3D DNA refers to several related concepts revolving around the three-dimensional structure and manipulation of DNA. It's not a single, unified concept, but rather an umbrella term encompassing different approaches and applications.
1. The Intrinsic 3D Structure of DNA
At its core, DNA's fundamental structure is inherently three-dimensional. The well-known double helix is a 3D configuration: two chains of nucleotides paired and twisted into a right-handed helix, resembling a spiral staircase. [Reference: The 3-dimensional structure of DNA is called a double helix because each DNA molecule consists of two chains of nucleotides that are paired along their lengths and twisted into a right-handed helix that resembles a spiral staircase (see below).] This foundational 3D structure is crucial for DNA's function in carrying genetic information. [Reference: Deoxyribonucleic acid or DNA is a molecule which is the carrier of genetic information in nearly all the living organisms.]
2. DNA Nanotechnology and 3D DNA Origami
Scientists leverage DNA's base-pairing properties to create custom-designed, self-assembling 3D structures. This field, known as DNA nanotechnology, allows for the construction of intricate nanoscale shapes and devices. Software like caDNAno aids in designing DNA sequences for folding into precise 3D structures, such as honeycomb shapes. [References: Rapid prototyping of 3D DNA-origami shapes with caDNAno, DNA nanotechnology exploits the programmable specificity afforded by base-pairing to produce self-assembling macromolecular objects of custom shape., Rapid prototyping of 3D DNA-origami shapes with caDNAno ... ] This opens avenues for applications in drug delivery, biosensors, and more. [Reference: Polyhedra self-assembled from DNA tripods and characterized with ... ] Furthermore, researchers are working on creating robust 3D DNA crystals through post-assembly ligation. [Reference: Making Engineered 3D DNA Crystals Robust | Journal of the ... ]
3. 3D Genome Organization and 3D DNA Assembly
The term "3D DNA" can also refer to the three-dimensional organization of a genome within a cell's nucleus. Techniques like Hi-C sequencing map these interactions, revealing how different regions of the genome are spatially arranged and how this organization impacts gene regulation. Pipelines like the one available on GitHub (https://github.com/aidenlab/3d-dna) are used to assemble this 3D genome data, including options for both haploid and diploid modes. [Reference: The pipeline consists of one bash wrapper script run-asm-pipeline.sh that calls individual modules to assemble a genome., 3d-dna "-m" parameter is : -m haploid/diploid - specifies whether to run the pipeline in the haploid (Hs2-HiC) or diploid (AaegL4) mode.]
4. 3D DNA Microarrays
Commercial applications also utilize the term "3D DNA." For example, Toray's 3D-Gene technology involves high-sensitivity DNA chips for various applications, including genomic research. [References: 3D-Gene®【Toray DNA Chips、Contract Microarray 】 | TORAY, 3D-Gene® Scanner | 3D-Gene® [Toray DNA Chips] | TORAY] These are examples of how the term "3D DNA" is used in a commercial context.
