journal article·2025-01-21Open access

Autonomous Nucleic Acid and Protein Nanocomputing Agents Engineered to Operate in Living Cells

Martin Panigaj, Tanaya Basu Roy, Elizabeth Skelly, Morgan R. Chandler, Jian Wang, Srinivasan Ekambaram, Kristin Bircsak, Nikolay V. Dokholyan, Kirill A. Afonin

ACS Nano· Volume 19· Issue 2

Abstract

In recent years, the rapid development and employment of autonomous technology have been observed in many areas of human activity. Autonomous technology can readily adjust its function to environmental conditions and enable an efficient operation without human control. While applying the same concept to designing advanced biomolecular therapies would revolutionize nanomedicine, the design approaches to engineering biological nanocomputing agents for predefined operations within living cells remain a challenge. Autonomous nanocomputing agents made of nucleic acids and proteins are an appealing idea, and two decades of research has shown that the engineered agents act under real physical and biochemical constraints in a logical manner. Throughout all domains of life, nucleic acids and proteins perform a variety of vital functions, where the sequence-defined structures of these biopolymers either operate on their own or efficiently function together. This programmability and synergy inspire massive research efforts that utilize the versatility of nucleic and amino acids to encode functions and properties that otherwise do not exist in nature. This Perspective covers the key concepts used in the design and application of nanocomputing agents and discusses potential limitations and paths forward.
Source: openalex_inverted_index · Quality: baseline

Research context

OpenAlex topics: Advanced biosensing and bioanalysis techniques · RNA Interference and Gene Delivery · DNA and Nucleic Acid Chemistry

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States

Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States

MIMETAS US, INC, Gaithersburg, Maryland 20878, United States

Funding

National Institute of General Medical Sciences · Division of Materials Research · Passan Foundation

References (100+)

Show source-provided references
1. Ezenkwu, C. P.; Starkey, A. In Machine Autonomy: Definition, Approaches, Challenges and Research Gaps, Intelligent Computing; Arai, K.; Bhatia, R.; Kapoor, S., Eds. Springer International Publishing: Cham, 2019; pp 335–358.10.1007/978-3-030-22871-2_24 ↗
2. 10.1358/dot.2017.53.11.272575410.1358/dot.2017.53.11.2725754 ↗
3. 10.1016/S0140-6736(20)31366-010.1016/S0140-6736(20)31366-0 ↗
4. 10.1056/NEJMoa202485010.1056/NEJMoa2024850 ↗
5. 10.1056/NEJMoa211320610.1056/NEJMoa2113206 ↗
6. 10.3389/fonc.2024.135972510.3389/fonc.2024.1359725 ↗
7. 10.3389/fmolb.2022.83484110.3389/fmolb.2022.834841 ↗
8. 10.1038/s41564-024-01750-610.1038/s41564-024-01750-6 ↗
9. 10.1006/mthe.2000.021810.1006/mthe.2000.0218 ↗
10. 10.1038/s41579-018-0025-010.1038/s41579-018-0025-0 ↗
11. 10.1126/sciadv.aau212410.1126/sciadv.aau2124 ↗
12. 10.1038/s41467-023-36996-x10.1038/s41467-023-36996-x ↗
13. 10.1039/D3LC00860F10.1039/D3LC00860F ↗
14. 10.1038/nature0141010.1038/nature01410 ↗
15. 10.1038/s41467-017-00459-x10.1038/s41467-017-00459-x ↗
16. 10.1021/nl502385k10.1021/nl502385k ↗
17. 10.1038/s41467-018-04652-410.1038/s41467-018-04652-4 ↗
18. 10.1021/acs.bioconjchem.3c0016710.1021/acs.bioconjchem.3c00167 ↗
19. 10.1038/nature1111710.1038/nature11117 ↗
20. 10.1038/nature0603210.1038/nature06032 ↗
21. 10.1016/j.ymeth.2019.04.02210.1016/j.ymeth.2019.04.022 ↗
22. 10.5936/csbj.20120900210.5936/csbj.201209002 ↗
23. 10.1007/978-1-4939-7366-8_210.1007/978-1-4939-7366-8_2 ↗
24. 10.1021/acs.chemrev.1c0026010.1021/acs.chemrev.1c00260 ↗
25. 10.1038/nnano.2010.16010.1038/nnano.2010.160 ↗
26. 10.1038/nnano.2010.23110.1038/nnano.2010.231 ↗
27. 10.1016/S1097-2765(00)80124-010.1016/S1097-2765(00)80124-0 ↗
28. 10.1016/j.nantod.2012.06.01010.1016/j.nantod.2012.06.010 ↗
29. 10.1021/nn500625410.1021/nn5006254 ↗
30. 10.1021/ar500076k10.1021/ar500076k ↗
31. 10.1038/nature0659710.1038/nature06597 ↗
32. 10.1126/science.125392010.1126/science.1253920 ↗
33. 10.1038/nature0458610.1038/nature04586 ↗
34. 10.1021/nn502253c10.1021/nn502253c ↗
35. 10.1038/nnano.2012.7310.1038/nnano.2012.73 ↗
36. 10.1038/s41580-020-00315-910.1038/s41580-020-00315-9 ↗
37. 10.1016/j.cell.2021.04.02310.1016/j.cell.2021.04.023 ↗
38. 10.1016/j.cell.2023.12.03310.1016/j.cell.2023.12.033 ↗
39. 10.1038/s41565-021-00898-010.1038/s41565-021-00898-0 ↗
40. 10.1002/smo.2023002310.1002/smo.20230023 ↗
41. 10.1021/acsabm.4c0043210.1021/acsabm.4c00432 ↗
42. 10.1021/acsnano.0c1024010.1021/acsnano.0c10240 ↗
43. 10.1016/j.csbj.2022.11.00710.1016/j.csbj.2022.11.007 ↗
44. 10.1016/j.tibs.2015.09.00110.1016/j.tibs.2015.09.001 ↗
45. 10.1016/S0092-8674(02)01134-010.1016/S0092-8674(02)01134-0 ↗
46. 10.1073/pnas.152300411310.1073/pnas.1523004113 ↗
47. 10.1073/pnas.21262889910.1073/pnas.212628899 ↗
48. 10.1016/j.addr.2021.04.01110.1016/j.addr.2021.04.011 ↗
49. 10.1002/smll.20220494110.1002/smll.202204941 ↗
50. 10.1002/adfm.20220558110.1002/adfm.202205581 ↗
51. 10.1038/s41596-020-0393-610.1038/s41596-020-0393-6 ↗
52. 10.1093/nar/gkx00810.1093/nar/gkx008 ↗
53. 10.3390/molecules2406109410.3390/molecules24061094 ↗
54. 10.1021/acs.nanolett.8b0128310.1021/acs.nanolett.8b01283 ↗
55. 10.1002/smll.20170125510.1002/smll.201701255 ↗
56. 10.1093/nar/gky121510.1093/nar/gky1215 ↗
57. 10.1002/adfm.20180595910.1002/adfm.201805959 ↗
58. 10.1038/s41576-021-00439-410.1038/s41576-021-00439-4 ↗
59. 10.1016/j.nano.2019.10209410.1016/j.nano.2019.102094 ↗
60. 10.1016/j.ajpath.2016.02.02310.1016/j.ajpath.2016.02.023 ↗
61. 10.1093/nar/gkac114310.1093/nar/gkac1143 ↗
62. 10.1016/j.cell.2013.02.01410.1016/j.cell.2013.02.014 ↗
63. 10.1038/nature0255110.1038/nature02551 ↗
64. 10.3390/ijms2308426510.3390/ijms23084265 ↗
65. 10.1093/nar/gkq11710.1093/nar/gkq117 ↗
66. 10.1093/nar/gks63610.1093/nar/gks636 ↗
67. 10.1093/nar/gks133010.1093/nar/gks1330 ↗
68. 10.1126/science.120552710.1126/science.1205527 ↗
69. 10.1021/acs.nanolett.5b0465110.1021/acs.nanolett.5b04651 ↗
70. 10.1038/nnano.2013.4410.1038/nnano.2013.44 ↗
71. 10.1038/nnano.2015.27810.1038/nnano.2015.278 ↗
72. 10.1021/sb500072510.1021/sb5000725 ↗
73. 10.1093/nar/gkt100110.1093/nar/gkt1001 ↗
74. 10.1021/nn504508s10.1021/nn504508s ↗
75. 10.1038/1643710.1038/16437 ↗
76. 10.1038/nnano.2009.8310.1038/nnano.2009.83 ↗
77. 10.1038/ncomms134010.1038/ncomms1340 ↗
78. 10.1038/nnano.2013.9210.1038/nnano.2013.92 ↗
79. 10.1002/anie.20090708210.1002/anie.200907082 ↗
80. 10.1111/j.1574-6976.2005.004.x10.1111/j.1574-6976.2005.004.x ↗
81. 10.1093/plcell/koad02610.1093/plcell/koad026 ↗
82. 10.1126/science.113249310.1126/science.1132493 ↗
83. 10.1088/1478-3975/ad5d6b10.1088/1478-3975/ad5d6b ↗
84. 10.1038/3502052410.1038/35020524 ↗
85. 10.1021/ja047543j10.1021/ja047543j ↗
86. 10.1002/anie.20050126210.1002/anie.200501262 ↗
87. 10.1002/smll.20090007810.1002/smll.200900078 ↗
88. 10.1002/anie.20045377910.1002/anie.200453779 ↗
89. 10.1038/nature0901210.1038/nature09012 ↗
90. 10.1126/science.121408110.1126/science.1214081 ↗
91. 10.1038/nature0797110.1038/nature07971 ↗
92. 10.1038/nbt.407110.1038/nbt.4071 ↗
93. 10.1038/nnano.2014.5810.1038/nnano.2014.58 ↗
94. U.S. Securities and Exchange Commission. Archemix and Nuvelo Close Phase 1 Trial for Thrombin Inhibitor, ARC183 12/05/2024, https://www.sec.gov/Archives/edgar/data/907654/000119312505189963/dex991.htm.
95. 10.1021/acs.nanolett.2c0201910.1021/acs.nanolett.2c02019 ↗
96. 10.1038/s41540-021-00176-810.1038/s41540-021-00176-8 ↗
97. 10.1126/science.aah340410.1126/science.aah3404 ↗
98. 10.1073/pnas.121831911010.1073/pnas.1218319110 ↗
99. Garst A. · Cell Syst. · 2017 · 4 · 310.1016/j.cels.2017.01.006 ↗
100. 10.1073/pnas.240571712110.1073/pnas.2405717121 ↗