383 Index a binary-coded decimal (BCD) code 236 actuator 125, 126 biocompatibility 125, 147, 166, 241, Adleman’s DNA computer 16–17 329 allosteric biosensors 64 biomolecular computing 1, 2, 3, 5, 15, allosteric effector 111, 113 353, 371, 381 allosteric inhibiter 113 (bio)molecular realizations 363 allosteric toehold 266 biomolecular scaffolds 80–81 -Hemolysin (HL) 331 biomolecular switches 105 7-amino-4-methyl coumarin (AMC) Black Hole Quencher 374 131 blocking amplitude 331 AND Boolean logic 68, 164 Boolean algebra 65, 279 3-AND gate 359, 360 Boolean logic gate 1, 2, 10, 88, 133, AND gate implementation 38 134, 140, 155, 156, 157, 164, 282, 3-AND logic gate operation 358 284, 362 anti-anti-terminator/anti-terminator Boolean operations 1, 113, 155, 279, hairpin (aat/at-HP) 255 363 anti-fuel strand complementary 270 branch migration 97, 158, 248, 249, anti-gRNA bind 257 254, 258, 265–268, 282, 285, 287, antioxidant indicator 241 297, 298 application-specific integrated circuits Broccoli RNA aptamer 68–70 (ASICs) 39 aptamer–fluorophore complex 61 c aptamer ligand binding 125 cadmium chalcogenide semiconductors Arbona’s biophysical model 313 159 arithmetic DNA logic devices carbon dots (CDs) 159, 174–175 full-adder, full-subtractor 234 Cas9 + gRNA 255 half-adder, half-subtractor 232–234 catalytic hairpin assembly (CHA) 131, asynchronization circuits 38 261 asynchronous circuits 38 cationic conjugated polymers (CCPs) automatic writing–reading DNA 176 processes 9, 10 cell entry vehicles 81, 82 Cello computing language 7 b cellular environment 93, 251, 281, 285, bi-dynamic DNA origami 289 nanostructures 309 central processing unit (CPU) 275 DNA- and RNA-Based Computing Systems, First Edition. Edited by Evgeny Katz. © 2021 WILEY-VCH GmbH. Published 2021 by WILEY-VCH GmbH. 384 Index Chao’s model 24 deoxyribozyme 46, 96, 293, 359 chemical reaction network (CRN) deoxyribozyme gate-based theory 31, 32, 35, 287 computational systems 362 application-specific integrated deoxyribozyme ligase-based 2iAND gate circuits (ASICs) 39 46 chemical reaction computer 31 deoxyribozyme logic gates 46–47, 50, complex functional computing 280–282, 357 systems 32 depletant molecule 119 decoding signal 37 3,5-difluoro-4-hydroxybenzylidene encoding 35, 37 imidazolinone (DFHBI) 138 history-free method 33 3,5-difluoro-4-hydroxybenzylidene-1- LDPC and polar codes 39 trifluoroethyl-imidazolinone mapping methods 31 (DFHBI-1T) 138 mass action kinetics 35 N-digit binary string 23 stochastic chemical reaction networks digital signal processing (DSP) modules (SCRNs) model 31 39 clustered regularly interspaced short direct representation, encoding 35 palindromic repeats (CRISPR) DNA-based digital data storage 83, 96, 255–258, 281 components of clustered regularly interspaced short data retrieval 348–349 palindromic repeats interference decoding 349–350 (CRISPRi) 257 encoding 346 communicating enzyme-DNA circuits storage 348 353 writing 346–348 computing core 241 density and coding capacity 345 concatenated logic circuits 232, durability and energy efficiency 345 239–240, 242 synthesis and sequencing conjugated polymers (CPs) 159, technologies 346 175–177 DNA-based logic gates 40, 157, 158, connecting DNA logic gates in circuits 171, 175, 266, 284, 379 deoxyribozymes 46–47 DNA catenanes 270 DNA strand displacement 47–50 DNA circuit construction techniques four-way junction (4WJ) 50–53 40 molecular computation field 45 DNA-coated QDs 160 construct multi-output circuits DNA computing system multifunctional probes 142 Adleman’s experiment 4, 5 signal transducers 138–141 advantages of 4, 329 contrary logic pairs 134, 241, 242 benefit of 379 conventional DNA computation 329 Cello computing language 7 CRISPR-Cas9 83, 86, 88, 95, 255 chemical structure of 3, 4 current-signal blockage 331 circuits application-specific integrated d circuits (ASICs) 39 data writing 346–348 clock signals 38 demultiplexer (DEMUX) 128, encoding representations 35 139–141, 144, 145 feed forward digital circuits 40 dendritic DNA strands 270 implementations 31–35 Index 385 logic gates 40 DNA hybridization 125 sequential digital logic circuits 38 DNA implementations conventional digital electronic chemical reaction networks (CRNs) computing 327 31, 32 developments in 6 diagrams of 35, 37 Adleman’s model 16 DNA strand displacement reactions challenges 27 34, 35 Chao’s model 24 stochastic chemical reaction networks DNA origami 24 (SCRNs) model 31 data storage 26 Turing machines 33 Lipton’s model 18 DNA keypad locks 236–238 Ouyang’s model 22 DNA logic circuits Sakamoto’s model 21 actuators 125 satisfiability (SAT) problem 16 arithmetic Smith’s model 19 full-adder, full-subtractor 234 DNA double helix 3, 5 half-adder, half-subtractor DNA logic circuits 231 232–234 DSD tool 7, 8 classification 231–232 future advancements of 380 concatenated 239–240 Hamiltonian path problem 327, 328 definition of 231–232 infancy 381 fluorescent signal design 125 information processing systems 3 innovative multifunctional DNA logic information storage systems 8 library 241 in vivo molecular computing devices intelligent bio-applications 241–244 329 logical principle 231–232 logic gate 329 non-arithmetic massive data 329 DNA keypad locks 236–237 microarrays 6, 7 DNA voter 236–237 motivation and application 1 encoders/decoders 235–236 nanopore decoding even/odd natural numbers 236 in medical diagnosis 335–338 multiplexers/demultiplexers rapid and label-free decoding 235–236 330–335 non-Boolean ternary logic gates nanorobots in living organisms 6 239 origami structures 6, 7 parity generator/checker (pG/pC) PCR method 9 error detection 237–238 second generation of 328 processors 125 switches 379 sensors 125 time-consuming process 329 universal input-output mechanism tic-tac-toe game 6 125, 126 travelling salesman problem 3, 6 DNA logic gates 45–53, 81, 85, 87, DNA dolphin-shaped structure 58 128, 130, 157–159, 175, 177, 239, DNA double helix 3, 5 241, 281, 282, 332, 360, 361, DNA gate motif 40 380 DNA G-quadruplex structures 107 DNA memory 8, 288, 381 DNA hairpin formation, Sakamoto’s DNA-MTC supramolecular logic model 21 platform 144, 145 386 Index DNA nanoparticles 58 e DNA nanotechnology 58, 80, 83, 85, electrochemical analysis 117, 118 88, 89, 90, 92–95, 247, 250, 261, electrochemical impedance 265, 287–289, 293, 304 spectroscopy (EIS) 118 DNA origami transformers electronic computing kernel 87 applications 318–321 encoders/decoders 235, 236 bi-dynamic 308 endonuclease activity 88, 134, 296 biophysical models 307 energy transfer upconversion (ETU) design 312–316 mechanism 165 disadvantage of 309 engineering DNA switches 105, 379 experimental demonstrations allosteric activator 316–318 AND gate 113, 114 hybridization reactions 312 DNAzyme 113 nanostructures 77, 79, 307 OR gate 113, 114 Raman signal 308 allosteric effectors 111, 113 self-assembly 310 allosteric inhibiter 113 staple strand 310 conformational changes 108 static 308 DNA tetrahedron 115, 116 technique 58, 270 dose–response profile 118 2D rectangular 310 logic output function response zip and unzip primitives design 308 117–118 zippering process 312 population-shift mechanism 108, DNA recognition element 107–111, 109 114, 118 recognition element, input 107–108 DNA-related problems 328 steps 106 DNA secondary structure 57, 108, 126, structure-switching mechanism 111 127, 132, 136, 157, 159, 171, 176 entropy driven DNA networks 250 DNA strand displacement (DSD) enzyme-based computing 3 reactions bioelectronic interface DNA logic gates connections 47–50 3-AND gate 360 logic operations 40 binary operation 354 MNIST database 41 DNA-based reversible logic gates programming language 287 362–363 Rule 110 Automata 33, 34 Fredkin gate 363–368 switching circuits 41 logic systems 354, 355, 360–362 DNA-templated AgNCs 142, 170, 235 NADH 354 DNA tetrahedron 115, 116, 270 output signal 356–357 DNA translators 282–285 reactions catalyzed 354 DNA tweezer 268, 269 releasing electrode 354 DNA voter 236–237 reversible logic operations 363 DNA walker system 271 sensing electrode 354 DNAzymes 113 communicating enzyme-DNA history of 293–296 circuits 353 function 125 selective and sensitive receptors 353 dual-rail logic 49, 284 ET-based logic gates 158 dual-rail representation, encoding 35 even/odd natural numbers 234–236 Index 387 f framework nucleic acids (FNA) feed forward digital circuits 40 biomolecular engineering, living Feynman gate 373 systems (bio)molecular realizations 363 biomolecular scaffolds 80–81 oligonucleotides 373 cell entry vehicles 82 reversible DNA-based 368–371 error correction and resilience finite automaton system 329 84–85 first-generation riboregulators isothermal construction 83 251–252 logic units 81–82 fluorescence labeling 330 signal readout 84 fluorescence-producing targeting and editing 83 structure-switching molecular triggers and switches 84 107 definition 77, 80 fluorescence techniques 330 electronic computing kernel 87 fluorescent RNA motifs 81, 84, 90 environmental or cellular signals 92 fluorescent signal design information storage 90–91 construct multi-output circuits I/O and human-computer interfacing multi-functional probes 142 89–90 signal transducers 138–141 targeted applications DNA secondary structure cellular imaging 85–86 Hoogsteen hydrogen bond cellular pathway investigation 86 132–138 drug delivery 85 Watson–Crick hydrogen bond metabolic engineering 86 127–132 fraying 248 fluorogenic RNA aptamers Fredkin gate 365, 367, 368 biocomputing applications 59 (bio)molecular realizations 363 electrochemical and colorimetric bioelectronic interface 363–368 approach 61