Construction of a simple and intelligent DNA-based computing system for multiplexing logic operations
Source abstract
Abstract
Over the past few decades, DNA-based computing technology has become a rapidly developing technology and shown remarkable capabilities in handling complex computational problems. However, most of the logical operations that DNA computer can achieve are still very basic or using large-scale operations to realize complex functions, especially in mathematics. Graphene oxide (GO) is an ideal nanomaterial for biological computing, which has been used in our previous work to perform basic logic operations. Here, we utilize GO to implement far more complex and large-scale logical computing. For the first time, in this work, we utilize the unique interaction between GO and a variety of classified single-stranded DNAs as the reaction platform, by segmenting and encoding the DNA sequences, and programming the interactions between inputs and between the inputs and reaction platform, two relative large-scale logic operations, 6-bit square-root and 9-bit cube-root logical circuits are realized. This study provides a simple but efficient method for advanced and large-scale logical mathematic operations in biotechnology, opening a new horizon for building biocomputer-based innovative functional devices.
Source: europepmc · Quality: candidate unverified · Source record ↗
Research context
OpenAlex topics: Advanced biosensing and bioanalysis techniques · DNA and Biological Computing · Quantum-Dot Cellular Automata
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
References (55)
Show source-provided references
1. Digital logic gate using quantum-dot cellular automata10.1126/science.284.5412.289 ↗
2. Logic gates and computation from assembled nanowire building blocks10.1126/science.1066192 ↗
3. Molecular logic and computing10.1038/nnano.2007.188 ↗
4. An intelligent universal system yields double results with half the effort for engineering a DNA ‘‘Contrary Logic Pairs’’ library and various DNA combinatorial logic circuits10.1039/C7MH00564D ↗
5. A molecular photoionic AND gate based on fluorescent signalling10.1038/364042a0 ↗
6. Molecular computation of solutions to combinatorial problems10.1126/science.7973651 ↗
7. Enzyme-free nucleic acid logic circuits10.1126/science.1132493 ↗
8. Programmable and multiparameter DNA-based logic platform for cancer recognition and targeted therapy10.1021/ja509263k ↗
9. Multi‐level logic gate operation based on amplified aptasensor performance10.1002/anie.201502315 ↗
10. Concatenated logic circuits based on a three‐way DNA junction: a keypad‐lock security system with visible readout and an automatic reset function10.1002/anie.201408334 ↗
11. Sequential logic operations with a molecular keypad lock with four inputs and dual fluorescence outputs10.1002/anie.201406002 ↗
12. Bridging the two worlds: a universal interface between enzymatic and DNA computing systems10.1002/anie.201411148 ↗
13. Computation with finite stochastic chemical reaction networks10.1007/s11047-008-9067-y ↗
14. Chemical reaction networks10.1109/TCS.1974.1083946 ↗
15. Computational functions in biochemical reaction networks10.1016/S0006-3495(94)80516-8 ↗
16. Chemical implementation of neural networks and Turing machines10.1073/pnas.88.24.10983 ↗
17. Structural sources of robustness in biochemical reaction networks10.1126/science.1183372 ↗
18. An autonomous molecular computer for logical control of gene expression10.1038/nature02551 ↗
19. Logic goes in vitro10.1038/nnano.2007.23 ↗
20. Surface-confined assemblies and polymers for molecular logic10.1021/ar200002v ↗
21. Smart molecules at work—Mimicking advanced logic operations10.1039/B820280J ↗
22. Exercises in molecular computing10.1021/ar5000538 ↗
23. Nucleic acids and smart materials: advanced building blocks for logic systems10.1002/adma.201401617 ↗
24. A resettable and reprogrammable DNA-based security system to identify multiple users with hierarchy10.1021/nn406523y ↗
25. Molecular computation of solutions to combinatorial problems10.1126/science.7973651 ↗
26. Scaling up digital circuit computation with DNA strand displacement cascades10.1126/science.1200520 ↗
27. Nucleic-acid junctions and lattices10.1016/0022-5193(82)90002-9 ↗
28. Functional DNA switches: rational design and electrochemical signaling10.1039/C3CS60264H ↗
29. Molecular beacons: probes that fluoresce upon hybridization10.1038/nbt0396-303 ↗
30. Entropy-driven DNA logic circuits regulated by DNAzyme10.1093/nar/gky663 ↗
31. Nanomaterials based on DNA10.1146/annurev-biochem-060308-102244 ↗
32. Potassium-lead-switched G-quadruplexes: a new class of DNA logic gates10.1021/ja9051075 ↗
33. Design of enzyme-interfaced DNA logic operations (AND, OR and INHIBIT) with an assaying application for single-base mismatch10.1039/C5CC02835C ↗
34. Metal ions triggered ligase activity for rolling circle amplification and its application in molecular logic gate operations10.1039/c3sc00043e ↗
35. Enzyme-free nucleic acid logic circuits10.1126/science.1132493 ↗
36. Engineering a 3D DNA-logic gate nanomachine for bispecific recognition and computing on target cell surfaces, J10.1021/jacs.8b04319 ↗
37. Multifunctional graphene/DNA-based platform for the construction of enzyme-free ternary logic gates10.1021/acsami.6b09021 ↗
38. An enzyme-free and DNA-based Feynman gate for logically reversible operation10.1039/C5CC02865E ↗
39. Effective construction of a AuNPs–DNA system for the implementation of various advanced logic gates10.1039/C6RA21585H ↗
40. Integration of DNA and graphene oxide for the construction of various advanced logic circuits10.1039/C6NR01213B ↗
41. Engineering nucleic acid structures for programmable molecular circuitry and intracellular biocomputation10.1038/nchem.2852 ↗
42. Combination of graphene oxide and thiol‐activated DNA metallization for sensitive fluorescence turn‐on detection of cysteine and their use for logic gate operations10.1002/adfm.201101584 ↗
43. Multiplexed aptasensors and amplified DNA sensors using functionalized graphene oxide: application for logic gate operations10.1021/nn300598q ↗
44. Molecular encoder−decoder based on an assembly of graphene oxide with dye-labelled DNA10.1039/C4CC01242A ↗
45. Incorporating graphene oxide and gold nanoclusters: a synergistic catalyst with surprisingly high peroxidase-like activity over a broad pH range and its application for cancer cell detection10.1002/adma.201204419 ↗
46. A reversible fluorescent DNA logic gate based on graphene oxide and its application for iodide sensing10.1039/c2cc17906g ↗
47. Combination of graphene oxide and thiol-activated DNA metallization for sensitive fluorescence turn-on detection of cysteine and their use for logic gate operations10.1002/adfm.201101584 ↗
48. Graphene-section10.1021/nn300997f ↗
49. Three-dimensional self-assembly of graphene oxide and DNA into multifunctional hydrogels10.1021/nn1027104 ↗
50. Graphene oxide-assisted nucleic acids assays using conjugated polyelectrolytes-based fluorescent signal transduction10.1021/ac504658a ↗
51. Graphene nanoprobes for real-time monitoring of isothermal nucleic acid amplification10.1021/acsami.7b01134 ↗
52. Programmable DNA nanoindicator-based platform for large-scale square root logic biocomputing10.1002/smll.201903489 ↗
53. DNA-based digital comparator systems constructed by multifunctional nanoswitches10.1039/C9NR08216F ↗
54. Preparation of graphitic oxide10.1021/ja01539a017 ↗
55. Design of DNA-based innovative computing system of digital comparison10.1016/j.actbio.2018.09.018 ↗