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

• formed an exciplex [15], and conjugates formed of pyrene and an amino acid-fluorescent nucleobase derivative qAN1, differing in length and flexibility between fluorophores [16]. Due to pre-organization, both conjugates strongly interacted with ds-DNA/RNA grooves with similar affinity but opposite

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

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

• 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

• dyes by its ability to intercalate into ds-DNA/RNA by “threading” through the polynucleotide double helix [21][22]. Such “threading intercalation” indicates that a large aromatic moiety with bulky groups at opposite ends is inserted between two DNA or RNA base pairs, whereby bulky substituents end in

• molecules. In addition to the pH value, the hydrolysis also depends on the position of cationic ammonium groups, namely, the distance of the charged group from the imide position is proportional to its stability [24]. However, too long side chains can interfere with threading intercalation into ds-DNA/RNA

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

• least partially aligned (Figure 9a). Flow LD is therefore a very useful method for the characterization of ds-DNA or ds-RNA conformation (base inclination), and of the flexibility and binding geometry of ds-DNA (RNA)/small molecule complexes [33][34]. The aforementioned flow cell is a cylindrical

• (Figure 7). Provided that at least factor S is known, one may in principle use LD measurements to estimate the angle by which a transition of a bound molecule is oriented relative to the axis of the DNA helix. 4.3.1. Changes in DNA absorbing region (<300 nm): The LD spectrum of ds-DNA/RNA can change upon

• of the negative LD amplitude at 260 nm with the addition of a small molecule could imply that the DNA/RNA becomes better-oriented in flow, due to a stiffening of the ds-DNA/RNA structure [33][34]. 4.3.2. Induced LD (>300 nm): When the compound is added to the DNA, and if the compound’s absorbing

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

• in contrast to the majority of previously studied DBTAA analogues (DNA/RNA intercalators). Only DBTAA–propyladenine conjugates revealed the molecular recognition of AT-DNA by an ICD band pattern > 300 nm, whereas significant ICD bands did not appear for other ds-DNA/RNA. A structure–activity relation

• 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

• ] (Supporting Information File 1). Study of interactions of DBTAA derivatives with ds-DNA/RNA in aqueous medium Previous studies [11] revealed intriguing recognition of single stranded DNA dT sequences by AP3 (but not AP6, APH), whereby intercalation of AP3, AP6, APH in double stranded ct-DNA was excluded. Here