towards RNA [5] as well as improved resistance against biodegradation [6]. Furthermore, PNA can be applied to block miRNA functions in cell culture
- experiments [7]. PNA conjugates of both metal-containing and metal-free RNA cleavers have been effectively used as artificial nucleases towards different substrates [8][9][10][11]. Most notable is a copper-based PNAzyme which cleaves RNA site-specifically with substrate half-lifes as low as 30 minutes [12]. A
NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A–T phosphoramidite building blocks
Beilstein J. Org. Chem. 2015, 11, 50–60, doi:10.3762/bjoc.11.8
- manipulate the charge pattern in the backbone and to enhance nuclease stability. The electroneutral nucleic acid mimic 'peptide nucleic acid' (PNA) [10][11][12] is capable of sequence-specific binding to nucleic acids, but it was found to display limited water solubility and a peptide-like folding behaviour
Synthesis of aromatic glycoconjugates. Building blocks for the construction of combinatorial glycopeptide libraries
Beilstein J. Org. Chem. 2014, 10, 2453–2460, doi:10.3762/bjoc.10.256
- focus was on glycosylated amino acid building blocks derived from aspartic acid and from the PNA-like N-(2-aminoethyl)glycine (AEG) backbone to which the sugar moieties were attached through either simple alkyl chains [5][6], amino alcohols [7][8] or 1,2,3-triazoles [9][10][11]. These building blocks
- usefulness for the preparation of corresponding glycosylated or non-glycosylated dipeptides. The benzoic acid derived building blocks described here will be used in combination with previously described similar glycopeptoids based on asparaginic acid or PNA-like backbones for automated SPOT syntheses of
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