Chemical modifications and reactions in DNA nanostructures
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Conjugation of functional groups to DNA nanostructures DNA is chemically a rather inert molecule and, in Nature, the function of DNA is to store and transfer information. Its chemical inertness provides DNA with the advantages of high stability and high fidelity in forming predesigned DNA structures by DNA hybridization. DNA nanostructures built by self-assembly of DNA strands, therefore, have limited chemical functionality, and DNA is mainly used as a molecular scaffold. Exceptions include artificially selected DNA aptamers that provide selective recognition of other (bio)molecules1 and artificial DNA structures, the so-called DNAzymes that can catalyze chemical reactions.2 To make functional DNA nanostructures, integration of other materials and molecules is most often required and, with a few exceptions, this requires chemical functionalization of DNA strands. Fortunately, a variety of chemical modifications are available from commercial DNA suppliers, allowing for the introduction of desired artificial functional groups into the DNA sequence. Custom oligonucleotides with any desired sequence are prepared by automated synthesis using phosphoramidite nucleoside building blocks, which are made up of an activated
phosphate bridge precursor linked to the protected deoxyribose ring and the nucleobase (Figure 1a).3 A vast variety of non-nucleosidic phosphoramidites or phosphoramidite nucleoside analogues are available for the introduction of chemical modifications. Some linkers are only used for the introduction of modifications at the 5′-end of oligonucleotides (Figure 1b), while others can be used to introduce nonnucleosidic modifiers at the 3′, 5′ (positions indicated in Figure 1a), or internally in the sequence (Figure 1c). The nucleosidic modifiers contain the modification on the nucleobase (Figure 1d). These modifications can be placed at any position in a DNA strand and conserve the hybridization ability. DNA strands containing such bases may also be compatible with enzymes (e.g., in polymerase chain reaction [PCR] reactions).4 When such modified DNA sequences are integrated in large DNA nanostructures, the functional groups can be placed at almost any specific position in the structure. The integration of modified DNA strands into DNA nanostructures (e.g., to DNA origami) can essentially be done in two different ways. In the first method, the modified strand(s) is also a staple strand (i.e., an integral part of the origami structure itself) that hybridizes to the long scaffold strand. In the second method, the modified strands are not staple strands.
Kurt V. Gothelf, Centre for DNA Nanotechnology, Aarhus University, Denmark; [email protected] doi:10.1557/mrs.2017.276
• VOLUME © 2017 Materials Research Society MRS 42 • ofDECEMBER 2017 •atwww.mrs.org/bulletin Downloaded from https://www.cambridge.org/core. RMIT University Library, on 08 Dec 2017 at 13:05:32, subject to theBULLETIN Cambridge Core terms use, available https://www.cambridge.org/core/terms. https://doi.org/10.1557/mrs.2017.276
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