Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides

• Mathias B. Danielsen and
• Jesper Wengel

Beilstein J. Org. Chem. 2021, 17, 1828–1848, doi:10.3762/bjoc.17.125

• solid-phase DNA synthesis, circumventing some of the laborious work involved in the synthesis of some internucleotide linkages. The authors demonstrated that this new modification could enhance the stability of the ON/RNA duplex, although no significant change was observed for the ON /DNA duplex (100 mM

DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies

• Yongdong Su,
• Maitsetseg Bayarjargal,
• Tracy K. Hale and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2021, 17, 749–761, doi:10.3762/bjoc.17.65

• section are shown: nuclear DNA (blue), 4Ts-FAM/ON (magenta), cell membrane (yellow). Scale bar: 20 μm. The synthesis of ONs with Ts and N+ modification using the Staudinger reaction during the solid-phase DNA synthesis. Conditions: (i) 0.5 M TsN3, MeCN, 37 °C, 30 min for Ts modification; 0.7 M 4

6’-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations

• Sibylle Frei,
• Andrei Istrate and
• Christian J. Leumann

Beilstein J. Org. Chem. 2018, 14, 3088–3097, doi:10.3762/bjoc.14.288

• cyclopropane ring opening which proceeded in high yields. The two phosphoramidite building blocks were successfully incorporated into oligonucleotides by automated solid-phase DNA synthesis with tert-butyl hydroperoxide as the oxidation agent. The CD spectra of the 6’F-bc4,3-T or -C-modified oligonucleotides

Preparation of trinucleotide phosphoramidites as synthons for the synthesis of gene libraries

• Ruth Suchsland,
• Bettina Appel and
• Sabine Müller

Beilstein J. Org. Chem. 2018, 14, 397–406, doi:10.3762/bjoc.14.28

• to 49% [23]. 5. Phosphitylation and coupling of trinucleotide synthons in solid phase DNA synthesis To be used as building blocks in standard phosphoramidite synthesis, fully protected trimers need to be converted in phosphoramidites (Figure 7). This has been described in a number of reports [19][22

DNA display of glycoconjugates to emulate oligomeric interactions of glycans

• Alexandre Novoa and
• Nicolas Winssinger

Beilstein J. Org. Chem. 2015, 11, 707–719, doi:10.3762/bjoc.11.81

• achieve conjugation during solid-phase DNA synthesis or in solution post DNA cleavage [28]. Subsequently, the same group reported a method to introduce two different glycans sequentially on the DNA strand at the 2’-position using an azido and a bromo-modified thymidine 6 and 7 (Scheme 5) [29]. Krauss and

• density. Synthesis of glycoconjugate DNA by diazo-coupling. β-Galactose-modified deoxyuridine phosphoramidite used for solid-phase DNA synthesis and DNA display of glycan. (NHS)-carboxy-dT phosphoramidite as a general entry for the solid-phase synthesis of glycan–DNA conjugates. Preparation of the DNA

Versatile synthesis of amino acid functionalized nucleosides via a domino carboxamidation reaction

• Vicky Gheerardijn,
• Jos Van den Begin and
• Annemieke Madder

Beilstein J. Org. Chem. 2014, 10, 2566–2572, doi:10.3762/bjoc.10.268

• have a stable and predictable structure allowing the design of engineered active sites through the carefully planned introduction of extra catalytic functionalities via solid phase DNA synthesis. We have further recently shown that the combination of solid phase synthesis and molecular modeling

• groups for later incorporation into nucleic acid duplexes via solid phase DNA synthesis [33]. Results and Discussion As mentioned earlier, a number of research groups have used the SELEX or in vitro selection protocol for the incorporation of amino acid-like modifications into DNA or RNA where there is

• using palladium-based coupling chemistry to the pyrimidine C5 or the 7-position of 7-deaza-2’-deoxyadenosine [38][39][40]. During enzymatic incorporation the extra functionalities do not need to be protected. However, solid phase DNA synthesis implies an appropriate protection of the extra

Autonomous assembly of synthetic oligonucleotides built from an expanded DNA alphabet. Total synthesis of a gene encoding kanamycin resistance

• Kristen K. Merritt,
• Kevin M. Bradley,
• Daniel Hutter,
• Mariko F. Matsuura,
• Diane J. Rowold and
• Steven A. Benner

Beilstein J. Org. Chem. 2014, 10, 2348–2360, doi:10.3762/bjoc.10.245

• systems; solid-phase DNA synthesis; synthetic biology; Introduction It has been nearly 50 years since the first solid-phase synthesis of DNA by Letsinger and Mahadevan [1][2]. This work laid the platform for new strategies in oligonucleotide synthesis, culminating in the development of phosphoramidite

Reversibly locked thionucleobase pairs in DNA to study base flipping enzymes

• Christine Beuck and
• Elmar Weinhold

Beilstein J. Org. Chem. 2014, 10, 2293–2306, doi:10.3762/bjoc.10.239

• extrahelical side and thus has an important contribution to the overall DNA-binding energy of M.TaqI. Experimental Solid-phase DNA synthesis was performed on an ABI DNA Synthesizer 392 in 1 µmol scale following the standard cycles recommended by Applied Biosystems with a coupling time of 30 s for the natural

Second generation silver(I)-mediated imidazole base pairs

• Susanne Hensel,
• Nicole Megger,
• Kristina Schweizer and
• Jens Müller

Beilstein J. Org. Chem. 2014, 10, 2139–2144, doi:10.3762/bjoc.10.221

• ) ions from minor and major groove, respectively. Synthesis of methylimidazole-based nucleosides and their corresponding phosphoramidites required for automated solid-phase DNA synthesis. a) 1. NaH, 2. Hoffer’s chloro sugar, CH3CN, 0 °C to ambient temperature, 3 h; b) aqueous NH3 (25%), CH3OH, ambient

A new building block for DNA network formation by self-assembly and polymerase chain reaction

• Holger Bußkamp,
• Sascha Keller,
• Marta Robotta,
• Malte Drescher and
• Andreas Marx

Beilstein J. Org. Chem. 2014, 10, 1037–1046, doi:10.3762/bjoc.10.104

• that was successfully used in solid phase DNA synthesis. In thermal denaturation studies Y-shaped bDNA indicates comparable behavior to the linear non-branched counterpart, thus forming a B-DNA conformation. Furthermore, the branched DNA self assembles into stable networks when short self-complimentary