Nucleic acid biosensing

doi:10.12211/2096-8280.2025-015

Abstract

Abstract:

Deoxyribonucleic acid (DNA) molecules store and transmit genetic information in all living organisms and some viruses. In vitro, it can be utilized as a programmable and versatile molecular self-assembling building block to construct functional materials. On the basis of the DNA double helix model and the specific rules of base complementary pairing, where adenine (A) with thymine (T) and cytosine (C) pairs with guanine (G) researchers have developed various DNA self-assembly techniques including the DNA tile technique, DNA origami and laterally developed single strand tile methods over the past few decades. These technologies have been employed to construct a variety of two- or three-dimensional nanoscale structures and devices with controllable sizes and morphologies, as well as dynamic response properties to external environmental stimulus. Researchers have continually demonstrated the exceptional construction capabilities of DNA molecules and have constructed a variety of DNA nanostructures (from simple four-arm nucleic acid junction to origami arrays up to 2-3 microns in size, from two-dimensional planar shapes to three-dimensional complex and twisted structures, and from simple nano-tweezers to command-executing DNA walkers). Due to the unparalleled programmability, precise addressability, editable biological functions, tissue permeability and inherent biocompatibility of DNA nanostructures, they have hold significant potential in molecular biology research fields such as biosensing, bioimaging, tissue engineering, and drug delivery. In this review, first, we summarize the construction of two-dimensional and three-dimensional DNA nanostructures using various DNA self-assembly technologies. Then, the dynamic transformation of DNA nanostructures driven by two distinct types of driving forces have been categorized and discussed. Finally, the prospects of biosensors based on DNA self-assembly technology, as well as the challenges in this field including enhancing the efficiency and stability of synthesized structures, advancing dynamic monitoring technology in vivo, establishing multiplex and rapid detection methods, and exploring new directions for integration with CRISPR technology, have been explored.

Key words: DNA self-assembly, 2D DNA nanostructure, 3D DNA nanostructure, dynamic DNA nanostructure, biosensing, biomarkers

摘要：

脱氧核糖核酸（DNA）分子在生命体内发挥储存和传递遗传信息的生物学功能，在体外，它还可以作为一种可编程的分子自组装纳米材料。基于DNA双螺旋模型和碱基互补配对原则，研究人员开发了多种DNA自组装技术并以此构建了尺寸、形貌可控以及具有动态响应特性的二维和三维纳米结构。鉴于DNA纳米结构具有可控的尺寸、精确的寻址能力、可定制的生物功能、良好的生物相容性等特点，其已被广泛用于生物传感、生物成像、组织工程、药物递送等分子生物学研究领域。本篇综述首先概述了利用DNA自组装技术构建的二维和三维DNA纳米结构；然后分类讨论了DNA链置换驱动以及环境刺激驱动的DNA纳米结构动态变构；并重点介绍了DNA纳米结构的生物传感应用；最后，本综述展望了基于DNA自组装技术构建的生物传感器的发展前景与面临挑战，包括提高DNA纳米结构的合成效率和稳定性、开发体内动态监测技术、建立多重检测与快速诊断方法以及探索与CRISPR技术联用的新发展方向。

关键词: DNA自组装技术, 2D DNA纳米结构, 3D DNA纳米结构, 动态DNA纳米结构, 生物传感, 生物标志物

CLC Number:

YAO Linxin, SONG Lu, LI Min, ZUO Xiaolei. Nucleic acid biosensing[J]. Synthetic Biology Journal, DOI: 10.12211/2096-8280.2025-015.

姚林欣, 宋璐, 李敏, 左小磊. 核酸生物传感[J]. 合成生物学, DOI: 10.12211/2096-8280.2025-015.

Figures/Tables 11

Fig. 1 History of DNA self-assembly technology(a) Four-arm junction, origins of DNA nanotechnology[1,6]; (b) The first 3D DNA nanostructure[7]; (c) The first 2D periodic DNA lattices[8]; (d) The 2D lattices breaking through the millimeter scale[9]; (e) DNA origami self-assembly technique[3]; (f) 3D hollow origami box[10]; (g) Three-dimensional structures built by multi-layer origami stack[11]; (h) 3D twisted origami[12]; (i) Two-dimensional arrays constructed using origami as a tile[13]; (j)Single strand tiles assembly technique[4]; (k) 3D teddy bear[14]; (l) Gigadalton-scale dodecahedron built by V-brick[15]; (m) The proposal of the concept of framework nucleic acids (FNAs)[16-17]; (n) Meta-DNA assembly technique[5]; (o) Right-handed dsM-DNA[5]

Fig. 2 2D DNA nanostructures(a) DNA tile: DX (DNA Double Crossover) (left), 4 × 4 tile (center), 6 × 4 tile (right) and the images of 2D arrays constructed from these structures (bottom)[34]; (b) 2D DNA origami smiley face[3]; (c) Asymmetric Chinese map origami[29]and concentric circle origami with curvature[28]; (d) Grid origami constructed by four-arm junctions[31] and bird and flower patterns constructed by multi-arm junctions[32]; (e) Mona Lisa image constructed with origami as a tile[33]; (f) Synthesized Chinese characters constructed by Single Strand Tile (SST) self-assembly strategy[4]

Fig. 3 3D DNA nanostructures(a) DNA cube[7] (left), DNA tetrahedron[35] (center), DNA-truncated octahedron[36] (right); (b) DNA polyhedra constructed by N-arms junctions[37]; (c) Square nut and railed bridge built based on honeycomb-pleated DNA origami strategy[11] (top), beachballs constructed by base pair insertions and deletions in the honeycomb lattice[12] (bottom); (d) Introduction of dihedral angles between adjacent planes (left), 3D nanoflask and sphere (right)[28]; (e) Single strand tile self-assembly strategy for synthesizing 3D teddy bear[14]; (f) Various siliconized framework nucleic acids[42]

Fig. 4 Strand displacement-driven dynamic variational configurations(a) DNA nanotweezer[43]; (b) Nanotweezer using two DX as dual arms[44]; (c) DNA walker[47]

Fig. 5 Environmental stimulus-driven dynamic deformation(a) Enzyme-driven DNA walker [50]; (b) DNA plasmonic nanoclock[51]; (c) I-motif structure[57]; (d) G-quadruplex structure[57]; (e) pH-responsive TDF structure[54]; (f) Light-induced conformational changes of origami nanostructures[56]

Fig. 6 Nucleic acids sensing based on DNA nanotechnology(a) TDF probes for detection of miRNA-141[62]; (b) A "soft lithography" approach to engineer the interface of electrochemical sensors[64]; (c) Detection of miRNAs using the HCR (Hybridization Chain Reaction) amplification strategy[65]; (d) DNA nanocubes for detection of miRNA[67]; (e) Ultrafast dual-layer 3D DNA nanosensor[69]; (f) The DNA origami for visual detection of SNP (Single Nucleotide Polymorphism)[79]

Fig. 7 Ion sensing based on DNA nanotechnology(a) Artificial enzyme hydrogel for detection of Pb2+[88]; (b) Multiplex detection of Metal Ions in TDF-encoded microchannels[89]; (c) Hybridization of i-motif with complementary chains narrows pH response range for more sensitive detection of extracellular pH changes[99]; (d) DNA triplexes with different levels of C-G-C enable programmable pH detection range[100]

Fig. 8 Small molecules sensing based on DNA nanotechnology(a) TPF for detection of Cocaine[107]; (b) Artificial enzyme hydrogel for detection of Cocaine[108]; (c) DNA nanotweezer for detection of ATP[112]; (d) Simultaneous detection of AFB1 and OTA by dual DNA nanotweezers[113]

Fig. 9 Proteins sensing based on DNA nanotechnology(a) Fiber optic surface plasmon resonance biosensor for detection of thrombin[122]; (b) DNA nanobelt based on the ELASA method for PSA detection[126]; (c) Concentric square DNA origami for single molecule C-reactive protein biosensing[133]; (d) DNA walker for exosomes detection[139]

Fig. 10 Cells sensing based on DNA nanotechnology(a) Detection of cancer cells with TDF probes and multibranched hybridization chain reaction amplification[144]; (b) Hydrogel used for cloaking and decloaking circulating tumor cells[145]; (c) PDN-based CTC fluorescence analysis[146]; (d) DNA walker-powered ratiometric SERS cytosensor of circulating tumor cells[147]

Fig. 11 Bacteria sensing based on DNA nanotechnology(a) Streptococcus pneumoniae biosensor based on TDF[152]; (b) Sensitive detection of Staphylococcus aureus by spherical nucleic acid triggered CRISPR/Cas12a and Poly T-CuNP[154]; (c) Simultaneous determination of different bacteria based on colorimetric enzyme assay[156]; (d) Super-multiplexed, high-throughput bacterial sensor[158]

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