Peptide-DNA conjugates as building blocks for de novo design of hybrid nanostructures
Source abstract
Abstract
Inspired by nature, modern nanotechnology has enabled the bottom-up construction of molecular machines and nanorobots using two different biomolecular building blocks, DNAs or peptides. As an emerging research field, synergizing these two biomolecular codes into a single nanostructure has provided super-powerful molecular tools into the arsenal of modern nanotechnology. Among them, peptide-DNA conjugates possess both attributes of peptide and DNA and can be arbitrarily predefined in given structural configurations, standing out as unique nanoscale building blocks for de novo design of instrumental nanostructures that otherwise could not be composed by using DNA or peptides only. Herein, the term peptide is used in the broadest sense, including oligopeptide, polypeptide, and protein. In this tutorial review, we survey the main progress made within the past decade in how to use peptide-DNA conjugates as nanoscale bricks to self-assemble hybrid nanostructures for different chemical and biological purposes. A concise perspective is included for existing challenges and potential future research directions. Looking to the horizon, peptide-DNA conjugates may serve as key structural elements in the coming decade to enable the bottom-up construction of advanced molecular machines, even comparable to those cellular organelles evolved by nature.
Source: openalex_inverted_index · Quality: baseline
Research context
OpenAlex topics: Advanced biosensing and bioanalysis techniques · RNA Interference and Gene Delivery · Supramolecular Self-Assembly in Materials
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
References (100+)
Show source-provided references
1. Nucleic acid junctions and lattices10.1016/0022-5193(82)90002-9 ↗
2. DNA in a material world10.1038/nature01406 ↗
3. Folding DNA to create nanoscale shapes and patterns10.1038/nature04586 ↗
4. Functional DNA sensors integrated with nucleic acid signal amplification strategies for non-nucleic acid targets detection10.1016/j.bios.2023.115282 ↗
5. Aptamers as targeted therapeutics: current potential and challenges10.1038/nrd.2016.199 ↗
6. Aptamers 101: aptamer discovery and in vitro applications in biosensors and separations10.1039/D3SC00439B ↗
7. Biosensing with DNAzymes10.1039/D1CS00240F ↗
8. Current signal amplification strategies in aptamer-based electrochemical biosensor: A review10.1016/j.cclet.2020.12.054 ↗
9. The current landscape of nucleic acid therapeutics10.1038/s41565-021-00898-0 ↗
10. Antisense oligonucleotides: the next frontier for treatment of neurological disorders10.1038/nrneurol.2017.148 ↗
11. Three's a crowd – stabilisation, structure, and applications of DNA triplexes10.1039/D2SC01793H ↗
12. Molecular beacon strategies for sensing purpose10.1016/j.trac.2020.116143 ↗
13. mRNA-based therapeutics: powerful and versatile tools to combat diseases10.1038/s41392-022-01007-w ↗
14. Principles and applications of nucleic acid strand displacement reactions10.1021/acs.chemrev.8b00580 ↗
15. DNA nanotechnology10.1038/natrevmats.2017.68 ↗
16. RNA-targeted therapeutics10.1016/j.cmet.2018.03.004 ↗
17. Drug delivery systems for RNA therapeutics10.1038/s41576-021-00439-4 ↗
18. Recent advances in DNA origami-engineered nanomaterials and applications10.1021/acs.chemrev.3c00028 ↗
19. The coming of age of de novo protein design10.1038/nature19946 ↗
20. The physical properties of supramolecular peptide assemblies: from building block association to technological applications10.1039/C4CS00164H ↗
21. Catalysis and electron transfer in de novo designed helical scaffolds10.1002/anie.201907502 ↗
22. Recent advances in de novo protein design: principles, methods, and applications10.1016/j.jbc.2021.100558 ↗
23. De novo metalloprotein design10.1038/s41570-021-00339-5 ↗
24. Hybrid nanostructures from the self-assembly of proteins and DNA10.1016/j.chempr.2020.01.012 ↗
25. Supramolecular architectures of nucleic acid/peptide hybrids10.3390/ijms21249458 ↗
26. Engineering functional DNA–protein conjugates for biosensing, biomedical, and nanoassembly applications10.1007/s41061-020-00305-7 ↗
27. Emerging applications of peptide–oligonucleotide conjugates: bioactive scaffolds, self-assembling systems, and hybrid nanomaterials10.1039/C8OB02436G ↗
28. New functions emerging from peptide–DNA materials
29. Actin binding proteins: regulation of cytoskeletal microfilaments10.1152/physrev.00026.2002 ↗
30. Controlled aggregation of peptide–DNA hybrids into amyloid-like fibrils10.1016/j.eurpolymj.2015.02.009 ↗
31. Label-free, optical sensing of the supramolecular assembly into fibrils of a ditryptophan–DNA hybrid10.1039/C4CC02631D ↗
32. Self-assembling DNA–peptide hybrids: morphological consequences of oligonucleotide grafting to a pathogenic amyloid fibrils forming dipeptide10.1039/c2cc31458d ↗
33. Natural nanochemical building blocks: icosahedral virus particles organized by attached oligonucleotides10.1021/nl0493850 ↗
34. Self-assembly and reassembly of fiber-forming dipeptides for pH-triggered DNA delivery10.1002/pola.27319 ↗
35. Functional assemblies emerging in complex mixtures of peptides and nucleic acid–peptide chimeras10.1002/chem.201800500 ↗
36. Noncovalent template-assisted mimicry of multiloop protein surfaces: assembling discontinuous and functional domains10.1021/ja305360q ↗
37. Periodic Operation of a dynamic DNA origami structure utilizing the hydrophilic–hydrophobic phase-transition of stimulus-sensitive polypeptides10.1002/smll.201903541 ↗
38. Reciprocal self-assembly of peptide–DNA conjugates into a programmable sub-10-nm supramolecular deoxyribonucleoprotein10.1002/anie.201605696 ↗
39. Short intrinsically disordered polypeptide–oligonucleotide conjugates for programmed self-assembly of nanospheres with temperature-dependent size controllability10.1039/D0SM01817A ↗
40. Programmed co-assembly of DNA-peptide hybrid microdroplets by phase separation10.1016/j.cclet.2021.08.116 ↗
41. DNA-controlled assembly of a NaTl lattice structure from gold nanoparticles and protein nanoparticles10.1038/nmat2877 ↗
42. Self-assembling cyclic peptide-oligonucleotide conjugates: synthetic strategies and the effect of cyclic topology on self-assembly and base pairing10.1002/pep2.24193 ↗
43. Peptide–oligonucleotide conjugates as nanoscale building blocks for assembly of an artificial three-helix protein mimic10.1038/ncomms12294 ↗
44. Folding topology of a short coiled-coil peptide structure templated by an oligonucleotide triplex10.1002/chem.201700971 ↗
45. Reversible self-assembly of superstructured networks10.1126/science.aat6141 ↗
46. Self-assembly of DNA–peptide supermolecules: coiled-coil peptide structures templated by D-DNA and L-DNA triplexes exhibit chirality-independent but orientation-dependent stabilizing cooperativity10.1002/chem.201905636 ↗
47. Encoding reversible hierarchical structures with supramolecular peptide–DNA materials10.1021/acs.bioconjchem.9b00271 ↗
48. Chirality transmission in macromolecular domains10.1038/s41467-021-27708-4 ↗
49. Hierarchical assembly of nucleic acid/coiled-coil peptide nanostructures10.1021/jacs.9b11158 ↗
50. DNA-mediated engineering of multicomponent enzyme crystals10.1073/pnas.1503533112 ↗
51. Modulating nanoparticle superlattice structure using proteins with tunable bond distributions10.1021/jacs.6b11893 ↗
52. Encoding hierarchical assembly pathways of proteins with DNA10.1073/pnas.2106808118 ↗
53. Tunable nanoscale cages from self-assembling DNA and protein building blocks10.1021/acsnano.8b09798 ↗
54. Correction to tunable nanoscale cages from self-assembling DNA and protein building blocks10.1021/acsnano.0c02484 ↗
55. Peptide assembly directed and quantified using megadalton DNA nanostructures10.1021/acsnano.9b04251 ↗
56. Diels-Alder cycloadditions in water for the straightforward preparation of peptide–oligonucleotide conjugates10.1093/nar/gnj020 ↗
57. Diene-modified nucleotides for the Diels–Alder-mediated functional tagging of DNA10.1093/nar/gkn1066 ↗
58. Inverse electron demand Diels–Alder reactions in chemical biology10.1039/C7CS00184C ↗
59. Protein nanotube selectively cleavable with DNA: supramolecular polymerization of “DNA-appended molecular chaperones”10.1021/jacs.7b09892 ↗
60. DNA-functionalized, bivalent proteins10.1021/jacs.8b03403 ↗
61. Self-assembly of a designed nucleoprotein architecture through multimodal interactions10.1021/acscentsci.8b00745 ↗
62. DNA scaffolds support stable and uniform peptide nanopores10.1038/s41565-018-0139-6 ↗
63. DNA-modified artificial viral capsids self-assembled from DNA-conjugated β-annulus peptide10.1002/psc.2967 ↗
64. Bioactive DNA-peptide nanotubes enhance the differentiation of neural stem cells into neurons10.1021/nl504079q ↗
65. Multivalent traptavidin–DNA conjugates for the programmable assembly of nanostructures10.1021/acsnano.8b06170 ↗
66. DNA-directed three-dimensional protein organization10.1002/anie.201108710 ↗
67. A monovalent streptavidin with a single femtomolar biotin binding site10.1038/nmeth861 ↗
68. Redefining protein interfaces within protein single crystals with DNA10.1021/jacs.1c04191 ↗
69. A facile method for reversibly linking a recombinant protein to DNA10.1002/cbic.200900165 ↗
70. NTA directed protein nanopatterning on DNA origami nanoconstructs10.1021/ja901407j ↗
71. Template-directed covalent conjugation of DNA to native antibodies, transferrin and other metal-binding proteins10.1038/nchem.2003 ↗
72. Structural Mimics of Viruses Through Peptide/DNA Co-Assembly10.1021/ja507833x ↗
73. Aptamer-directed self-assembly of protein arrays on a DNA nanostructure10.1002/anie.200501089 ↗
74. Incorporation of native antibodies and Fc-fusion proteins on DNA nanostructures via a modular conjugation strategy10.1039/C7CC04178K ↗
75. Zinc-finger proteins for site-specific protein positioning on DNA-origami structures10.1002/anie.201108199 ↗
76. Spatially organized enzymes drive cofactor-coupled cascade reactions10.1021/jacs.5b10198 ↗
77. DNA origami scaffolds as templates for functional tetrameric Kir3 K+ channels10.1002/anie.201709982 ↗
78. Design of modular protein tags for orthogonal covalent bond formation at specific DNA sequences10.1021/jacs.7b01640 ↗
79. Casting metal nanowires within discrete self-assembled peptide nanotubes10.1126/science.1082387 ↗
80. Molecular basis for amyloid-β polymorphism10.1073/pnas.1112600108 ↗
81. SOCKET: a program for identifying and analysing coiled-coil motifs within protein structures10.1006/jmbi.2001.4545 ↗
82. The crystal structure of the designed trimeric coiled coil coil-VaLd: implications for engineering crystals and supramolecular assemblies10.1002/pro.5560060109 ↗
83. Stereodivergence in asymmetric catalysis10.1021/jacs.6b13340 ↗
84. Exploiting attractive non-covalent interactions for the enantioselective catalysis of reactions involving radical intermediates10.1038/s41557-020-00561-6 ↗
85. Exploiting non-covalent π interactions for catalyst design10.1038/nature21701 ↗
86. Dynamic foldamer chemistry10.1039/C6CC00788K ↗
87. Supramolecular helical systems: helical assemblies of small molecules, foldamers, and polymers with chiral amplification and their functions10.1021/acs.chemrev.6b00354 ↗
88. Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases10.1038/nature04088 ↗
89. Applications of biological pores in nanomedicine, sensing, and nanoelectronics10.1016/j.copbio.2010.05.002 ↗
90. Continuous base identification for single-molecule nanopore DNA sequencing10.1038/nnano.2009.12 ↗
91. Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore10.1038/s41587-019-0345-2 ↗
92. Nanopore sequencing and assembly of a human genome with ultra-long reads10.1038/nbt.4060 ↗
93. A dual-constriction biological nanopore resolves homonucleotide sequences with high fidelity10.1038/s41587-020-0570-8 ↗
94. Building membrane nanopores10.1038/nnano.2017.99 ↗
95. FraC nanopores with adjustable diameter identify the mass of opposite-charge peptides with 44 dalton resolution10.1038/s41467-019-08761-6 ↗
96. A monodisperse transmembrane α-helical peptide barrel10.1038/nchem.2647 ↗
97. Protein detection by nanopores equipped with aptamers10.1021/ja2105653 ↗
98. Membrane pores: from structure and assembly, to medicine and technology10.1098/rstb.2016.0208 ↗
99. Bioactive fibronectin-III10–DNA origami nanofibers promote cell adhesion and spreading10.1021/acsabm.2c00303 ↗
100. Physical chemistry of biological free energy transduction as demonstrated by elastic protein-based polymers10.1021/jp972167t ↗