Programmable Engineering of a Biosensing Interface with Tetrahedral DNA Nanostructures for Ultrasensitive DNA Detection

Abstract

Self-assembled DNA nanostructures with precise sizes allow a programmable "soft lithography" approach to engineer the interface of electrochemical DNA sensors. By using millimeter-sized gold electrodes modified with several types of tetrahedral DNA nanostructures (TDNs) of different sizes, both the kinetics and thermodynamics of DNA hybridization were profoundly affected. Because each DNA probe is anchored on an individual TDN, its lateral spacing and interactions are finely tuned by the TDN size. By simply varying the size of the TDNs, the hybridization time was decreased and the hybridization efficiency was increased. More significantly, the detection limit for DNA detection was tuned over four orders of magnitude with differentially nanostructured electrodes, and achieved attomolar sensitivity with polymeric enzyme amplification.

Electrochemical detection of nucleic acids, proteins, small molecules and cells using a DNA-nanostructure-based universal biosensing platform

“…As a universal biosensing platform, we have tested this protocol to detect DNA, microRNA (mir-21, mir-141 and others), proteins (antigens such as prostate-specific antigen (PSA), thrombin and others) and small molecules (cocaine) [19][20][21][22][23][24][25][26] . Furthermore, we have used our detection platform to detect target molecules in complicated biological fluids such as cell lysates, tissue extracts and human serum, and we observed excellent sensing performance.…”

“…Next, we thoroughly investigated the programmability of the DNA-nanostructure-based biosensing interface. We demonstrated that the use of TDNs with various precise sizes supported a 'soft lithography'-like means to engineer the interface for electrochemical DNA sensing 20 . Then, we generalized our with the aid of structural prediction tools (e.g., RNAstructure and NUPACK software) to predict the secondary structure 20 .…”

“…We demonstrated that the use of TDNs with various precise sizes supported a 'soft lithography'-like means to engineer the interface for electrochemical DNA sensing 20 . Then, we generalized our with the aid of structural prediction tools (e.g., RNAstructure and NUPACK software) to predict the secondary structure 20 . The important design principle is that each sequence has minimal or no undesired secondary structures, but after hybridization with three other sequences, every two complementary parts have more negative free energy to form a stable structure.…”

“…We have demonstrated that one can finely tune the kinetics and thermodynamics of interfacial biomolecular recognition by varying the size of TDNs. Under optimal conditions, this TDN-based biosensing platform can greatly increase target accessibility and improve the sensitivity by several orders of magnitude for various types of molecular targets (DNA, RNA, proteins and small molecules) and even whole cells [19][20][21][22][23][24][25][26] .…”

“…We also translated the DNA-based biosensing interface into an immunological one by site-specifically anchoring antibodies on individual TDNs, which led to a versatile protein-sensing platform 21 . Overall, our protocol has been standardized in our laboratory and successfully used to detect various types of targets, including DNA, RNA, proteins, small molecules and whole cells [19][20][21][22][23][24][25][26][27] . A comprehensive overview of the protocol is provided in Figure 1.…”