Synthesis of functionalized, 13-alkyl-substituted coralyne derivatives and investigation of their interactions with duplex and abasic site-containing DNA

• Laurin Beckmann,
• Jason Lennard Kunze,
• Hannah Karola Strunk,
• Maurice Michel and
• Heiko Ihmels

Beilstein J. Org. Chem. 2026, 22, 1057–1066, doi:10.3762/bjoc.22.84

• abasic site-containing DNA (AP-DNA), different synthetic routes towards the functionalization of coralyne were tested. In particular, the alkylation of the benzylic position in papaverine and subsequent cyclization by treatment with acetic anhydride in sulfuric acid led to the synthesis of a coralyne

• -binding units. Specifically, we proposed that the attachment of an (aminooxy)alkyl functionality may lead to a highly selective ligand for abasic site-containing DNA (AP-DNA) [36][37]. The latter is duplex DNA with apurinic/apyrimidinic (AP) sites, more generally named abasic sites (Scheme 1). Such AP

• nm and a weaker negative one at 400–460 nm, which both increased with increasing ligand-to-DNA ratio (LDR) (Figure 2D). Interaction of 2g with abasic site-containing DNA To investigate whether the aminooxy-functionalized coralyne derivative 2g interacts with AP sites in DNA and whether such binding

DNA functionalization by dynamic chemistry

• Zeynep Kanlidere,
• Oleg Jochim,
• Marta Cal and
• Ulf Diederichsen

Beilstein J. Org. Chem. 2016, 12, 2136–2144, doi:10.3762/bjoc.12.203

• ][18][19][20][21] constitutes an attractive choice for oligonucleotide functionalization. Threoninol can be introduced in oligonucleotides via the corresponding phosphoramidite generating a ribose-free abasic site on the backbone that provides the amine group for later functionalization [22][23][24][25

• influence of the DNA template on nucleobase incorporation into the strands at abasic site through imine attachment to the amine group, four reactions were carried out under identical conditions (pH 6, 20 mM phosphate buffer), but differing in the applied template strand. The 13mer oligonucleotide ON1 was

Come-back of phenanthridine and phenanthridinium derivatives in the 21st century

• Lidija-Marija Tumir,
• Marijana Radić Stojković and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2930–2954, doi:10.3762/bjoc.10.312

• (abasic site X). Though, ethidium 2’-deoxyribofuranoside (17) [88] revealed chemical instability and was therefore replaced with an acyclic linker system [87]. However, in a later work the acyclic linker was again modified to correspond by length to the deoxyribofuranoside, whereby it was proven that

• sensitive to major erroneous ds-DNA sites (e.g., abasic sites) [91]. Namely, by using the well-known system of EB-fluorescence quenching by 7-deazaguanine incorporated within modified oligonucleotides, it showed that the abasic site (S) either one base pair away (DNA1-XY and DNA2-XY) or two base pairs away

Synthesis, characterization and DNA interaction studies of new triptycene derivatives

• Sourav Chakraborty,
• Snehasish Mondal,
• Rina Kumari,
• Sourav Bhowmick,
• Prolay Das and
• Neeladri Das

Beilstein J. Org. Chem. 2014, 10, 1290–1298, doi:10.3762/bjoc.10.130

• spectrometry, and elemental analyses techniques. The study of the interaction of these trisubstituted triptycenes with various forms of DNA revealed interesting dependency on the functional groups of the triptycene core to initiate damage or conformational changes in DNA. Keywords: abasic site; DNA damage

• generated when a purine (A/G) or a pyrimidine (C/T) base is stripped off from the DNA strand and this is considered as the most common type of DNA damage lesions. We generated one abasic site in a 48-base pair long oligomer duplex by treating the DNA (Figure 3) with Uracil DNA Glycosylase (UDG) enzyme

• the abasic site by hydrolysis of the phosphate backbone (Figure 3). This signifies that though few compounds are able to hydrolyse phosphodiester bonds in plasmids, none of the compounds are able to reproduce that act, when a base is missing from the DNA duplex. Thus the interaction of the compounds

Synthesis of novel derivatives of 5-hydroxymethylcytosine and 5-formylcytosine as tools for epigenetics

• Anna Chentsova,
• Era Kapourani and
• Athanassios Giannis

Beilstein J. Org. Chem. 2014, 10, 7–11, doi:10.3762/bjoc.10.2

• catalyzed by TET enzymes followed by removal of 5fC and 5caC by thymine DNA glycosylase (TDG). Excision of 5fC and 5caC generates an abasic site, which is further repaired resulting in replacement of 5mC with unmodified cytosine (C) [15][16][17][18]. (2) The second alternative scenario still remains