Binary DNA Nanostructures for Data Encryption
Open accessAbstract
We present a simple and secure system for encrypting and decrypting information using DNA self-assembly. Binary data is encoded in the geometry of DNA nanostructures with two distinct conformations. Removing or leaving out a single component reduces these structures to an encrypted solution of ssDNA, whereas adding back this missing "decryption key" causes the spontaneous formation of the message through self-assembly, enabling rapid read out via gel electrophoresis. Applications include authentication, secure messaging, and barcoding.
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
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.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Halvorsen and Wong used electrophoresis to demonstrate the readout of an 11 byte ASCII message.
“The authors used electrophoresis to demonstrate the readout of an 11 byte ASCII message.113”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [113]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
The Proceedings of the National Academy of Sciences
Richards, J. W. (1915) · Science · doi:10.1126/science.42.1074.161 · Cited by 13,941 · see citing works
Folding DNA to create nanoscale shapes and patterns
Rothemund, P. W. K. (2006) · Nature · doi:10.1038/nature04586 · Cited by 7,391 · see citing works
Molecular Computation of Solutions to Combinatorial Problems
Adleman, L. M. (1994) · Science · doi:10.1126/science.7973651 · Cited by 4,474 · see citing works
Self-assembly of DNA into nanoscale three-dimensional shapes
Douglas, S. M., Dietz, H., Liedl, T., Högberg, B., Graf, F., & Shih, W. M. (2009) · Nature · doi:10.1038/nature08016 · Cited by 2,579 · see citing works
A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads
Douglas, S. M., Bachelet, I., & Church, G. M. (2012) · Science · doi:10.1126/science.1214081 · Cited by 2,187 · see citing works
Self-assembly of a nanoscale DNA box with a controllable lid
Andersen, E. S., Dong, M., Nielsen, M. M., Jahn, K., Subramani, R., Mamdouh, W., Golas, M. M., Sander, B. O., Stark, H., Oliveira, C. L. P., et al. (2009) · Nature · doi:10.1038/nature07971 · Cited by 1,628 · see citing works
Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades
Qian, L., & Winfree, E. (2011) · Science · doi:10.1126/science.1200520 · Cited by 1,440 · see citing works
DNA Solution of Hard Computational Problems
Lipton, R. J. (1995) · Science · doi:10.1126/science.7725098 · Cited by 1,058 · see citing works
Mechanically controlled binary conductance switching of a single-molecule junction
Quek, S. Y., Kamenetska, M., Steigerwald, M. L., Choi, H. J., Louie, S. G., Hybertsen, M. S., Neaton, J. B., & Venkataraman, L. (2009) · Nature Nanotechnology · doi:10.1038/nnano.2009.10 · Cited by 718 · see citing works
Hiding messages in DNA microdots
Clelland, C. T., Risca, V. I., & Bancroft, C. (1999) · Nature · doi:10.1038/21092 · Cited by 638 · see citing works
DNA Solution of the Maximal Clique Problem
Ouyang, Q., Kaplan, P. D., Liu, S., & Libchaber, A. J. (1997) · Science · doi:10.1126/science.278.5337.446 · Cited by 625 · see citing works
Solution of a 20-Variable 3-SAT Problem on a DNA Computer
Braich, R. S., Chelyapov, N. V., Johnson, C., Rothemund, P. W. K., & Adleman, L. M. (2002) · Science · doi:10.1126/science.1069528 · Cited by 567 · see citing works
Programming DNA Tube Circumferences
Yin, P., Hariadi, R. F., Sahu, S., Choi, H. M. T., Park, S. H., LaBean, T. H., & Reif, J. H. (2008) · Science · doi:10.1126/science.1157312 · Cited by 486 · see citing works
An Overview of Structural DNA Nanotechnology
Seeman, N. C. (2007) · Molecular Biotechnology · doi:10.1007/s12033-007-0059-4 · Cited by 450 · see citing works
Journal of The American Society for Mass Spectrometry
(2020) · Journal of the American Society for Mass Spectrometry · doi:10.1007/13361.1879-1123 · Cited by 347 · see citing works
The Tohoku Journal of Experimental Medicine
(1938) · Tubercle · doi:10.1016/s0041-3879(38)80099-4 · Cited by 327 · see citing works
Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices
Yan, H., LaBean, T. H., Feng, L., & Reif, J. H. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1032954100 · Cited by 312 · see citing works
Gehani, A., LaBean, T. H., & Reif, J. H. (2003) · Lecture notes in computer science · doi:10.1007/978-3-540-24635-0_12 · Cited by 290 · see citing works
Cryptography with DNA binary strands
Leier, A., Richter, C., Banzhaf, W., & Rauhe, H. (2000) · Biosystems · doi:10.1016/s0303-2647(00)00083-6 · Cited by 288 · see citing works
A review of DNA sequencing techniques
França, L. T. C., Carrilho, E., & Kist, T. B. L. (2002) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583502003797 · Cited by 249 · see citing works
A Sticker-Based Model for DNA Computation
Roweis, S. T., Winfree, E., Burgoyne, R., Chelyapov, N. V., Goodman, M. F., Rothemund, P. W. K., & Adleman, L. M. (1998) · Journal of Computational Biology · doi:10.1089/cmb.1998.5.615 · Cited by 218 · see citing works
Guarnieri, F., Fliss, M., & Bancroft, C. (1996) · Science · doi:10.1126/science.273.5272.220 · Cited by 189 · see citing works
An encryption scheme using DNA technology
Cui, G., Qin, L., Wang, Y., & Zhang, X. (2008) · International Conference on Bio-Inspired Computing: Theories and Applications (BIC-TA) · doi:10.1109/bicta.2008.4656701 · Cited by 148 · see citing works
Public-key system using DNA as a one-way function for key distribution
Tanaka, K., Okamoto, A., & Saito, I. (2005) · Biosystems · doi:10.1016/j.biosystems.2005.01.004 · Cited by 110 · see citing works
Photochemical Single-Molecule Affinity Switch
Schäfer, C. G., Eckel, R., Ros, R., Mattay, J., & Anselmetti, D. (2007) · Journal of the American Chemical Society · doi:10.1021/ja067734h · Cited by 67 · see citing works
Nanoengineering a single-molecule mechanical switch using DNA self-assembly
Halvorsen, K., Schaak, D., & Wong, W. P. (2011) · Nanotechnology · doi:10.1088/0957-4484/22/49/494005 · Cited by 61 · see citing works
Self-citationLee, I. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh196 · Cited by 61 · see citing works
Development of Biometric DNA Ink for Authentication Security
Hashiyada, M. (2004) · The Tohoku Journal of Experimental Medicine · doi:10.1620/tjem.204.109 · Cited by 57 · see citing works
Automated de novo sequencing of nucleic acids by liquid chromatography-tandem mass spectrometry
Oberacher, H., Mayr, B. M., & Huber, C. G. (2003) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2003.09.005 · Cited by 36 · see citing works
De Novo Sequence Determination of Modified Oligonucleotides
Farand, J., & Gosselin, F. (2009) · Analytical Chemistry · doi:10.1021/ac802452p · Cited by 29 · see citing works
DNA BookPreprint
Kawai, J., & Hayashizaki, Y. (2003) · Genome Research · doi:10.1101/gr.914203 · Cited by 28 · see citing works
Bio-Inspired Computing - Theories and Applications
(2014) · Communications in computer and information science · doi:10.1007/978-3-662-45049-9 · Cited by 27 · see citing works
On the use of ESI‐QqTOF‐MS/MS for the comparative sequencing of nucleic acids
Oberacher, H., & Pitterl, F. (2009) · Biopolymers · doi:10.1002/bip.21156 · Cited by 23 · see citing works
Automated de novo sequencing of nucleic acids by liquid chromatography-tandem mass spectrometry
Oberacher, H. (2003) · Journal of the American Society for Mass Spectrometry · doi:10.1016/s1044-0305(03)00708-6 · Cited by 2 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Emerging Approaches to DNA Data Storage: Challenges and Prospects
Doricchi, A., Platnich, C. M., Gimpel, A., Horn, F., Earle, M., Lanzavecchia, G., Cortajarena, A. L., Liz-Marzán, L. M., Liu, N., Heckel, R., et al. (2022) · ACS Nano · doi:10.1021/acsnano.2c06748 · Cited by 235 · see citing works
Kumar, M., Iqbal, A., & Kumar, P. (2016) · Signal Processing · doi:10.1016/j.sigpro.2016.01.017 · Cited by 214 · see citing works
Nanopore-Based DNA Hard Drives for Rewritable and Secure Data Storage
Chen, K., Zhu, J., Bošković, F., & Keyser, U. F. (2020) · Nano Letters · doi:10.1021/acs.nanolett.0c00755 · Cited by 134 · see citing works
Lossless chaotic color image cryptosystem based on DNA encryption and entropy
Wu, X., Wang, K., Wang, X., & Kan, H. (2017) · Nonlinear Dynamics · doi:10.1007/s11071-017-3698-4 · Cited by 117 · see citing works
“Naturally, DNA computing is applied in the field of encryption, which is called DNA cryptography [41].”
MethodWang, S., Mao, X., Wang, F., Zuo, X., & Fan, C. (2023) · Advanced Materials · doi:10.1002/adma.202307499 · Cited by 85 · see citing works
Addressable configurations of DNA nanostructures for rewritable memory
Chandrasekaran, A. R., Levchenko, O., Patel, D. S., MacIsaac, M., & Halvorsen, K. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx777 · Cited by 79 · see citing works
“Our memory system is also compatible with an encryption scheme that we previously presented (14), giving it further applications in secure messaging, authentication, and anti-counterfeiting.”
BackgroundMethodSelf-citationNucleic Acid Databases and Molecular-Scale Computing
Song, X., & Reif, J. (2019) · ACS Nano · doi:10.1021/acsnano.9b02562 · Cited by 73 · see citing works
Image Encoding Using Multi‐Level DNA Barcodes with Nanopore Readout
Zhu, J., Ermann, N., Chen, K., & Keyser, U. F. (2021) · Small · doi:10.1002/smll.202100711 · Cited by 66 · see citing works
Security in Wireless Body Area Networks: From In-Body to Off-Body Communications
Usman, M., Asghar, M. R., Ansari, I. S., & Qaraqe, M. (2018) · IEEE Access · doi:10.1109/access.2018.2873825 · Cited by 59 · see citing works
Xie, T., Liu, Y., & Tang, J. (2014) · Optik · doi:10.1016/j.ijleo.2014.07.111 · Cited by 52 · see citing works
DNA Nanoswitch Barcodes for Multiplexed Biomarker Profiling
Chandrasekaran, A. R., MacIsaac, M. F., Vilcapoma, J., Hansen, C. H., Yang, D., Wong, W. P., & Halvorsen, K. (2021) · Nano Letters · doi:10.1021/acs.nanolett.0c03929 · Cited by 50 · see citing works
Self-citationCryptanalysis of a chaos-based image encryption scheme combining DNA coding and entropy
Su, X. B., Li, W., & Hu, H. (2016) · Multimedia Tools and Applications · doi:10.1007/s11042-016-3800-9 · Cited by 49 · see citing works
“Secondly, the encoded DNA sequence is substituted and permuted to generate a key image based on DNA operation rules and form the cipher image [3, 7, 10].”
MethodNovel Modalities in DNA Data Storage
Lim, C. K., Nirantar, S., Yew, W. S., & Poh, C. L. (2021) · Trends in biotechnology · doi:10.1016/j.tibtech.2020.12.008 · Cited by 44 · see citing works
Zhu, J., Tivony, R., Bošković, F., Pereira-Dias, J., Sandler, S. E., Baker, S. G., & Keyser, U. F. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.3c01649 · Cited by 38 · see citing works
An Overview of Security Threats, Solutions and Challenges in WBANs for Healthcare
Mucchi, L., Jayousi, S., Martinelli, A., Caputo, S., & Marcocci, P. (2019) · International Symposium on Medical Information and Communication Technology · doi:10.1109/ismict.2019.8743798 · Cited by 36 · see citing works
“Biochemical cryptography is proposed to address the challenge of the key structure (such as DNA nano-structures for data encryption [43]).”
BackgroundEngineering surface patterns on nanoparticles: new insights into nano-bio interactions
Hu, B., Liu, R., Liu, Q., Lin, Z., Shi, Y., Li, J., Wang, L., Li, L., Xiao, X., & Wu, Y. (2022) · Journal of Materials Chemistry B · doi:10.1039/d1tb02549j · Cited by 36 · see citing works
Na, D. (2020) · Microbial Cell Factories · doi:10.1186/s12934-020-01387-0 · Cited by 31 · see citing works
Programmable DNA Nanoswitch Sensing with Solid-State Nanopores
Beamish, E., Tabard‐Cossa, V., & Godin, M. (2019) · ACS Sensors · doi:10.1021/acssensors.9b01053 · Cited by 30 · see citing works
Image watermarking using chaotic map and DNA coding
Wang, B., Zhou, S., Zheng, X., Zhou, C., Dong, J., & Zhao, L. (2015) · Optik · doi:10.1016/j.ijleo.2015.09.217 · Cited by 29 · see citing works
Recent Advances in Noninvasive Biosensors for Forensics, Biometrics, and Cybersecurity
McGoldrick, L. K., & Halámek, J. (2020) · Sensors · doi:10.3390/s20215974 · Cited by 25 · see citing works
DNA nanotechnology: new adventures for an old warhorse
Zakeri, B., & Lu, T. K. (2015) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2015.05.020 · Cited by 20 · see citing works
“Information can also be embedded in the artificial 3D architectures of programmed and self-assembled DNA [35].”
BackgroundProcessing DNA Storage through Programmable Assembly in a Droplet‐Based Fluidics System
Yu, M., Lim, D., Kim, J.-W., & Song, Y. (2023) · Advanced Science · doi:10.1002/advs.202303197 · Cited by 17 · see citing works
RADIANT - hybrid multilayered chaotic image encryption system for color images
Sasikaladevi, N., Geetha, K., Sriharshini, K., & Aruna, M. D. (2018) · Multimedia Tools and Applications · doi:10.1007/s11042-018-6711-0 · Cited by 18 · see citing works
Abdolahi, M., Jiang, H., & Kamińska, B. (2019) · Nanotechnology · doi:10.1088/1361-6528/ab2d3b · Cited by 18 · see citing works
An Image Encryption Scheme Based on DNA Computing and Cellular Automata
Zhou, S., Wang, B., Zheng, X., & Zhou, C. (2016) · Discrete Dynamics in Nature and Society · doi:10.1155/2016/5408529 · Cited by 14 · see citing works
“The sixth one [21] uses DNA self-assembly technique.”
Aims and methods of biosteganography
Brunet, T. D. P. (2016) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2016.03.044 · Cited by 11 · see citing works
Current and emerging opportunities in biological medium‐based computing and digital data storage
Bennet, D., Vo‐Dinh, T., & Zenhausern, F. (2021) · Nano Select · doi:10.1002/nano.202100275 · Cited by 9 · see citing works
SemiSynBio: A new era for neuromorphic computing
Liu, R., Liu, T., Liu, W., Luo, B., Li, Y., Fan, X., Zhang, X., Cui, W., & Teng, Y. (2024) · Synthetic and Systems Biotechnology · doi:10.1016/j.synbio.2024.04.013 · Cited by 8 · see citing works
“DNA molecules have complementary base pairing properties that allow for specific molecular recognition [13], self-assembly [14], and large-scale parallel reactions [15 – 18].”
BackgroundEncrypted Oligonucleotide Arrays for Molecular Authentication
Holden, M. T., & Smith, L. M. (2019) · ACS Combinatorial Science · doi:10.1021/acscombsci.9b00088 · Cited by 7 · see citing works
An enhanced DNA structure for one-time pad together with graph labeling techniques
Deepa, B., & Maheswari, V. (2022) · AIP conference proceedings · doi:10.1063/5.0071283 · Cited by 6 · see citing works
A watermarking system for labeling genomic DNA
Yamamoto, N., Kajiura, H., Takeno, S., Suzuki, N., & Nakazawa, Y. (2014) · Plant Biotechnology · doi:10.5511/plantbiotechnology.14.0609b · Cited by 5 · see citing works
“DNA watermark technologies are generally comprised of three processes: encryption, labeling and detection (Halvorsen and Wong 2012; Jupiter et al. 2010).”
MethodThe power of deoxyribonucleic acid and bio-robotics in creating new global revolution: a review
Kasegn, M. M., Gebremedhn, H. M., Yaekob, A. T., & Mesele, E. (2025) · Health Nanotechnology · doi:10.1186/s44301-024-00002-0 · Cited by 4 · see citing works
“Although all lanes contain an equal amount of DNA, only the double-stranded pieces are visible when stained [58] as shown in Fig.2.”
A DNA-Based Semantic Fusion Model for Remote Sensing Data
Sun, H., Weng, J., Yu, G., & Massawe, R. H. J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077090 · Cited by 3 · see citing works
Secure data storage on DNA hard drivesPreprint
Chen, K., Zhu, J., Bošković, F., & Keyser, U. F. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/857748 · Cited by 4 · see citing works
“More importantly, our system enables data encryption by physical keys (specific molecules bound to target positions) (24).”
BackgroundPhotoresponsive DNA steganography for secure information transmission by nanopore
Hu, Z., Wang, J., Liu, S.-C., Wang, J.-H., Ma, H., Yang, C. C. C.-C., Ying, Y., Yan, F., & Long, Y.-T. (2026) · National Science Review · doi:10.1093/nsr/nwag196 · Cited by 2 · see citing works
“…letter encoding using 5–25 nucleotides (e.g. ‘E’ = 00001, 5 nt; ‘L’ = 10010, 10 nt), thereby achieving an average logical storage density of 0.2–1.0 bits/nt, which is about one order of magnitude higher than those of conventional DNA-structure-based encryption methods [14 ,17 ,18 ,40 ,41 ].”
InfluentialAddressable DNA Information Processing System with a Fluorescent Readout for Rewritable Memory
Xi, Z., Yang, M., Hu, Y., & Wu, T. (2023) · Chinese Journal of Chemistry · doi:10.1002/cjoc.202300272 · Cited by 1 · see citing works
Cryptographic keys management system based on DNA strands
Miśkiewicz, M., & Ksi̜eżopolski, B. (2019) · Annals of Computer Science and Information Systems · doi:10.15439/2019f313 · Cited by 1 · see citing works
“Halvorsen and Wong in his paper [9] showed an interesting, simple and secure system for encrypting and decrypting information using self-assembly DNA structures and PCR based decoded information reading method.”
BackgroundBiochemical and chemical methods of key derivation for cryptographic ciphers
McGoldrick, L. K. (2020) · doi:10.54014/6tmb-psdz · Cited by 1 · see citing works
Constructing artificial neural networks using genetic circuits to realize neuromorphic computing
Yang, S., Liu, R., Liu, T., Zhuang, Y., Li, J., & Teng, Y. (2021) · Chinese Science Bulletin (Chinese Version) · doi:10.1360/tb-2021-0501
Strong and Efficient Cipher with Dynamic Symbol Substitution and Dynamic Noise Insertion
Al-Daraiseh, A. A., & Al-Muhammed, M. J. (2022) · Symmetry · doi:10.3390/sym14112372
An improved DNA cryptosystem based graph labeling techniques
Deepa, B., & Maheswari, V. (2022) · AIP conference proceedings · doi:10.1063/5.0108504
Uncover the Hidden Message in DNA
(2023) · Archives of Health Science · doi:10.31829/2641-7456/ahs2023-7(1)-001
Dynamic Operations in Macromolecular Data Storage
Ossowski, J., Affenberger, O., Lutz, J., & Nerantzaki, M. (2026) · Angewandte Chemie International Edition · doi:10.1002/anie.5128253
“Nevertheless, readers are directed to representative examples for further reference [26, 65, 66].”
Dynamic Operations in Macromolecular Data Storage
Ossowski, J., Affenberger, O., Lutz, J., & Nerantzaki, M. (2026) · Angewandte Chemie · doi:10.1002/ange.5128253
Nontraditional molecular-bit DNA storage
Liu, X., Wu, R., Liang, Y., Gong, Y., Zhang, Y., & Zhang, C. (2026) · Chinese Science Bulletin (Chinese Version) · doi:10.1360/csb-2026-0924
- Authors
- Halvorsen, K., & Wong, W. P.
- Affiliations
- Boston Children's Hospital (US)
- Corresponding author
- Wong, Wesley P.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-09-11
- Volume
- 7
- Issue
- 9
- Pages
- e44212
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3439488
- OpenAlex
- W2130537383
- Cited by
- 45
- References
- 34
- Citations by year
- 2026: 4 · 2025: 1 · 2024: 1 · 2023: 5 · 2022: 5 · 2021: 5 · 2020: 4 · 2019: 7 · 2018: 2 · 2017: 2 · 2016: 4 · 2015: 2 · 2014: 2 · 2013: 1
- FWCI
- 0.64
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Physical Sciences › Computer Science › Artificial Intelligence › Cryptography and Data Security
- Keywords
- DNA self-assembly, DNA nanostructures, data encryption, binary encoding, single-stranded DNA, decryption keys, authentication, secure messaging, DNA barcoding
- MeSH terms
- DNA, Electrophoresis, Agar Gel, Computer Security, Nanostructures
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