(51f) Spherical Nucleic Acids As Stimuli-Responsive Synthons and Live-Cell Probes

Spherical nucleic acids (SNAs), nanoparticles functionalized with a dense and radially oriented layer of DNA, have emerged as a unique class of nanomaterials and opened new opportunities in materials synthesis and biodiagnostics. The presence of DNA makes these structures responsive to stimuli. In this talk, I will discuss two specific examples that show how the inherent responsiveness of the DNA sequences to a variety of different chemical species can be leveraged to (i) engineer dynamic materials assembled from SNAs and (ii) design SNA-based chemical probes for live-cell analysis.

In the first example, I will focus on how multivalent cations induce structural changes in DNA which alter interparticle distances in crystalline assemblies of SNAs. In the context of materials synthesis, the SNA platform represents a powerful synthon owing to (i) its modular structure, (ii) the specific interactions between SNAs functionalized with complementary DNA, and (iii) the ease of synthesis of sequence-defined SNAs with desired DNA lengths. SNAs can be analogized as programmable atom equivalents (PAEs) in which the nanoparticle core is the “atom” and the DNA forms the programmable “bond”. Unlike atomic systems, PAEs allow the atom and bond to be varied independently. Therefore, by changing the nanoparticle size, shape, and composition and the DNA sequence, length, and density, a rich phase-space of matter can be accessed. By modulating the DNA length post-synthetically, a new class of dynamic metamaterials can be accessed. Here, I will discuss how multivalent metal cations induce the contraction and re-expansion of the DNA bonds by >85% in length, resulting in >65% changes in crystal volume, all while maintaining crystallinity. This new approach represents a powerful strategy to alter superlattice structure and stability, which can impact diverse applications through dynamic control of material properties, including optical, magnetic, and mechanical properties.

In the second example, I will describe how different DNA sequences change structure in response to specific chemical species and can, therefore, be utilized to develop SNA-based chemical probes for live-cell analysis. The detection of intracellular analytes in live single cells is a grand challenge as most current techniques require (i) the analysis of a bulk population of cells, (ii) cell lysis, or (iii) the use of transfection reagents. SNAs enable the design of highly tailorable intracellular probes because: (i) unlike linear DNA sequences, SNAs are taken up by cells without the need for transfection reagents and are resistant to nuclease degradation in the cellular environment; (ii) by judiciously choosing the DNA sequence (e.g. using aptamers that bind to specific analytes or complementary sequences that bind cellular RNA), it is possible to detect a wide range of analytes; and (iii) the modular structure allows different nanoparticle cores to be used for added functionality. I developed a new class of signaling aptamers called “FIT-aptamers”. These aptamers contain a visco-sensitive dye that is forced to intercalate or FIT between base pairs upon target binding, turning the fluorescence on due to the restricted rotation of the dye. The FIT strategy reduces false-positive signals common to all fluorophore-quencher systems, provides up to 20-fold fluorescence enhancement upon target binding, and allows target detection down to nanomolar concentrations in complex milieu such as human serum. Arranging the FIT-aptamers into an SNA-architecture allows them to be used as intracellular probes. Moreover, by using a functional enzyme as the nanoparticle core, it is possible to detect analytes for which aptamers are not known. We have validated the use of these protein-based SNAs as intracellular probes by detecting intracellular pH and glucose levels in 8 different cell lines. Taken together, these advances represent a promising step toward the use of SNAs as detection tools for the molecular profiling of cells and identification of diseases based on intracellular signatures.