PolyA-based DNA bonds with programmable bond length and bond energy
Source abstract
Abstract
Abstract DNA-functionalized Au nanoparticles (AuNPs) have been intensively exploited as programmable atom equivalents (PAEs) for the self-assembly of molecule-like structures. However, it remains challenging to build hierarchical PAE assemblies via discrete DNA bonds at different levels. Here, we report a strategy to program DNA bond length and bond energy on PAEs using DNA encoders carrying consecutive adenines (polyA). On AuNPs, we built three types of DNA motifs with different topologic configurations, which can form bonds for PAE self-assembly. By small-angle X-ray scattering (SAXS) analysis, we found that the bond length and flexibility between the coupled PAEs can be tuned by programming the bond structure. We also found that these bonds show different bond energies and thus differ, depending on their topologic configuration, leading to different PAE assembly efficiencies. We demonstrated that the bonds at different levels can be arranged in different directions on one nanoparticle, leading to asymmetric PAEs that allow ionic strength-controlled hierarchical assembly of multiparticle structures. This programmable bonding system may provide a new route for building complex plasmonic superstructures.
Source: crossref · Quality: baseline
Research context
OpenAlex topics: Advanced biosensing and bioanalysis techniques · Gold and Silver Nanoparticles Synthesis and Applications · RNA Interference and Gene Delivery
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
References (48)
Show source-provided references
1. Sanger, J. M., Mittal, B., Pochapin, M. & Sanger, J. W. Observations of microfilament bundles in living cells microinjected with fluorescently labelled contractile proteins. J. Cell Sci. 1986, 17–44 (1986).10.1242/jcs.1986.Supplement_5.2 ↗
2. Lane, T., Serwer, P., Hayes, S. J. & Eiserling, F. Quantized viral-DNA packaging revealed by rotating gel-electrophoresis. Virology 174, 472–478 (1990).10.1016/0042-6822(90)90101-V ↗
3. Bednar, J. et al. Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc. Natl Acad. Sci. USA 95, 14173–14178 (1998).10.1073/pnas.95.24.14173 ↗
4. Routh, A., Sandin, S. & Rhodes, D. Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure. Proc. Natl Acad. Sci. USA 105, 8872–8877 (2008).10.1073/pnas.0802336105 ↗
5. Conde, C. & Caceres, A. Microtubule assembly, organization and dynamics in axons and dendrites. Nat. Rev. Neurosci. 10, 319–332 (2009).10.1038/nrn2631 ↗
6. Ke, X., Zhong, G. & Zhuang, X. Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons. Science 339, 452–456 (2013).10.1126/science.1232251 ↗
7. Garzoni, M., Okuro, K., Ishii, N., Aida, T. & Pavan, G. M. Structure and shape effects of molecular glue on supramolecular tubulin assemblies. ACS Nano 8, 904–914 (2014).10.1021/nn405653k ↗
8. Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251–260 (1997).10.1038/38444 ↗
9. Suto, R. K., Clarkson, M. J., Tremethick, D. J. & Luger, K. Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nat. Struct. Biol. 7, 1121–1124 (2000).10.1038/81971 ↗
10. Davey, C. A., Sargent, D. F., Luger, K., Maeder, A. W. & Richmond, T. J. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9Å resolution. J. Mol. Biol. 319, 1097–1113 (2002).10.1016/S0022-2836(02)00386-8 ↗
11. Schreiber, R. et al. Hierarchical assembly of metal nanoparticles, quantum dots and organic dyes using DNA origami scaffolds. Nat. Nanotechnol. 9, 74–78 (2014).10.1038/nnano.2013.253 ↗
12. Park, S. Y. et al. DNA-programmable nanoparticle crystallization. Nature 451, 553–556 (2008).10.1038/nature06508 ↗
13. Jones, M. R. et al. DNA-nanoparticle superlattices formed from anisotropic building blocks. Nat. Mater. 9, 913–917 (2010).10.1038/nmat2870 ↗
14. Macfarlane, R. J., O’Brien, M. N., Petrosko, S. H. & Mirkin, C. A. Nucleic acid-modified nanostructures as programmable atom equivalents: forging a new “Table of Elements”. Angew. Chem. Int. Ed. 52, 5688–5698 (2013).10.1002/anie.201209336 ↗
15. Zhang, C. et al. A general approach to DNA-programmable atom equivalents. Nat. Mater. 12, 741–746 (2013).10.1038/nmat3647 ↗
16. Auyeung, E. et al. DNA-mediated nanoparticle crystallization into wulff polyhedra. Nature 505, 73–77 (2014).10.1038/nature12739 ↗
17. Lu, F., Yager, K. G., Zhang, Y., Xin, H. & Gang, O. Superlattices assembled through shape-induced directional binding. Nat. Commun. 6, 6912 (2015).
18. Zhang, Y. et al. Selective transformations between nanoparticle superlattices via the reprogramming of DNA-mediated interactions. Nat. Mater. 14, 840 (2015).10.1038/nmat4296 ↗
19. Kim, Y., Macfarlane, R. J., Jones, M. R. & Mirkin, C. A. Transmutable nanoparticles with reconfigurable surface ligands. Science 351, 579–582 (2016).10.1126/science.aad2212 ↗
20. Liu, W. et al. Diamond family of nanoparticle superlattices. Science 351, 582–586 (2016).10.1126/science.aad2080 ↗
21. Tian, Y. et al. Lattice engineering through nanoparticle-DNA frameworks. Nat. Mater. 15, 654–661 (2016).10.1038/nmat4571 ↗
22. Senesi, A. J. et al. Oligonucleotide flexibility dictates crystal quality in DNA-programmable nanoparticle superlattices. Adv. Mater. 26, 7235–7240 (2014).10.1002/adma.201402548 ↗
23. Thaner, R. V. et al. The significance of multivalent bonding motifs and “bond order” in DNA-directed nanoparticle crystallization. J. Am. Chem. Soc. 138, 6119–6122 (2016).10.1021/jacs.6b02479 ↗
24. Kraft, D. J. et al. Surface roughness directed self-assembly of patchy particles into colloidal micelles. Proc. Natl Acad. Sci. USA 109, 10787–10792 (2012).10.1073/pnas.1116820109 ↗
25. Wang, Y. et al. Colloids with valence and specific directional bonding. Nature 491, 51–55 (2012).10.1038/nature11564 ↗
26. Feng, L., Dreyfus, R., Sha, R. J., Seeman, N. C. & Chaikin, P. M. DNA patchy particles. Adv. Mater. 25, 2779–2783 (2013).10.1002/adma.201204864 ↗
27. Edwardson, T. G. W., Lau, K. L., Bousmail, D., Serpell, C. J. & Sleiman, H. F. Transfer of molecular recognition information from DNA nanostructures to gold nanoparticles. Nat. Chem. 8, 162–170 (2016).10.1038/nchem.2420 ↗
28. Liu, W. Y., Halverson, J., Tian, Y., Tkachenko, A. V. & Gang, O. Self-organized architectures from assorted DNA-framed nanoparticles. Nat. Chem. 8, 867–873 (2016).10.1038/nchem.2540 ↗
29. Zhang, Y. et al. Transfer of two-dimensional oligonucleotide patterns onto stereocontrolled plasmonic nanostructures through DNA-origami-based nanoimprinting lithography. Angew. Chem. Int. Ed. 55, 8036–8040 (2016).10.1002/anie.201512022 ↗
30. Xing, H. et al. Bottom-up strategy to prepare nanoparticles with a single DNA strand. J. Am. Chem. Soc. 139, 3623–3626 (2017).10.1021/jacs.7b00065 ↗
31. Yang, Z., Liu, H. & Liu, D. Spatial regulation of synthetic and biological nanoparticles by DNA nanotechnology. NPG Asia Mater. 7, e161 (2015).
32. Lan, X. & Wang, Q. DNA-programmed self-assembly of photonic nanoarchitectures. NPG Asia Mater. 6, e97 (2014).
33. Aldaye, F. A. & Sleiman, H. F. Dynamic DNA templates for discrete gold nanoparticle assemblies: control of geometry, modularity, write/erase and structural switching. J. Am. Chem. Soc. 129, 4130–4131 (2007).10.1021/ja070017i ↗
34. Shen, C. et al. Site-specific surface functionalization of gold nanorods using DNA origami clamps. J. Am. Chem. Soc. 138, 1764–1767 (2016).10.1021/jacs.5b11566 ↗
35. Yao, G. et al. Programming nanoparticle valence bonds with single-stranded DNA encoders. Nat. Mater. https://doi.org/10.1038/s41563-019-0549-3 (2019).10.1038/s41563-019-0549-3 ↗
36. Pei, H. et al. Designed diblock oligonucleotide for the synthesis of spatially isolated and highly hybridizable functionalization of DNA-gold nanoparticle nanoconjugates. J. Am. Chem. Soc. 134, 11876–11879 (2012).10.1021/ja304118z ↗
37. Yao, G. et al. Clicking DNA to gold nanoparticles: poly-adenine-mediated formation of monovalent DNA-gold nanoparticle conjugates with nearly quantitative yield. NPG Asia Mater. 7, e159 (2015).
38. Hartman, M. R. et al. Thermostable branched DNA nanostructures as modular primers for polymerase chain reaction. Angew. Chem. Int. Ed. 52, 8699–8702 (2013).10.1002/anie.201302175 ↗
39. Lin, C. et al. In vivo cloning of artificial DNA nanostructures. Proc. Natl Acad. Sci. USA 105, 17626–17631 (2008).10.1073/pnas.0805416105 ↗
40. Nielsen, S. S. et al. BioXTAS RAW, a software program for high-throughput automated small-angle X-ray scattering data reduction and preliminary analysis. J. Appl. Crystallogr. 42, 959–964 (2009).10.1107/S0021889809023863 ↗
41. Dobrynin, A. V., Rubinstein, M. & Obukhov, S. P. Cascade of transitions of polyelectrolytes in poor solvents. Macromolecules 29, 2974–2979 (1996).10.1021/ma9507958 ↗
42. Hartl, C. et al. Position accuracy of gold nanoparticles on DNA origami structures studied with small-angle X-ray scattering. Nano Lett. 18, 2609–2615 (2018).10.1021/acs.nanolett.8b00412 ↗
43. Wang, H., Li, Y., Liu, M., Gong, M. & Deng, Z. Overcoming the coupling dilemma in DNA-programmable nanoparticle assemblies by “Ag+ soldering”. Small 11, 2247–2251 (2015).10.1002/smll.201403108 ↗
44. Damke, P. P. et al. Identification of the periplasmic DNA receptor for natural transformation of Helicobacter pylori. Nat. Commun. 10, 5357 (2019).10.1038/s41467-019-13352-6 ↗
45. Hill, H. D., Hurst, S. J. & Mirkin, C. A. Curvature-induced base pair “slipping” effects in DNA-nanoparticle hybridization. Nano Lett. 9, 317–321 (2009).10.1021/nl8030482 ↗
46. Randeria, P. S. et al. What controls the hybridization thermodynamics of spherical nucleic acids? J. Am. Chem. Soc. 137, 3486–3489 (2015).10.1021/jacs.5b00670 ↗
47. He, Y. et al. Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 452, 198–201 (2008).10.1038/nature06597 ↗
48. Liu, N. & Liedl, T. DNA-assembled advanced plasmonic architectures. Chem. Rev. 118, 3032–3053 (2018).10.1021/acs.chemrev.7b00225 ↗