Concentric DNA Amplifier That Streamlines In-Solution Biorecognition and On-Particle Biocatalysis

Abstract

Colloidal nanoparticle biosensors capable of on-particle biocatalysis are powerful tools for amplified detection of biomolecules. The development and practical uses of such concentric amplifiers can be complicated because of the on-particle biorecognition that involves varying interfacial factors at the biomolecule–nanoparticle interfaces. Herein, we reason that a nanoparticle biosensor equipped with an in-solution biorecognition element may be better fabricated, predicted, controlled, and performed. The in-solution biorecognition shall also be streamlined with the on-particle biocatalysis so that the overall analytical and kinetic performance is not compromised. As a testbed, we introduce a concentric DNA amplifier driven by an enzyme-powered three-dimensional DNA nanomachine, where a DNA walker can be instantly assembled onto a spherical nucleic acid (SNA) track through a polyadenosine anchor. As such, the free DNA walker can participate in reactions in a homogeneous solution before assembling to the SNA track. The instant and stable assembly enabled by both adsorption and complementary base pairing also ensures rapid on-particle biocatalysis. We demonstrate that the in-solution biorecognition effectively eliminates the binding hindrance encountered by the on-particle biorecognition and thus significantly reduced energy barriers for the detection of nucleic acids and proteins. Because of the in-solution biorecognition, our system can also be plugged readily into complex DNA strand displacement networks for rapid signal amplification.

Stimuli-Responsive Three-Dimensional DNA Nanomachines Engineered by Controlling Dynamic Interactions at Biomolecule-Nanoparticle Interfaces

“…A salt-aging protocol that increased the concentration of NaCl to 0.75 M over a period of 24 h was then applied according to our previously established protocol. 43 After the salt-aging step, DNA-conjugated AuNPs were then washed three times using 1× PBS buffer and centrifuged at 13 500 rpm for 30 min. The obtained 3D DNA nanomachine was finally dispersed in 1× PBS buffer at a final concentration of 1 nM and stored at 4 °C.…”

“…The spherical nucleic acid (SNA) track was prepared using a previously reported protocol by our lab. ,− Briefly, a 20 μL solution containing 50 μM thiolated signal reporter sequence was mixed with 500 μL of 1 nM AuNPs. This mixture was incubated at room temperature for 12 h and then was slowly mixed with 20 μL of 3 M NaCl, followed by 10 s of sonication.…”

Target Extension‐Activated DNA Walker on Nanoparticles for Digital Counting‐Based Analysis of MicroRNA†

“…[ 20‐22 ] The DNA walking process is typically activated by the reaction of strand hybridization, enzymatic reaction (including nicking endonuclease, exonuclease, and DNAzyme), or environmental stimuli such as light irradiation. [ 23‐28 ] With the assistant of the target‐ activated “driving motor”, the DNA walking strand can “walk” steadily and progressively along the precisely designed DNA tracks. After cycles of automatically and directionally walking process, the signal to reflect the content of the target molecule will be amplified.…”

Intraparticle and Interparticle Transferable DNA Walker Supported by DNA Micelles for Rapid Detection of MicroRNA

“…Dynamic DNA nanotechnology with DNA as creating material has attracted much attention in the field of molecular and nanomachines due to the inherent molecular recognition property, programmable high-precision structure, and controllable motion of DNA. − A three-dimensional (3D) DNA walker is one of the most typical dynamic DNA nanomachines that concentrates DNA reaction strands on the surface of 3D particles (such as gold nanoparticles or silicon microparticles) and shows machine-like movements in response to external stimuli. − Owing to the excellent molecular recognition ability, self-driven capacity, accelerated reaction rate, and superior signal amplification capability, the 3D DNA walker has been applied in biosensing, intracellular imaging, molecular computation, and clinical diagnostics. − According to the anchoring type of walking arms, the 3D DNA walker can be divided into two categories: fixed-arm walker , and free-arm walker. , Nevertheless, these two types of walkers usually have to anchor the DNA tracks on the 3D landscapes via covalent or coordinate bonds, which complicates their construction processes. Moreover, the walkers have to at least statically anchor the tracks on the 3D landscapes, which hinders the relative motion between the tracks and arms, thereby reducing walking efficiency.…”