A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA

• Ekaterina A. Bryushkova,
• Erik R. Gandalipov and
• Julia V. Nuzhina

Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100

• diagnosis. Keywords: androgen receptor; 10–23 deoxyribozyme; nucleic acid sensor; malachite green aptamer; RNA cleavage; Introduction The fast and precise diagnostics of diseases are one of the key factors that allow choosing the most effective method of treatment. Disease markers can be found at a few

• -AR_RNA at 37 °C already in 6 hours. To estimate the functional activity of the SDFS we simultaneously evaluated the biosensor fluorescence intensity and the efficiency of the target RNA cleavage in the presence of SDFS under the same conditions. The complete assembled SDFS (100 nM), mix of Т1–Т5 (100 nM

In search of visible-light photoresponsive peptide nucleic acids (PNAs) for reversible control of DNA hybridization

• Lei Zhang,
• Greta Linden and
• Olalla Vázquez

Beilstein J. Org. Chem. 2019, 15, 2500–2508, doi:10.3762/bjoc.15.243

• targets without causing a permanent knockout. During the last years, the pioneering structural studies of reversible photoregulation of DNA/RNA duplex stability of Asanuma and Komiyama [16][17] have become functional ones, affecting DNA/RNA cleavage [18][19][20], transcription [21][22][23], and

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

• pseudorotation has almost exclusively used in mechanistic discussion of RNA cleavage. The stability of the phosphorane intermediate largely depends on its state of protonation. The first pKa value of the acyclic tetraalkoxy monohydroxy phosphorane has been estimated to be 8.6 for an equatorial hydroxy group and

• pH. In case a dianionic phosphorane is formed, its protonation to a monoanion expectedly is thermodynamically favored, but it is not clear whether the life-time is long enough to allow this. The cyclic phosphorane intermediate of RNA cleavage is in neutral form (IH2 in Figure 4) sufficiently stable

Sequence-specific RNA cleavage by PNA conjugates of the metal-free artificial ribonuclease tris(2-aminobenzimidazole)

• Friederike Danneberg,
• Alice Ghidini,
• Plamena Dogandzhiyski,
• Elisabeth Kalden,
• Roger Strömberg and
• Michael W. Göbel

Beilstein J. Org. Chem. 2015, 11, 493–498, doi:10.3762/bjoc.11.55

• PNA. Previous results for the corresponding DNA conjugates had shown sequence specific RNA cleavage with substrate half-lives in the range of 12 to 17 h [16]. Tris(2-aminobenzimidazole) 7 can be obtained in a six-step reaction sequence starting from tris(2-aminoethyl)amine (1) [15]. However, the use

• Information File 1), which proves that cleavage in the examined concentration range fully depends on Watson–Crick base pairing. Cleavage experiments with varying amounts of conjugates (Figure 4) show that – at concentrations below 1.5 µM – RNA cleavage by PNAs 10–12 and 14 obeys saturation kinetics. Full

Multicomponent synthesis of artificial nucleases and their RNase and DNase activity

• Anton V. Gulevich,
• Lyudmila S. Koroleva,
• Olga V. Morozova,
• Valentina N. Bakhvalova,
• Vladimir N. Silnikov and
• Valentine G. Nenajdenko

Beilstein J. Org. Chem. 2011, 7, 1135–1140, doi:10.3762/bjoc.7.131

• activity of the new compounds towards single-stranded RNA and double-stranded circular DNA. Keywords: DNA; isocyanide; multicomponent reaction; organocatalysis; peptidomimetic; RNA; Introduction RNA cleavage can serve as a molecular tool for biological research [1], as well as for development of

• centers of natural RNases A and T1 have been described [13][14][15]. RNA cleavage was shown to be more efficient in the presence of aliphatic hydrophobic linkers [16]. However, the potential role of the alkyl chain of the catalyst remains unclear. Interaction of hydrophobic residues in peptides was

• and 5g, the most hydrophobic among synthesized substances, might potentially penetrate through cellular or viral membranes and therefore the dependence of RNA cleavage on the concentration of the peptidomimetics was studied in detail. The concentration of compounds 5e and 5g, optimal for RNA cleavage