Paper Highlights

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.
 
 

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.

 

Block copolymer micellization as a protection strategy for DNA origami

Nayan P. Agarwal, Michael Matthies, Fatih F. N. Gür, Kensuke Osada, Thorsten L. Schmidt

Angew. Chem. Int. Ed. 2017, DOI:10.1002/anie.201608873
 
DNA nanotechnology enables the synthesis of nanometer-sized objects that can be site-specifically functionalized with a large variety of materials. For these reasons, DNA-based devices such as DNA origami are being considered for applications in molecular biology and nanomedicine. However, many DNA structures need a higher ionic strength than that of common cell culture buffers or bodily fluids to maintain their integrity and can be degraded quickly by nucleases. To overcome these deficiencies, we coated several different DNA origami structures with a cationic poly(ethylene glycol)–polylysine block copolymer, which electrostatically covered the DNA nanostructures to form DNA origami polyplex micelles (DOPMs). This straightforward, cost-effective, and robust route to protect DNA-based structures could therefore enable applications in biology and nanomedicine where unprotected DNA origami would be degraded.