Artificial bioconjugates with naturally occurring linkages: the use of phosphodiester

• Takao Shoji,
• Hiroki Fukutomi,
• Yohei Okada and
• Kazuhiro Chiba

Beilstein J. Org. Chem. 2018, 14, 1946–1955, doi:10.3762/bjoc.14.169

• ’-phosphitylation; phosphodiester bonds; Introduction Peptides and oligonucleotides are of exceptional importance since they are promising pharmaceutical candidates for the treatment of a range of diseases that are beyond traditional small molecule drugs [1][2][3][4][5][6][7]. Due to their iterative structures

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

• the next one are cleaved by a variety of enzymes [1]. The phosphodiester bonds of DNA are hydrolyzed, depending on the enzyme, either to a 3´- or 5´-phosphate, whereas the bonds in RNA, with few exceptions (above all RNase H-catalyzed cleavages) undergo transesterification to a 2´,3´-cyclic phosphate

• transphosphorylation by departure of the 5´-linked nucleoside [3]. The half-life at pH 6–7 and 25 °C is around 10 years [4][5], the enzymatic cleavage by RNase A being 3∙1011 times faster [6]. Interestingly, the RNA phosphodiester bonds are additionally subject to cleavage by RNA itself, viz. by RNA sequences known as

• position. Recent DFT calculations suggest the barrier to be about 30 kcal mol−1 [27]. While several lines of evidence suggest that the cleavage of the RNA phosphodiester bonds proceeds via a phosphorane intermediate rather than a phosphorane-like transition state [28][29][30], this is not necessarily the

Enzyme-free genetic copying of DNA and RNA sequences

• Marilyne Sosson and
• Clemens Richert

Beilstein J. Org. Chem. 2018, 14, 603–617, doi:10.3762/bjoc.14.47

• enzymes and ribozymes, relying on solely on base pairing for molecular recognition and chemical reactivity to drive the formation of phosphodiester bonds in aqueous media. This is what is usually referred to as "enzyme-free copying" (Figure 1). Studies on enzyme-free copying of genetic polymers date back

From chemical metabolism to life: the origin of the genetic coding process

• Antoine Danchin

Beilstein J. Org. Chem. 2017, 13, 1119–1135, doi:10.3762/bjoc.13.111

• hydroxyl groups of ribose, resulting in a mixture of 2′,5′- and 3′,5′-phosphodiester bonds. By contrast, when peptides are present in the mixture, polymerisation is essentially happens through 3′,5′-phosphodiester bonds [52], stressing again the importance of peptides at the onset of prebiotic nucleic-acid

Interactions between cyclodextrins and cellular components: Towards greener medical applications?

• Loïc Leclercq

Beilstein J. Org. Chem. 2016, 12, 2644–2662, doi:10.3762/bjoc.12.261

• phosphodiester bonds. There are two types of nucleic acids according to the sugar: deoxyribose and ribose for deoxyribonucleic acid, DNA, and ribonucleic acid, RNA. Nucleic acids function in encoding, transmitting and expressing genetic information. As nucleic acids allow the synthesis of proteins their

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

• the DNA [46]. Such an effect of significant change in Tm was not observed for compounds 1–4 and 7 and 8. Base selectivity: Restriction endonucleases recognise particular bases in the DNA and subsequently cleave the DNA by hydrolysis of the phosphodiester bonds. Inhibition of endonuclease activity in

• 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