The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
Modular Multi-Level Circuits from Immobilized DNA-Based Logic Gates
Abstract
One of the fundamental goals of molecular computing is to reproduce the tenets of digital logic, such as component modularity and hierarchical circuit design. An important step toward this goal is the creation of molecular logic gates that can be rationally wired into multi-level circuits. Here we report the design and functional characterization of a complete set of modular DNA-based Boolean logic gates (AND, OR, and AND-NOT) and further demonstrate their wiring into a three-level circuit that exhibits Boolean XOR (exclusive OR) function. The approach is based on solid-supported DNA logic gates that are designed to operate with single-stranded DNA inputs and outputs. Since the solution-phase serves as the communication medium between gates, circuit wiring can be achieved by designating the DNA output of one gate as the input to another. Solid-supported logic gates provide enhanced gate modularity versus solution-phase systems by significantly simplifying the task of choosing appropriate DNA input and output sequences used in the construction of multi-level circuits. The molecular logic gates and circuits reported here were characterized by coupling DNA outputs to a single-input REPORT gate and monitoring the resulting fluorescent output signals.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Electronics using hybrid-molecular and mono-molecular devices
Joachim, C., Gimzewski, J. K., & Aviram, A. (2000) · Nature · doi:10.1038/35046000 · Cited by 3,077
Balzani, V., Credi, A., Raymo, F. M., & Stoddart, J. F. (2000) · Angewandte Chemie · doi:10.1002/1521-3773(20001002)39:19<3348::aid-anie3348>3.0.co;2-x · Cited by 2,487
A DNA-fuelled molecular machine made of DNA
Yurke, B., Turberfield, A. J., Mills, A. P., Simmel, F. C., & Neumann, J. L. (2000) · Nature · doi:10.1038/35020524 · Cited by 2,448
Enzyme-Free Nucleic Acid Logic Circuits
Seelig, G., Soloveichik, D., Zhang, D. Y., & Winfree, E. (2006) · Science · doi:10.1126/science.1132493 · Cited by 1,540
DINAMelt web server for nucleic acid melting prediction
Markham, N. R., & Zuker, M. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki591 · Cited by 944
Digital Processing and Communication with Molecular Switches
Raymo, F. M. (2002) · Advanced Materials · doi:10.1002/1521-4095(20020318)14:6<401::aid-adma401>3.0.co;2-f · Cited by 656
A deoxyribozyme-based molecular automaton
Stojanovic, M. N., & Stefanovic, D. (2003) · Nature Biotechnology · doi:10.1038/nbt862 · Cited by 625
Logic Operations at the Molecular Level. An XOR Gate Based on a Molecular Machine
Credi, A., Balzani, V., Langford, S. J., & Stoddart, J. F. (1997) · Journal of the American Chemical Society · doi:10.1021/ja963572l · Cited by 519
A Unidirectional DNA Walker That Moves Autonomously along a Track
Yin, P., Yan, H., Daniell, X. G., Turberfield, A. J., & Reif, J. H. (2004) · Angewandte Chemie International Edition · doi:10.1002/anie.200460522 · Cited by 489
DNA Fuel for Free-Running Nanomachines
Turberfield, A. J., Mitchell, J. C., Yurke, B., Mills, A. P., Blakey, M. I., & Simmel, F. C. (2003) · Physical Review Letters · doi:10.1103/physrevlett.90.118102 · Cited by 377
Integration of Logic Functions and Sequential Operation of Gates at the Molecular-Scale
de Silva, A. P., Dixon, I. M., Gunaratne, H. Q. N., Gunnlaugsson, T., Maxwell, P. R. S., & Rice, T. E. (1999) · Journal of the American Chemical Society · doi:10.1021/ja982909b · Cited by 361
From genes to machines: DNA nanomechanical devices
Seeman, N. C. (2005) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2005.01.007 · Cited by 356
Magri, D. C., Brown, G. J., McClean, G. D., & de Silva, A. P. (2006) · Journal of the American Chemical Society · doi:10.1021/ja058295+ · Cited by 336
Molecular Photoionic AND Logic Gates with Bright Fluorescence and “Off−On” Digital Action
de Silva, A. P., Gunaratne, H. Q. N., & McCoy, C. P. (1997) · Journal of the American Chemical Society · doi:10.1021/ja9712229 · Cited by 328
Using DNA to Power Nanostructures
Yurke, B., & Mills, A. P. (2003) · Genetic Programming and Evolvable Machines · doi:10.1023/a:1023928811651 · Cited by 315
A Molecular Full-Adder and Full-Subtractor, an Additional Step toward a Moleculator
Margulies, D., Melman, G., & Shanzer, A. (2006) · Journal of the American Chemical Society · doi:10.1021/ja058564w · Cited by 309
A new class of homogeneous nucleic acid probes based on specific displacement hybridization
Li, Q. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.2.e5 · Cited by 279
Balzani, V., Credi, A., & Venturi, M. (2003) · ChemPhysChem · doi:10.1002/cphc.200390007 · Cited by 268
Influencing intramolecular motion with an alternating electric field
Bermudez, V., Capron, N., Gase, T., Gatti, F. G., Kajzar, F., Leigh, D. A., Zerbetto, F., & Zhang, S. (2000) · Nature · doi:10.1038/35020531 · Cited by 257
Boolean Logic Functions of a Synthetic Peptide Network
Ashkenasy, G., & Ghadiri, M. R. (2004) · Journal of the American Chemical Society · doi:10.1021/ja046745c · Cited by 229
Self-citationSimmel, F. C., & Dittmer, W. U. (2005) · Small · doi:10.1002/smll.200400111 · Cited by 228
Computational functions in biochemical reaction networks
Arkin, A., & Ross, J. (1994) · Biophysical Journal · doi:10.1016/s0006-3495(94)80516-8 · Cited by 222
DNA Hairpins: Fuel for Autonomous DNA Devices
Green, S. J., Lubrich, D., & Turberfield, A. J. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.084681 · Cited by 218
Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes
Penchovsky, R., & Breaker, R. R. (2005) · Nature Biotechnology · doi:10.1038/nbt1155 · Cited by 212
Elementary Arithmetic Operations by Enzymes: A Model for Metabolic Pathway Based Computing
Baron, R., Lioubashevski, O., Katz, E., Niazov, T., & Willner, I. (2006) · Angewandte Chemie International Edition · doi:10.1002/anie.200503314 · Cited by 208
Concatenated logic gates using four coupled biocatalysts operating in series
Niazov, T., Baron, R., Katz, E., Lioubashevski, O., & Willner, I. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0608319103 · Cited by 202
Beissenhirtz, M. K., & Willner, I. (2006) · Organic & Biomolecular Chemistry · doi:10.1039/b607033g · Cited by 201
The kinetics of oligonucleotide replacements
Reynaldo, L. P., Vologodskii, A. V., Neri, B. P., & Lyamichev, V. I. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3573 · Cited by 195
Deoxyribozyme-Based Three-Input Logic Gates and Construction of a Molecular Full Adder
Lederman, H., Macdonald, J., Stefanovic, D., & Stojanovic, M. N. (2006) · Biochemistry · doi:10.1021/bi051871u · Cited by 188
Medium Scale Integration of Molecular Logic Gates in an Automaton
Macdonald, J., Li, Y., Sutovic, M., Lederman, H., Pendri, K., Lu, W., Andrews, B. L., Stefanovic, D., & Stojanovic, M. N. (2006) · Nano Letters · doi:10.1021/nl0620684 · Cited by 179
Deoxyribozyme-Based Ligase Logic Gates and Their Initial Circuits
Stojanovic, M. N., Semova, S., Kolpashchikov, D., Macdonald, J., Morgan, C., & Stefanovic, D. (2005) · Journal of the American Chemical Society · doi:10.1021/ja043003a · Cited by 167
Miyoshi, D., Inoue, M., & Sugimoto, N. (2006) · Angewandte Chemie International Edition · doi:10.1002/anie.200602404 · Cited by 139
Miyoshi, D., Inoue, M., & Sugimoto, N. (2006) · Angewandte Chemie · doi:10.1002/ange.200602404 · Cited by 135
Evolutionary speed limits inferred from the fossil record
Kirchner, J. W. (2002) · Nature · doi:10.1038/415065a · Cited by 114
Two coupled enzymes perform in parallel the ‘AND’ and ‘InhibAND’ logic gate operations
Baron, R., Lioubashevski, O., Katz, E. Y., Niazov, T., & Willner, I. (2006) · Organic & Biomolecular Chemistry · doi:10.1039/b518205k · Cited by 79
Shaping Amorphous Calcium Carbonate Films into 2D Model Substrates for Bone Cell Culture
Popescu, D. C., van Leeuwen, E. N. M., Rossi, N. A. A., Holder, S. J., Jansen, J. A., & Sommerdijk, N. A. J. M. (2006) · Angewandte Chemie International Edition · doi:10.1002/anie.200502602 · Cited by 57
Software Tools for DNA Sequence Design
Feldkamp, U., Rauhe, H., & Banzhaf, W. (2003) · Genetic Programming and Evolvable Machines · doi:10.1023/a:1023985029398 · Cited by 42
Life, diversity and the pursuit of haplotypes
McCarthy, J. J. (2005) · Nature Biotechnology · doi:10.1038/nbt1105-1376 · Cited by 4
Cited by
Dynamic DNA nanotechnology using strand-displacement reactions
Zhang, D. Y., & Seelig, G. (2011) · Nature Chemistry · doi:10.1038/nchem.957 · Cited by 1,785
Control of DNA Strand Displacement Kinetics Using Toehold Exchange
Zhang, D. Y., & Winfree, E. (2009) · Journal of the American Chemical Society · doi:10.1021/ja906987s · Cited by 1,444
Wang, F., Lu, C.-H., & Willner, I. (2014) · Chemical Reviews · doi:10.1021/cr400354z · Cited by 649
Deng, R., Tang, L., Tian, Q., Wang, Y., Lin, L., & Li, J. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201309388 · Cited by 450
All-photonic multifunctional molecular logic device
Andréasson, J., Pischel, U., Straight, S. D., Moore, T. A., Moore, A. L., & Gust, D. (2011) · Journal of the American Chemical Society · doi:10.1021/ja203456h · Cited by 350
Metadata
- Authors
- Frezza, B. M., Cockroft, S. L., & Ghadiri, M. R.
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2007-11-10
- Volume
- 129
- Issue
- 48
- Pages
- 14875-14879
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W2069755600
- Cited by
- 276
- References
- 38
- FWCI
- 5.15
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
