Nucleotide Chemistry for RNA Nanoparticle Labeling, Conjugation, and Synthesis

Nanotechnology and Therapeutics ................................................................................. 181 9.2.1 Overview ................................................................................................................. 181 9.2.2 Stabilizing Modifications ...................................................................................... 182 9.2.3 Functional Modifications ...................................................................................... 183

9.3 Introducing Modifications to RNA through Chemical Synthesis .............................. 183 9.3.1 Overview ................................................................................................................. 183 9.3.2 Direct Incorporation of Conjugates and Reactive Groups during Solid

Phase RNA Synthesis ............................................................................................ 183 9.3.2.1 Modified Nucleotide Phosphoramidites Bearing Conjugate

Groups or Reactive Intermediates for Incorporation into Solid Phase Synthesis ....................................................................................... 185

9.3.2.2 Incorporating Conjugates through Nonnucleoside Linkers and Solid Supports ......................................................................................... 186

9.3.3 Postsynthetic Methods for Adding Labels and Conjugate Groups to RNA ......186 9.3.3.1 Chemistry for Postsynthesis Conjugation ........................................... 186

9.3.4 Functionality Transfer Reactions ......................................................................... 188 9.4 Introducing Conjugates and Labels through Combined Chemical and

Enzymatic Strategies ......................................................................................................... 190 9.5 Summary and Conclusions .............................................................................................. 191 Acknowledgments ...................................................................................................................... 191 References ..................................................................................................................................... 192

enabled the rapid expansion of the field of DNA nanotechnology first pioneered by Seeman and coworkers (Chen and Seeman, 1991; Seeman, 1991; Seeman, 2003). A large number of 2D and 3D DNA nanostructures have been constructed and characterized using standard, unmodified DNA building blocks for bottom up assembly (He et al., 2005; Seeman, 2010b). Recent activity in the field has focused on the creation of nanoscale devices that integrate sequence facilitated nanostructure assembly with functional activities, including biological activity as well as computational and physical operations (Krishnan and Simmel, 2011).