The wending rhombus: Self-assembling 3D DNA crystals

Lu, Brandon; Vecchioni, Simon; Ohayon, Yoel P.; Canary, James W.; Sha, Ruojie

doi:10.1016/j.bpj.2022.08.019

Cited by 5 publications

(2 citation statements)

References 91 publications

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“…After functionalization with ligands or DNA aptamers, 3D DNA crystals could serve as drug carriers to achieve selective targeting of macromolecule drugs (e.g., nucleic acids and proteins) to specific cells/organ, which of course cannot be achieved without further enhancements of the biocompatibility and stability of DNA crystals within biological systems [44] ; 6) After a lot of efforts, we may be able to achieve the modular design of 3D DNA crystals based on coupling of DNA molecular reaction networks with enzymatic processes, and further complete the construction of highly ordered DNA-based synthetic cells with energy conversion, communication, motion, and adaptation functions. [92][93] Seeman, who founded the area of structural DNA nanotechnology, has contributed most to its advancement and generated so much interest that it has grown into a separate discipline.…”

Section: Perspectivesmentioning

confidence: 99%

Exploring the Potential of Three‐Dimensional DNA Crystals in Nanotechnology: Design, Optimization, and Applications

Kong

Sun

et al. 2023

Advanced Science

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DNA has been used as a robust material for the building of a variety of nanoscale structures and devices owing to its unique properties. Structural DNA nanotechnology has reported a wide range of applications including computing, photonics, synthetic biology, biosensing, bioimaging, and therapeutic delivery, among others. Nevertheless, the foundational goal of structural DNA nanotechnology is exploiting DNA molecules to build three‐dimensional crystals as periodic molecular scaffolds to precisely align, obtain, or collect desired guest molecules. Over the past 30 years, a series of 3D DNA crystals have been rationally designed and developed. This review aims to showcase various 3D DNA crystals, their design, optimization, applications, and the crystallization conditions utilized. Additionally, the history of nucleic acid crystallography and potential future directions for 3D DNA crystals in the era of nanotechnology are discussed.

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Section: Perspectivesmentioning

confidence: 99%

Exploring the Potential of Three‐Dimensional DNA Crystals in Nanotechnology: Design, Optimization, and Applications

Kong

Sun

et al. 2023

Advanced Science

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“…We make use of the tensegrity triangle motif, which reliably self-assembles into 3D DNA crystals with designed unit cell parameters and space group based on the semantomorphic programming of DNA oligomers (Figures a and S1 and Table S1) and is stable across a wide range of pH values from at least pH 5.0 to pH 11.0. ,,,− Each triangle center contains one mmDNA base pair (Figure b) with two possible metal binding sites (Figure c), allowing us to test homoleptic coordination in thymine, uracil, and cytosine pairs (Figure d). Previously, we found that 5-methylcytosine pairs (PDB ID: 7SDJ) bind silver(I) exclusively at the major groove N4 position, while cytosine homopairs exhibit multiple binding sites within a single base pair (Figure e) .…”

Section: Introductionmentioning

confidence: 99%

Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals

Lu,

Ohayon,

Woloszyn

et al. 2023

J. Am. Chem. Soc.

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Metal-mediated DNA (mmDNA) presents a pathway toward engineering bioinorganic and electronic behavior into DNA devices. Many chemical and biophysical forces drive the programmable chelation of metals between pyrimidine base pairs. Here, we developed a crystallographic method using the three-dimensional (3D) DNA tensegrity triangle motif to capture single- and multi-metal binding modes across granular changes to environmental pH using anomalous scattering. Leveraging this programmable crystal, we determined 28 biomolecular structures to capture mmDNA reactions. We found that silver(I) binds with increasing occupancy in T–T and U–U pairs at elevated pH levels, and we exploited this to capture silver(I) and mercury(II) within the same base pair and to isolate the titration points for homo- and heterometal base pair modes. We additionally determined the structure of a C–C pair with both silver(I) and mercury(II). Finally, we extend our paradigm to capture cadmium(II) in T–T pairs together with mercury(II) at high pH. The precision self-assembly of heterobimetallic DNA chemistry at the sub-nanometer scale will enable atomistic design frameworks for more elaborate mmDNA-based nanodevices and nanotechnologies.

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Metal‐Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction

Vecchioni

Livernois

et al. 2023

Advanced Materials

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We are deeply grateful to the mentorship and friendship of Professor Nadrian C. Seeman, who passed away during the writing of this manuscript, and whose foundational work and guidance to DNA Nanotechnology was a light to all DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag + and Hg 2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination is explored. The tensegrity triangle is employed to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and generalized design rules for mmDNA construction are elucidated. Two binding modes are uncovered: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations show additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates.

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The wending rhombus: Self-assembling 3D DNA crystals

Cited by 5 publications

References 91 publications

Exploring the Potential of Three‐Dimensional DNA Crystals in Nanotechnology: Design, Optimization, and Applications

Exploring the Potential of Three‐Dimensional DNA Crystals in Nanotechnology: Design, Optimization, and Applications

Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals

Metal‐Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction

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