Search results
Search for "nucleic acid" in Full Text gives 83 result(s) in Beilstein Journal of Organic Chemistry.
Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme
Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40
- as a function of temperature. The absorbance scale was normalized. Tm values were the midpoints of the transition curves determined from the maximum of the first derivative and checked graphically by the tangent method. The ΔTm values were calculated subtracting Tm of the free nucleic acid from Tm of
Structural basis for endoperoxide-forming oxygenases
Beilstein J. Org. Chem. 2022, 18, 707–721, doi:10.3762/bjoc.18.71
- that play important roles in antimalarial activity by damaging membranes, inhibiting nucleic acid and protein syntheses, and so on [8][9]. The best studied endoperoxide-containing compound is probably prostaglandin H2 (PGH2), the common precursor of biologically active prostanoids [10][11][12
Synthetic strategies toward 1,3-oxathiolane nucleoside analogues
Beilstein J. Org. Chem. 2021, 17, 2680–2715, doi:10.3762/bjoc.17.182
- nucleic acid components. Therefore, it was assumed until recently that effective inhibition of the metabolic enzyme is only possible by ᴅ-nucleoside analogues, which have the stereochemistry of natural nucleosides. This was proved to be untrue when the antiviral activity of 1,3-oxathiolane nucleosides
Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides
Beilstein J. Org. Chem. 2021, 17, 1828–1848, doi:10.3762/bjoc.17.125
- endogenous nucleic acid targets, thereby inhibiting the gene expression. Although ASOs have great potential in the treatment of many diseases, the search for favorable toxicity profiles and distribution has been challenging and consequently impeded the widespread use of ASOs as conventional medicine. One
- nuclease resistance, increased binding to the nucleic acid target and improved cell uptake for oligonucleotides (ONs) and ASOs. The modifications highlighted in this review are some of the most prevalent cationic amine groups which have been attached as single modifications onto ONs/ASOs. The review has
- negatively charged phosphorus-based linkages. ASOs have the distinctive ability to bind endogenous nucleic acid targets in a sequence-specific manner, thereby inhibiting gene expression and offering opportunities for the treatment of a broad range of diseases. As ASOs interact with their RNA (or DNA) targets
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
- for innovative chemistry and biology to unlock the full potential of PNA in biomedical applications. Keywords: antisense; chemical modifications; diagnostics; peptide nucleic acid; PNA; Introduction Peptide nucleic acid (PNA) is a DNA mimic where the sugar–phosphate backbone of DNA is replaced with
- replaced by an achiral and neutral pseudopeptide backbone having the same number of atoms [2][3]. It is remarkable that this simple design resulted in a nucleic acid analogue that had the right degree of flexibility and favorable conformational properties, enforced by the rotational preferences around
Double-headed nucleosides: Synthesis and applications
Beilstein J. Org. Chem. 2021, 17, 1392–1439, doi:10.3762/bjoc.17.98
- , Bose Institute, P1/12 CIT Scheme VIIM, Kolkata-700 054, India 10.3762/bjoc.17.98 Abstract Double-headed nucleoside monomers have immense applications for studying secondary nucleic acid structures. They are also well-known as antimicrobial agents. This review article accounts for the synthetic
- showed a moderate cytostatic activity against human cervix carcinoma HeLa cells [37]. It is pertinent to mention that Sharma et al. [29] have reviewed the double-headed nucleotides in the recent past with a focus on their effects in nucleic acid duplexes and other secondary structures. Herein, we focused
- phosphitylation at the secondary hydroxy group afforded the double-headed nucleoside monomer 19 (Scheme 5) [45]. The synthesized double-headed nucleoside 19 was introduced in oligonucleotides and its impact on the secondary nucleic acid structure was studied. It was revealed that the double-headed nucleoside 19
A new glance at the chemosphere of macroalgal–bacterial interactions: In situ profiling of metabolites in symbiosis by mass spectrometry
Beilstein J. Org. Chem. 2021, 17, 1313–1322, doi:10.3762/bjoc.17.91
- conditions or with bacterial symbionts Roseovarius sp. MS2 and Maribacter sp. MS6. a) Images acquired after nucleic acid staining with SYBR gold and with confocal laser scanning microscopy. The protrusion of alga grown without bacterial symbiont is highlighted (red arrow). DIC: differential interference
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
- group between the sugars in DNA and RNA is at the origin of the vastly expanded fold [29][30][31][32] and functional spaces of RNA [33][34][35][36][37][38][39]. Perhaps less known is the fact that the sugar moiety in the backbone of a nucleic acid determines the base pairing priorities. For example, in
- DNA G:C > A:T whereas in homo-DNA (2',3'-β-ᴅ-dideoxyglucopyranose nucleic acid) G:C > A:A ≈ G:G > A:T (reverse Hoogsteen A:A and G:G pairs) ([40] and cited references). Messenger RNA is the target of both the antisense and RNAi strategies to interfere with biological information transfer prior to
- 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
- the nuclear DNA, confirmed that the Ts-ON foci are present within the cytoplasm as shown in Figure 4. Discussion Chemical modification provides an effective and efficient way of obtaining therapeutic antigene/antisense agents based on the nucleic acid scaffold. To regulate transcription or translation
- the factors that determines the thermodynamic stability of nucleic acid secondary structures. Neutral or positively charged oligonucleotide analogues should bind more tightly with complementary DNA or RNA. Several studies have focused on the introduction of positively charged groups to a nucleobase
- onto DNA is performed during DNA synthesis instead of a standard oxidation step. Moreover, N+ and Ts modifications can be introduced into any position in the sequence, which is not the case for SaRNA and BCNS nucleic acid analogues. Unlike PNAs and some of BCNS groups, N+ and Ts-modified ONs
Synthesis and properties of oligonucleotides modified with an N-methylguanidine-bridged nucleic acid (GuNA[Me]) bearing adenine, guanine, or 5-methylcytosine nucleobases
Beilstein J. Org. Chem. 2021, 17, 622–629, doi:10.3762/bjoc.17.54
- the stability against nucleases, binding affinity to the targets, and efficacy. We previously reported that oligonucleotides modified with an N-methylguanidine-bridged nucleic acid (GuNA[Me]) bearing the thymine (T) nucleobase show excellent biophysical properties for applications in antisense
- data indicate that GuNA[Me] could be a useful modification for therapeutic antisense oligonucleotides. Keywords: artificial nucleic acid; duplex-forming ability; oligonucleotide synthesis; Introduction The efficacy and safety of therapeutic oligonucleotides can be controlled by chemical modifications
- (ASOs) modified with 2',4'-bridged nucleic acid/locked nucleic acid (2',4'-BNA/LNA; Figure 1) are now widely used for gene regulation in vitro and in vivo because 2',4'-BNA/LNA greatly increases the affinity toward the target RNAs, thus enhancing the efficacy of the modified ASOs [1][2][3][4][5][6
19F NMR as a tool in chemical biology
Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28
- analysis of higher-ordered DNA and RNA G-quadruplex structures. G-quadruplexes are four-stranded nucleic acid secondary structures formed in specific guanine-rich sequences showing, in general, highly polymorphic structures and various folding topologies. These structures have been suggested to play an
Molecular basis for protein–protein interactions
Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1
- that a nucleic acid scaffold aids the assembly by concentrating assembly units and providing additional association energy. Some viral capsids can self-assemble around other scaffolds that mimic the viral genome in charge and size [89] or can also assemble without any scaffold to form empty capsid
Selected peptide-based fluorescent probes for biological applications
Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247
- , UMP, TBAP, MMP or other anions (SO42−, NO3−, HCO3−, CH3COO−) does not show any enhancement of fluorescence enabling the probe as selective for nucleoside triphosphates. The probe 1 is not toxic and has been demonstrated by fluorescence imaging of ATP in HeLa cells (Figure 2A, inset). Nucleic acid
- peptide shows “switch-on” fluorescence response upon interaction with nucleic acids. Reproduced with permission from [32], Maity et al., “Peptide‐Based Probes with an Artificial Anion‐Binding Motif for Direct Fluorescence “Switch‐On” Detection of Nucleic Acid in Cells”, Chem. – Eur. J. © 2017 Wiley‐VCH
- for Direct Fluorescence “Switch‐On” Detection of Nucleic Acid in Cells”, Chem. – Eur. J. © 2017 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim. A) Molecular structure of 6; B) possible binding mode of pyrene termini of 6 to CB[8] according to molecular modeling; C) cartoon representation of ratiometric
Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function
Beilstein J. Org. Chem. 2020, 16, 2870–2879, doi:10.3762/bjoc.16.236
- (or removal) of external triggers, allowing to switch the nucleic acid function [8]. For example, DNA can be used in nanotechnology to create mechanically moving systems such as walkers, fueled by the addition of appropriately designed oligonucleotides [9]. Moreover, external triggers can be applied
Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator
Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185
- the free nucleic acid from Tm of the complex. Every ΔTm value reported herein was the average of at least two measurements. The error in ΔTm is ±0.5 °C. Isothermal titration calorimetry (ITC) experiments were performed on a MicroCal VP-ITC microcalorimeter (MicroCal, Inc., Northampton, MA, USA
Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA
Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170
- calculated by subtracting the Tm value of the free nucleic acid from the Tm value of the complex. Every ΔTm value here reported was the average of at least two measurements. The error in ΔTm is ±0.5 °C. In a similar manner as described in [62] ITC were carried out at 293 K on a MicroCal VP-iTC instrument. In
Synthesis of new dihydroberberine and tetrahydroberberine analogues and evaluation of their antiproliferative activity on NCI-H1975 cells
Beilstein J. Org. Chem. 2020, 16, 1606–1616, doi:10.3762/bjoc.16.133
- various inflammatory diseases. The main component of this rhizome is berberine (BER), an alkaloid with numerous pharmacological properties, which include anticancer and anti-inflammatory activities [1]. However, the low bioavailability, poor solubility, and moderate nucleic acid binding affinity
A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA
Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100
- . Petersburg, 197101, Russian Federation 10.3762/bjoc.16.100 Abstract Nowadays a variety of biosensors are widely used in different fields, including biomedical diagnostics and self-testing. Nucleic acid-based biosensors are typically applied to detect another nucleic acid, proteins, ions, and several other
- mRNA molecule of the androgen receptor. The constructed sensor is easy to use, has high efficiency and selectivity for the RNA target, and can be reconstructed for the detection of various nucleic acid sequences due to its modular structure. Thus, similar biosensors may be useful for the differential
- diagnosis. Keywords: androgen receptor; 10–23 deoxyribozyme; nucleic acid sensor; malachite green aptamer; RNA cleavage; Introduction The fast and precise diagnostics of diseases are one of the key factors that allow choosing the most effective method of treatment. Disease markers can be found at a few
Synthesis and herbicidal activities of aryloxyacetic acid derivatives as HPPD inhibitors
Beilstein J. Org. Chem. 2020, 16, 233–247, doi:10.3762/bjoc.16.25
- balance of the plant, which interrupts nucleic-acid and protein metabolism, and is especially effective in broadleaf weeds, such as Amaranthus retroflexus and Alfalfa. The application of 2,4-D causes excessive growth that ultimately results in plant death. Consequently, 2,4-D has become one of the world’s
Reversible photoswitching of the DNA-binding properties of styrylquinolizinium derivatives through photochromic [2 + 2] cycloaddition and cycloreversion
Beilstein J. Org. Chem. 2020, 16, 111–124, doi:10.3762/bjoc.16.13
- structural changes of the nucleic acid. In turn, both of these processes interfere with biologically relevant recognition processes between DNA and enzymes, e.g., topoisomerase [10]. Therefore, many potential lead structures of chemotherapeutic anticancer drugs exhibit DNA-binding properties [1][2][3][4][5
- ][6][7][8][9][10]. Nevertheless, most DNA-binding ligands have an insufficient selectivity towards the targeted nucleic acid, and they also accumulate in healthy tissue, so that the chemotherapeutic treatment of tumors with DNA-binding drugs still suffers from severe side effects because of the
- these ligands with the nucleic acid [72]. In all cases, isosbestic points developed at the beginning of the titration and eventually became indistinct, which already indicated different binding modes at particular stages of the titration. The data from the photometric titrations are presented as binding
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
- 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
- -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
- switching capacities and duplex formation were analyzed. Our group has recently demonstrated that photoresponsive peptides can affect the transcription of genes via inhibition of histone-modifying enzymes [37]. Repression of enzymes is achievable at nucleic acid level too. Therefore, in this project we
Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye libraries
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
- and RNA structures The fluorimetric response of the dye library was investigated against a set of 14 diverse nucleic acid structures (Table 2), including ten G4-DNA structures of different topologies (parallel G4: c-kit2, 25CEB, c-kit87up, c-myc, c-src1; parallel dimer G4: c-myb; hybrid G4: 22AG, 46AG
- , presented as relative enhancement of fluorescence intensity in the presence of nucleic acids (I/I0, where I is the fluorescence intensity of the dye in the presence of two equivalents of nucleic acid and I0 is the fluorescence of the dye alone), are shown in the form of a heat-map in Figure 5 (for numeric
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
Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA
Beilstein J. Org. Chem. 2019, 15, 79–88, doi:10.3762/bjoc.15.9
- improved affinity for RNA as complement can be found in DNA oligonucleotides containing 2’-deoxy-2’-fluoro-RNA (F-RNA) [8] or 2’-deoxy-2’-fluoroarabino nucleic acid (F-ANA, Figure 1) [9]. In the former the sugar pucker adopts a C3’-endo conformation [10] and the duplex formation is entropically stabilized
- 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
Beilstein J. Org. Chem. 2018, 14, 3088–3097, doi:10.3762/bjoc.14.288
- , Figure 1) [23]. Another strategy to overcome some of the limitations deals with the insertion of one or several fluorine atom(s) in the sugar moiety of the nucleic acid analog. The polar hydrophobic nature [24] of the fluorine atom can positively alter the furanose conformation, basicity and/or
- ’-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
- -fluorinated tc-DNA was observed in fully modified 2’F-tc-ANA sequences [44]. In contrast, a significant stabilisation with RNA targets resulted in the case of the 2’F-tc-RNA modification due to conformational control of the furanose conformation [45]. To further widen the scope of fluorinated nucleic acid
Other Beilstein-Institut Open Science Activities
