Paper Highlights

Micellar Brønsted Acid Mediated Synthesis of DNA-Tagged Heterocycles

M. Klika Škopić, K. Götte, C. Gramse, M. Dieter, S. Pospich, S. Raunser, R. Weberskirch, A. Brunschweiger

DNA-encoded libraries are increasingly used of drug identification. However, the reactivity of the DNA imposes limitations on the choice of chemical methods for encoded library synthesis. Amphiphilic block copolymers covalently functionalized with sulfonic acid moieties in the lipophilic portion assemble in water and locate the Brønsted catalyst in micelles. These acid nanoreactors enabled the reaction of DNA-conjugated aldehydes to diverse substituted tetrahydroquinolines and aminoimidazopyridines by Povarov and Groebke–Blackburn–Bienaymé reactions, respectively.

Rolling circle amplification shows a sinusoidal template length-dependent amplification bias

Bastian Joffroy, Yavuz O. Uca, Domen Prešern, Jonathan P. K. Doye, Thorsten L. Schmidt

Nucleic Acids Res. 2018, DOI:10.1093/nar/gkx1238

Small DNA circles can serve as templates for rolling circle amplification (RCA), which is a common and extremely robust amplification mechanism for nucleic acids. We discovered a strong template length-dependent amplification efficiency bias of RCA with the same periodicity as B-DNA.

A cytidine phosphoramidite with protected nitroxide spin label: Synthesis of a full-Length TAR RNA and investigation by in-line probing and EPR spectroscopy

Timo Weinrich, Eva A. Jaumann, Ute Scheffer, Thomas F. Prisner, Michael W. Göbel

Chem. Eur. J. 2018, DOI:10.1002/chem.201800167

A photolabile 2-nitrobenzyloxy methyl group can protect nitroxide spin labels against all critical conditions of chemical RNA synthesis and enzymatic strand ligation.

Structural transformation of wireframe DNA origami via DNA polymerase assisted gap-filling

Nayan P. Agarwal, Michael Matthies, Bastian Joffroy, Thorsten L. Schmidt

ACS Nano 2018, DOI:10.1021/acsnano.7b08345

In this work, we have explored the possibility to synthesize the complementary sequences to single-stranded gap regions in the DNA origami scaffold cost effectively by a DNA polymerase rather than by a DNA synthesizer.

Reversible modification of DNA by methyltransferase-catalyzed transfer and light-triggered removal of photo-caging groups

L. Anhäuser, F. Muttach, A. Rentmeister

Chem. Commun. 2018, DOI:10.1039/C7CC08300A

Methyltransferases are powerful tools for site-specific transfer of non-natural functional groups from synthetic analogs of their cosubstrate S-adenosyl-L-methionine (AdoMet). We present a new class of AdoMet analogs containing photo-caging (PC) groups in their side chain, enzymatic transfer of PC groups by a promiscuous DNA MTase as well as light-triggered removal from the target DNA. This strategy provides a new avenue to reversibly modulate the functionality of DNA at MTase target sites.

Enzyme-free ligation of 5'-phosphorylated oligodeoxynucleotides in a DNA nanostructure

Markus Kramer, Clemens Richert

Chem. Biodiversity 2017, DOI:10.1002/cbdv.201700315 (open access)

Chemical ligation of synthetic oligonucleotides in small origami nanostructures is higher yielding than in linear duplexes.