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

• – binding to several different DNA or RNA structures but for each of them giving a different spectrophotometric response [17][18][19][20][21][22]. Until now we have studied aryl systems which behaved as ds-DNA/RNA intercalators, DNA/RNA groove binders, or nucleobase derivatives. In this work we focused our

• adjacent amino groups (pH 7, green) and decorated by two GCP arms protonated at pH 5 (red; pH-switchable DNA groove binders). Synthesis of compound 4. Conditions: a) mono-N-Boc-ethylenediamine, DMF, 90 °C; b) i) trifluoroacetic acid (TFA)/CH2Cl2 1:1, ii) Fmoc-Lys(Boc)-OH, DIPEA, HCTU; c) i) TFA/CH2Cl2 1:1

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

• in Figure 4 and Table 2, the addition of all studied compounds resulted in very strong stabilisation effects on both, poly(dA-dT)2 and poly(A)-poly(U). This similarity of stabilisation of ds-DNA and ds-RNA supports the presence of an intercalative binding mode because DNA groove binders are usually

Photocontrolled DNA minor groove interactions of imidazole/pyrrole polyamides

• Sabrina Müller,
• Jannik Paulus,
• Jochen Mattay,
• Heiko Ihmels,
• Veronica I. Dodero and
• Norbert Sewald

Beilstein J. Org. Chem. 2020, 16, 60–70, doi:10.3762/bjoc.16.8

• was proven amenable for the light-induced triggering of transcription [24], photoswitchable polyamides that can act as selective DNA minor groove binders displaying tunable affinity have not yet been reported [29][30]. We envisaged that control of the geometry and functionality could be achieved upon

• % P1; 67% P2; after 1 d: 76% P3). Analysis of polyamide–DNA interaction by induced circular dichroism CD spectroscopic analysis is suitable for the characterization of DNA minor groove binders, providing semiquantitative information about binding affinity and thermal stability of the target dsDNA [47

• polyamide groove binders on B-DNA at about 335 nm [47][52]. Initially, it was difficult to predict, which sequences would be optimal for the new polyamides containing the azobenzene linker. Hence, we employed the target sequences for the Im/Py hairpin polyamides based on Dervan’s pairing rules, such as 5

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

• 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

• guanine bases) to DNA is irreversible and causes permanent stall of transcription leading to cell death. Non-covalent interaction between small molecules and DNA is usually reversible and can further be classified as minor groove binders, intercalators, backbone binders, and major groove binders. There

• (groove binders, intercalators and alkylating agents), which includes both classical DNA binders and new advancements in the recent years (with emphasis on research advances reported in the last five years). For a focused work, we have excluded triplex and quadruplex DNA binders for this review. In

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

• 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

Application of Cu(I)-catalyzed azide–alkyne cycloaddition for the design and synthesis of sequence specific probes targeting double-stranded DNA

• Svetlana V. Vasilyeva,
• Vyacheslav V. Filichev and
• Alexandre S. Boutorine

Beilstein J. Org. Chem. 2016, 12, 1348–1360, doi:10.3762/bjoc.12.128

• synthesis of conjugates of pyrrole–imidazole polyamide minor groove binders (MGB) with fluorophores and with triplex-forming oligonucleotides (TFOs). Diverse bifunctional linkers were synthesized and used for the insertion of terminal azides or alkynes into TFOs and MGBs. The formation of stable triple

• ]. Besides natural and engineered peptides or proteins, two synthetic substances are known to recognize and bind dsDNA in a sequence-specific manner: triplex-forming oligonucleotides (TFOs) [4][5] and pyrrole–imidazole polyamide minor groove binders (MGBs) [6][7]. TFOs recognize polypurine stretches in