Branched Oligonucleotide Hybrids

Branched Oligonucleotide Hybrids

One of the non-biological applications for DNA is nanostructuring. Because oligo- and polynucleotides engage in predictable base pairing interactions, designed three-dimensional structures can be generated, based on the hybridization and folding of such strands. A wide array of structures on the scale of nanometers have been created using unmodified DNA. For applications in material sciences, branched oligonucleotides are being synthesized that consist of an organic molecule as branching element and oligonucleotides appended to it through covalent bonds. Because these synthetic species are constructed from two different classes of compounds, they are called 'hybrids'.

References

DNA nanostructuring

a)  P. W. K. Rothemund, Folding DNA to create nanoscale shapes and patterns. Nature 2006, 440, 297-302.

b)  Jones, M. R.; Seeman, N. C.; Mirkin, C. A. Programmable materials and the nature of the DNA bond. Science 2015, 347, 840.

Branched oligonucleotide hybrids

a)  M. Meng, C. Ahlborn, M. Bauer, O. Plietzsch, S. A. Soomro, A. Singh, T. Muller, W. Wenzel, S. Bräse, C. Richert, Two base pair duplexes suffice to build a novel material. ChemBioChem 2009, 10 , 1335-1339.

b)  A. Singh, M. Tolev, M. Meng, K. Klenin, O. Plietzsch, C. I. Schilling, T. Muller, M. Nieger, S. Bräse, W. Wenzel, C. Richert, Branched DNA that forms a solid at 95 °C. Angew. Chem. Int. Ed. 2011, 50, 3227-3231.

c)  H. Griesser, M. Tolev, A. Singh, T. Sabirov, C. Gerlach, C. Richert, Solution-phase synthesis of branched DNA hybrids based on dimer phosphoramidites and phenolic or nucleosidic cores. J. Org. Chem. 2012, 77, 2703-2717.

d)  A. Singh, M. Tolev, C. Schilling, S. Bräse, H. Griesser, C. Richert, Solution-phase synthesis of branched DNA hybrids via H-phosphonate dimers. J. Org. Chem. 2012, 77, 2718-2728.

e)  A. Schwenger, T.P. Jurkowski, C. Richert, Capturing and stabilizing folded proteins in lattices formed with branched oligonucleotide hybrids. ChemBioChem 2018, 19, 1523-1530.

f)  V. Damakoudi, T. Feldner, E. Dilji, A. Belkin, C. Richert, Hybridization networks of mRNA and branched RNA hybrids. ChemBioChem 2020, 22, 924-930.