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Search for "intercalation" in Full Text gives 47 result(s) in Beilstein Journal of Organic Chemistry.

Switchable molecular tweezers: design and applications

  • Pablo Msellem,
  • Maksym Dekthiarenko,
  • Nihal Hadj Seyd and
  • Guillaume Vives

Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45

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  • et al. exploited the same scaffold to control the physical properties of materials. They incorporated planar terpyridine-alkyne Pt complexes as functional units and studied the intercalation of a Pt-complex guest in order to obtain Pt–Pt interactions in solution [23]. In the native state of 3, both
  • arms with planar Pt complexes are parallel and the distance between them allows for the intercalation of another terpy-Pt complex. The guest intercalation coupled with the induction of short-range Pt–Pt interactions was followed by UV–vis absorption and emission spectroscopies with characteristic MMLCT
  • . This larger system adds two more chelating sites and moves farther the functional unit allowing the intercalation of electron-rich polyaromatic guests such as pyrene [39]. In general, these hydrazone-based systems have the advantage of being more synthetically accessible than the terpyridine-based
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Published 01 Mar 2024

Photoinduced in situ generation of DNA-targeting ligands: DNA-binding and DNA-photodamaging properties of benzo[c]quinolizinium ions

  • Julika Schlosser,
  • Olga Fedorova,
  • Yuri Fedorov and
  • Heiko Ihmels

Beilstein J. Org. Chem. 2024, 20, 101–117, doi:10.3762/bjoc.20.11

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  • organic solvents (78–20% in MeCN). The quinolizinium derivatives bind to DNA by intercalation with binding constants of 6–11 × 104 M−1, as shown by photometric and fluorimetric titrations as well as by CD- and LD-spectroscopic analyses. These ligand–DNA complexes can also be established in situ upon
  • ; heterocycles; photocyclization; photosensitizer; styrylpyridines; Introduction DNA intercalators – most often represented by small planar heteroaromatic compounds – play an important role as chemotherapeutic agents [1][2][3][4]. Specifically, upon intercalation into the DNA double helix such ligands can cause
  • intercalators, and some currently applied anticancer drugs actually operate on the basis of intercalation [3]. Hence, several classes of compounds have been established, whose DNA-binding properties can be tailored and fine-tuned for that purpose, for example anthracyclines [5], indolocarbazoles [6], acridines
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Published 18 Jan 2024

Anion–π catalysis on carbon allotropes

  • M. Ángeles Gutiérrez López,
  • Mei-Ling Tan,
  • Giacomo Renno,
  • Augustina Jozeliūnaitė,
  • J. Jonathan Nué-Martinez,
  • Javier Lopez-Andarias,
  • Naomi Sakai and
  • Stefan Matile

Beilstein J. Org. Chem. 2023, 19, 1881–1894, doi:10.3762/bjoc.19.140

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  • insensitivity of fullerene monomers 22 thus supported that 38 and 40 activate and inactivate fullerene dimers 37 by intercalation in-between the two fullerenes. Replacement of the second fullerene in dimer 37 with a poorly polarizable naphthalenediimide (NDI) in 44 increased the catalytic activity of fullerene
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Published 12 Dec 2023

Synthesis and biological evaluation of Argemone mexicana-inspired antimicrobials

  • Jessica Villegas,
  • Bryce C. Ball,
  • Katelyn M. Shouse,
  • Caleb W. VanArragon,
  • Ashley N. Wasserman,
  • Hannah E. Bhakta,
  • Allen G. Oliver,
  • Danielle A. Orozco-Nunnelly and
  • Jeffrey M. Pruet

Beilstein J. Org. Chem. 2023, 19, 1511–1524, doi:10.3762/bjoc.19.108

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  • ]. Similar to berberine, results have demonstrated that the antibacterial activity of chelerythrine can be tied to DNA intercalation and disruption to cell membrane permeability [11][24]. One particular mechanism of action noted for chelerythrine’s antitumor bioactivity is through the inhibition of protein
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Published 29 Sep 2023

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

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  • extinction coefficient and long emission lifetime (>100 ns) [3]. Their large aromatic hydrophobic surface allows the intercalation between DNA/RNA base pairs and binding within the minor groove. Pyrenes are also prominent protein probes that can monitor protein conformational changes because of pyrene
  • -helical structure is favorable for intercalation and/or major groove binding. Calf thymus DNA (ct-DNA, 58% AT and 42% GC base pairs) and poly rA–poly rU (RNA) were chosen as models for a classical B-helical and A-helical structure, respectively [35]. Unlike Phen-Py-2, compound Phen-Py-1 showed notable
  • 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
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Published 26 Apr 2023

Efficient synthesis of polyfunctionalized carbazoles and pyrrolo[3,4-c]carbazoles via domino Diels–Alder reaction

  • Ren-Jie Fang,
  • Chen Yan,
  • Jing Sun,
  • Ying Han and
  • Chao-Guo Yan

Beilstein J. Org. Chem. 2021, 17, 2425–2432, doi:10.3762/bjoc.17.159

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  • used to treat joint pain and postoperative pain [6] (Figure 1). Ellipticine was considered to be based mainly on DNA intercalation and topoisomerase II inhibition [7]. Midostaurin and carvediol have been approved by the FDA for tumor therapy and treatment of congestive heart failure [8]. On the other
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Published 16 Sep 2021

Strategies for the synthesis of brevipolides

  • Yudhi D. Kurniawan and
  • A'liyatur Rosyidah

Beilstein J. Org. Chem. 2021, 17, 2399–2416, doi:10.3762/bjoc.17.157

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  • revealed various results, including toxicity to brine shrimp [9], DNA intercalation as well as antibacterial and fungal [4][9], and strong insecticidal activity against the 3rd instar larva of the cotton leaf worm Spodoptera littoralis (Biosd.) [7]. The essential oil extracted from the leaf of Hyptis
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Published 14 Sep 2021

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

  • Nikita Brodyagin,
  • Martins Katkevics,
  • Venubabu Kotikam,
  • Christopher A. Ryan and
  • Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

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  • intercalation, triplex formation, and backbone chirality shifts [44]. A similar P-form helix having a wide and deep major groove and a shallow and narrow minor groove was also observed for an NMR solution structure of a self-complementary PNA–PNA duplex [45]. Taken together, these results confirmed that, while
  • binding strongly to either U–A or C–G base pairs [111]. The low mismatch discrimination suggests that S may have binding modes other than the hydrogen bonding depicted in Figure 7, for example, intercalation as has been previously observed for other similar unnatural nucleobases in DNA [116]. At the time
  • modified natural nucleobase that did not quench the fluorescence upon hybridization [148]. Köhler and Seitz introduced thiazole orange (TO, Figure 10), an intercalator dye originally designed for DNA [149], as a forced intercalation (FIT) probe in PNA. Because of rotation around the methine bond connecting
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Published 19 Jul 2021

Selected peptide-based fluorescent probes for biological applications

  • Debabrata Maity

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

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  • 4 binds with dsDNA in a combined intercalation and minor groove binding mode, whereas probe 5 binds with the outer surface of dsDNA. These two probes are low cytotoxic and probe 4 has been successfully used for imaging of nuclear DNA (Figure 5B, inset). Protein detection Specific peptides and
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Published 03 Dec 2020

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

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  • naphthalene diimde analogue (NDI) equipped at the imide positions with two guanidinio-carbonyl-pyrrole (GCP) pendant arms interacted significantly stronger with ds-DNA at pH 5 than at pH 7, due to reversible protonation of the GCP arms. This was consequence of a pH-switchable threading intercalation into ds
  • attention to a less common DNA/RNA binding motif: threading intercalation. This sterically very demanding binding mode is characterised by a central large aromatic moiety, in this case the well-known naphthalene diimide (NDI), equipped at both sides of the long axis with large substituents, which have to
  • thread through DNA double helix and are therefore positioned in the minor and major groove, respectively [23][24][25]. Since GCP units always interact within DNA/RNA grooves, thus our particular interest in threading intercalation is the positioning of side chains simultaneously in both, the minor and
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Published 08 Sep 2020

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

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  • interacted with ds-DNA/RNA by threading intercalation. Different from a reference NDI dye with identical visible range absorbance (520–540 nm) and Stokes shifts in emission (+60 nm, quantum yield > 0.2), only these amino acid–NDI conjugates showed selective fluorimetric response for GC-DNA in respect to AT(U
  • 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
  • several decades, consequently becoming increasingly complex [5][6][7]. This includes examples incorporating several types of non-covalent interaction with DNA/RNA (intercalation, groove binding, positive–negative charge interaction [5][8]) in one molecule or even modified biomacromolecules (e.g., proteins
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Published 19 Aug 2020

Highly selective Diels–Alder and Heck arylation reactions in a divergent synthesis of isoindolo- and pyrrolo-fused polycyclic indoles from 2-formylpyrrole

  • Carlos H. Escalante,
  • Eder I. Martínez-Mora,
  • Carlos Espinoza-Hicks,
  • Alejandro A. Camacho-Dávila,
  • Fernando R. Ramos-Morales,
  • Francisco Delgado and
  • Joaquín Tamariz

Beilstein J. Org. Chem. 2020, 16, 1320–1334, doi:10.3762/bjoc.16.113

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  • stereoselective approaches of substrates and reagents or catalysts in a variety of processes. Examples include the substrate–enzyme recognition (the host–guest interaction) responsible for inducing pharmacological activity, the DNA-intercalation capable of generating biomolecular activity, molecular dynamics [63
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Published 17 Jun 2020

p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies

  • Panagiotis S. Gritzapis,
  • Panayiotis C. Varras,
  • Nikolaos-Panagiotis Andreou,
  • Katerina R. Katsani,
  • Konstantinos Dafnopoulos,
  • George Psomas,
  • Zisis V. Peitsinis,
  • Alexandros E. Koumbis and
  • Konstantina C. Fylaktakidou

Beilstein J. Org. Chem. 2020, 16, 337–350, doi:10.3762/bjoc.16.33

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  • typical intercalator while compound 12 may initially interact to CT DNA probably by nonclassical intercalation (i.e., as groove-binder) and as a subsequent step it may probably intercalate within the CT DNA base pairs [11]. Such features may obviously shed light to the findings from the UV–vis
  • spectroscopic studies. Given the results derived from DNA-viscosity measurements suggesting intercalation as possible interaction mode between compounds 11 and 12 and CT DNA, the determination of the ability of the compounds to displace EB from the EB–DNA conjugate may further clarify and verify their
  • conditions (λexcitation = 540 nm at room temperature). Thus, the quenching observed in an EB–DNA solution upon addition of the compounds 11 and 12 may reveal their competition to EB for the DNA-intercalation sites as monitored by fluorescence emission spectroscopy with λexcitation = 540 nm. A significant
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Published 09 Mar 2020

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

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  • lower ligand:DNA ratios (≤1.5), these compounds bind to duplex DNA by intercalation, with binding constants ranging from Kb = 4.1 × 104 M to 2.6 × 105 M (four examples), as shown by photometric and fluorimetric titrations as well as by CD and LD spectroscopic analyses. Upon irradiation at 450 nm, the
  • relative to the ones of the DNA base pairs [75][76]. Considering a dipole moment of the donor–acceptor systems 3a–c along the long molecular axis, a binding mode in which the ligand is accommodated in the intercalation site with its long molecular axis perpendicular to the long axis of the binding site
  • observed. It should be noted that the DNA-bound ligand did not dimerize upon irradiation because within the intercalation site, it could not approach another quinolizinium molecule that was required for the photoreaction. Instead, the photodimerization most likely involved the free or loosely backbone
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Published 23 Jan 2020

Influence of the cis/trans configuration on the supramolecular aggregation of aryltriazoles

  • Sara Tejera,
  • Giada Caniglia,
  • Rosa L. Dorta,
  • Andrea Favero,
  • Javier González-Platas and
  • Jesús T. Vázquez

Beilstein J. Org. Chem. 2019, 15, 2881–2888, doi:10.3762/bjoc.15.282

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  • from 0° or 180°, since this interaction is governed by an equation with a vectorial product. The lack of exciton pairwise interactions between the two chromophores in positions 1 and 2 of each molecule could be due to the intercalation of a third chromophore between the two former in a parallel
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Published 28 Nov 2019

Nanopatterns of arylene–alkynylene squares on graphite: self-sorting and intercalation

  • Tristan J. Keller,
  • Joshua Bahr,
  • Kristin Gratzfeld,
  • Nina Schönfelder,
  • Marcin A. Majewski,
  • Marcin Stępień,
  • Sigurd Höger and
  • Stefan-S. Jester

Beilstein J. Org. Chem. 2019, 15, 1848–1855, doi:10.3762/bjoc.15.180

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  • nanopores from the gas phase [15], the intercalation of organic molecules into nanopores is rather difficult to tailor from scratch, however, with prominent examples [16][17]. Likewise, larger polycyclic aromatic hydrocarbons (PAHs) and nanographenes form robust adsorbate films in a certain size range, and
  • –alkynylene macrocycles 1a/b (Figure 1), and the intercalation of solvent molecules and polycyclic aromatic hydrocarbons (PAHs). Our way towards nanoporous quadratic templates containing long (OC16H33) alkoxy side chains on two opposite sides of the square and two shorter (OC10H21, OC6H13) side chains on the
  • solvent molecules are sometimes resolved as intercalation adducts in STM of self-assembled monolayers. On the other hand, reports on intercalated TCB molecules are rather rare. Two exceptions are the observations of TCB in monolayers of arylene–alkynylene pentagons as well as triphenylene/azobenzene-based
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Published 02 Aug 2019

Synthesis and photophysical studies of a multivalent photoreactive RuII-calix[4]arene complex bearing RGD-containing cyclopentapeptides

  • Sofia Kajouj,
  • Lionel Marcelis,
  • Alice Mattiuzzi,
  • Adrien Grassin,
  • Damien Dufour,
  • Pierre Van Antwerpen,
  • Didier Boturyn,
  • Eric Defrancq,
  • Mathieu Surin,
  • Julien De Winter,
  • Pascal Gerbaux,
  • Ivan Jabin and
  • Cécile Moucheron

Beilstein J. Org. Chem. 2018, 14, 1758–1768, doi:10.3762/bjoc.14.150

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  • . Barton et al. demonstrated in 1990 that [Ru(bpy)2(dppz)]2+ behaves as a light-switch for DNA [5]: this complex is not luminescent in water but upon intercalation within the DNA base pairs stack, the complex luminescence is restored. Derivatives of [Ru(bpy)2(dppz)]2+ and complexes bearing similar aromatic
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Published 16 Jul 2018

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

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  • . Therefore, HeLa and MCF-7 cells were exposed to the chemotherapeutic drug doxorubicin (DOX) that is already clinically applied in cancer therapy [37]. Doxorubicin interacts with DNA by intercalation and thereby inhibits the macromolecular biosynthesis [38]. Instead of covalent conjugation of the drug, we
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Published 07 Jun 2018

A three-armed cryptand with triazine and pyridine units: synthesis, structure and complexation with polycyclic aromatic compounds

  • Claudia Lar,
  • Adrian Woiczechowski-Pop,
  • Attila Bende,
  • Ioana Georgeta Grosu,
  • Natalia Miklášová,
  • Elena Bogdan,
  • Niculina Daniela Hădade,
  • Anamaria Terec and
  • Ion Grosu

Beilstein J. Org. Chem. 2018, 14, 1370–1377, doi:10.3762/bjoc.14.115

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  • , 1,5-dihydroxynaphthalene was chosen as another candidate for intercalation in the cryptand system. The pyrene molecule was replaced by 1,5-dihydroxynaphthalene in such way that its OH fragment arrived near the N atom of the 3,5-dicyanopyridine fragment. However, at the end of the energy optimization
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Published 06 Jun 2018

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

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  • . This review presents the latest findings in the pursuit of novel synthetic DNA binders. This article provides recent coverage of major strategies (such as groove recognition, intercalation and cross-linking) adopted in the duplex DNA recognition by small molecules, with an emphasis on major works of
  • all DNA binding agents, this review article intends to provide a substantial coverage of new advancements made in the discovery of major leads in three most visited areas (groove recognition, intercalation and cross linking agents) of DNA recognition. 2. Minor groove binders (MGBs) DNA groove binding
  • binding affinity using sophisticated molecular dynamics approach with eight different nucleotides having variety of sequences. It has been observed that QUE appears to be a minor groove binder, whereas FLP involves in combined mode of interaction such as minor groove binding and intercalation. A set of
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Published 16 May 2018

On the design principles of peptide–drug conjugates for targeted drug delivery to the malignant tumor site

  • Eirinaios I. Vrettos,
  • Gábor Mező and
  • Andreas G. Tzakos

Beilstein J. Org. Chem. 2018, 14, 930–954, doi:10.3762/bjoc.14.80

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  • sugar moiety. The difference between Dau and Dox is a hydroxy group substituted at the C-14 carbon atom on Dox providing an extra conjugation site for ester linkage (Figure 6). The mechanism of action of anthracyclines is based on their intercalation to DNA inhibiting the macromolecular biosynthesis
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Published 26 Apr 2018

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

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Published 10 Apr 2018

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

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  • (Dox), daunorubicin (Dau) or epirubicin are frequently used anticancer drugs. Their mode of action is based on a planar ring system which is important for intercalation into DNA [10]. In this way, anthracyclines can affect a broad range of DNA processes leading to an inhibited synthesis of
  • the drug within cancer cells is of high relevance. In this study the anthracycline daunorubicin was used as anticancer agent. This drug interacts with DNA by intercalation and affects a broad range of DNA processing [11][41]. Orbán et al. recently reported that next to the free drug, also small Dau
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Published 04 Apr 2018

Fluorogenic PNA probes

  • Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17

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  • ) partner, and the combination of short linear PNA probes with environment-sensitive dyes, such as in light-up and forced intercalation (FIT) PNA probes. PNA probes carrying two or more interacting dyes in the same strand The very first PNA probe of this type were independently reported in 1998 by Ortiz et
  • duplexes by various mechanisms, such as groove binding or intercalation. This fluorescent label may be a stand-alone entity (referred to as a tethered label) or combined with a nucleobase that integrates the base pairing and the fluorescence sensing in a single event. The latter strategy should allow a
  • fluorescence enhancement was observed in the case of a single pyrene-labeled acpcPNA probe [170]. This is in sharp contrast to pyrene-tethered DNA probes, which are usually quenched after hybridization due to intercalation of the pyrene in the DNA–DNA duplex [173][174], unless the pyrene is attached to the
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Published 29 Jan 2018

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

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  • between nucleic acids and small ligands. This tutorial aims to help researchers entering the research field to organize experiments accurately and to interpret the obtained data reliably. Keywords: circular dichroism; emission-based dichroism; groove binding; intercalation; linear dichroism; non-covalent
  • . Among the methods discussed, primary focus will be centered on the most frequently employed techniques, ECD and LD. Moreover, we will elaborate the interpretation of results not only for the most common DNA, RNA/ligand binding modes (intercalation, groove binding) but also for increasingly appearing
  • range indicates a disruption of helical chirality by intercalation or severe kinking of the helix by sterically demanding groove binders. At variance, if the ECD spectrum of the DNA and RNA does not change significantly, the biopolymer helical structure is preserved, suggesting a ligand groove binding
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Published 08 Jan 2018
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