A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis

• Theodore Groth,
• Rudiyanto Gunawan and
• Sriram Neelamegham

Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119

• their tissue-specific expression, DNA binding domains, and nucleosome interaction sequences [3]. Additional factors regulating transcriptional activity include: i) cofactors and small molecules that enable TF-DNA recognition and RNA polymerase recruitment [3]; ii) chromatin modifications, such as

Synthesis of 10-O-aryl-substituted berberine derivatives by Chan–Evans–Lam coupling and investigation of their DNA-binding properties

• Peter Jonas Wickhorst,
• Mathilda Blachnik,
• Denisa Lagumdzija and
• Heiko Ihmels

Beilstein J. Org. Chem. 2021, 17, 991–1000, doi:10.3762/bjoc.17.81

• -DNA by terminal stacking. Keywords: berberine alkaloids; Cu-mediated coupling reactions; DNA recognition; nucleic acids; quadruplex DNA; Introduction Berberine (1a) is the most prominent member of the protoberberine family, i.e., a group of tetracyclic isoquinolinium alkaloids [1]. Like many members

Synthesis and investigation of quadruplex-DNA-binding, 9-O-substituted berberine derivatives

• Jonas Becher,
• Daria V. Berdnikova,
• Heiko Ihmels and
• Christopher Stremmel

Beilstein J. Org. Chem. 2020, 16, 2795–2806, doi:10.3762/bjoc.16.230

• ; DNA recognition; G4-DNA; nucleic acids; Introduction In nucleic acids chemistry, quadruplex DNA (G4-DNA) has been established as an attractive target [1][2][3]. This noncanonical DNA form is assembled through stacking of at least two guanine quartets and has been observed with highly diverse

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

• . 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

• the past few years. Keywords: alkylators; antibiotic; anticancer; antineoplastic; antiproliferative; DNA recognition; groove binders; hairpin polyamides; Hoechst 33258; intercalators; Review 1. Introduction DNA is one of the central components of cellular machinery and storage unit of genetic

• structures. These variations in the groove widths and shapes shed light on the challenges in programmed DNA recognition in a sequence and shape selective manner. DNA recognition by small molecules can be divided in two broad categories: covalent and non-covalent. Covalent binding (e.g., cis-platin binding to

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• reporting pyrenyl group and hydrogen-bonding biological nucleobase vector to be tested in DNA recognition and bioimaging applications. Results and Discussion A straightforward, one-pot two-step methodology for aryl–nucleobases has been recently developed in our laboratory and was examined in respect to

Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives

• Marijana Radić Stojković,
• Marko Škugor,
• Łukasz Dudek,
• Jarosław Grolik,
• Julita Eilmes and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2175–2185, doi:10.3762/bjoc.10.225

• the DBTAA-ICD pattern proposed for the AT-DNA recognition is an intermolecularly stacked system formed by two DBTAA moieties or, alternatively, a single intramolecularly stacked DBTAA–adenine molecule. The solubility of the system prevented NMR experiments. So we relied on structural differences

• intramolecular aromatic stacking between DBTAA and adenine. The observed AT-DNA-ICD pattern differs from previously reported ss-DNA (poly dT) ICD recognition by a strong negative ICD band at 350 nm, which allows for the dynamic differentiation between ss-DNA (poly dT) and coupled ds-AT-DNA. Keywords: AT-DNA

• recognition; circular dichroism; DBTAA-adenine conjugate; ds-DNA/RNA; minor groove binding; nucleic acids; Introduction The majority of natural and artificial applications involving small molecule-DNA/RNA recognition depend on several non-covalent binding modes. Typical examples are double-stranded (ds) DNA