Design and Visualization of DNA/RNA Nanostructures from Branched Oligonucleotides Using Blender Software

• Published in: Russian journal of bioorganic chemistry Vol. 45; no. 6; pp. 608 - 618
• Main Authors: Bakulina, A. Yu, Rad’kova, Z. V., Burakova, E. A., Benassi, E., Zatsepin, T. S., Fokina, A. A., Stetsenko, D. A.
• Format: Journal Article
• Language: English
• Published: Moscow Pleiades Publishing 01-11-2019; Springer Nature B.V
• Subjects: Biochemistry; Biomedical and Life Sciences; Biomedicine; Bioorganic Chemistry; Chain branching; Deoxyribonucleic acid; DNA; Fullerenes; Life Sciences; Nanostructure; Oligonucleotides; Organic Chemistry; Ribonucleic acid; RNA; Software; Tetrahedra; Three dimensional models; branched oligonucleotides; template-directed assembly; DNA nanotechnology; click chemistry; nucleic acids; computer modelling; solid-phase synthesis
• ISSN: 1068-1620; 1608-330X
• DOI: 10.1134/S1068162019060062

Recently, three-dimensional nucleic acid nanostructures have attracted great interest, which have been made available through the DNA origami technique. We have proposed a different way of constructing nucleic acid nanoobjects, namely, template-directed assembly employing branched oligonucleotides as templates and building blocks, which include nonnucleotidic linkers, particularly, branching units for connecting three or more oligonucleotide chains. For the design and 3D modelling of such nanostructures as DNA tetrahedron, DNA cube and DNA fullerene C24, we have used Blender software. As we found, Blender not only allows one to visualize complex DNA and RNA nanostructures, but also helps to choose the parameters for their synthesis.