Sage Journals: Discover world-class research

Abstract

DNA molecules are increasingly being synthesized in the laboratory. A major concern in this domain is that a malicious actor can potentially tweak a benevolent synthesized DNA molecule and create a DNA molecule with harmful properties (Biodefense in the Age of Synthetic Biology (2018) The National Academies Press). To detect if a synthesized DNA molecule has been modified from the original version created in the laboratory, the authors in (In Proceedings of the New Security Paradigms Workshop (2018) ACM) proposed a digital signature protocol for creating a signed DNA molecule. However, several challenges arise in more complex molecules because of various forms of DNA mutations as well as size restrictions of the molecule that impact its properties. The current work extends (In Proceedings of the New Security Paradigms Workshop (2018) ACM) in several directions to address these problems. A second concern with synthesized DNA is that it is an intellectual property. In order to allow its use by third parties, an annotated document of the molecule needs to be distributed. However, since the molecule and document are two different entities, one being a physical product and the other being a digital one, ensuring that both are distributed correctly together without tampering is challenging. This work also addresess this problem by transforming the document into a DNA molecule and embedding it within the original molecule together with the signature.

Keywords

Cyber-bio security identity-based signatures Reed–Solomon codes pairing-based cryptography synthetic DNA

Get full access to this article

View all access options for this article.

References

Boneh and

Franklin, Identity-based encryption from the Weil pairing, in: Advances in Cryptology – CRYPTO 2001,

Kilian, ed., Lecture Notes in Computer Science, Vol. 2139, 2001.

J.C.

Choon and

Hee Cheon, An identity-based signature from gap Diffie–Hellman groups, in: Public Key Crytpography – PKC 2003,

Y.G.

Desmedt, ed., Lecture Notes in Computer Science, Vol. 2567, Springer, Berlin, 2003.

F.J.

Damerau, A technique for computer detection and correction of spelling errors, Communications of ACM 7(3) (1964), 171–176. doi:10.1145/363958.363994.

De Caro and

Iovino, jPBC: Java pairing based cryptography, in: Proceedings of the 16th IEEE Symposium on Computers and Communications, ISCC 2011, Kerkyra, Corfu, Greece, June 28–July 1, IEEE, 2011, pp. 850–855.

J.E.

Gallegos,

D.M.

Kar,

Ray,

Ray and

Peccoud, Securing the exchange of synthetic genetic constructs using digital signatures, bioRxiv, 2019. https://www.biorxiv.org/content/early/2019/09/26/750927. doi:10.1101/750927.

D.G.

Gibson,

J.I.

Glass,

Lartigue,

V.N.

Noskov,

R.-Y.

Chuang,

M.A.

Algire,

G.A.

Benders,

M.G.

Montague,

Ma,

M.M.

Moodie,

Merryman,

Vashee,

Krishnakumar,

Assad-Garcia,

Andrews-Pfannkoch,

E.A.

Denisova,

Young,

Z.-Q.

Qi,

T.H.

Segall-Shapiro,

C.H.

Calvey,

P.P.

Parmar,

C.A.

Hutchison,

H.O.

Smith and

J.C.

Venter, Creation of a bacterial cell controlled by a chemically synthesized genome, Science 329(5987) (2010), 52–56. doi:10.1126/science.1190719.

Heider and

Barnekow, DNA-based watermarks using the DNA-crypt algorithm, BMC Bioinformatics 8 (2007), 176. doi:10.1186/1471-2105-8-176.

C.A.

Hutchison,

R.-Y.

Chuang,

V.N.

Noskov,

Assad-Garcia,

T.J.

Deerinck,

M.H.

Ellisman,

Gill,

Kannan,

B.J.

Karas,

Ma,

J.F.

Pelletier,

Z.-Q.

Qi,

R.A.

Richter,

E.A.

Strychalski,

Sun,

Suzuki,

Tsvetanova,

K.S.

Wise,

H.O.

Smith,

J.I.

Glass,

Merryman,

D.G.

Gibson and

J.C.

Venter, Design and synthesis of a minimal bacterial genome, Science 351(6280) (2016), aad6253. doi:10.1126/science.aad6253.

Jaccard, Etude de la distribution florale dans une portion des alpes et du jura, Bulletin de la Societe Vaudoise des Sciences Naturelles 37(142) (1901), 547–579.

10.

Jaccard, Distribution de la Flore Alpine dans le Bassin des Dranses et dans quelques régions voisines., Bulletin de la Societe Vaudoise des Sciences Naturelles 37(140) (1901), 241–272.

11.

M.A.

Jaro, Advances in record-linkage methodology as applied to matching the 1985 Census of Tampa, Florida, Journal of the American Statistical Association 84(406) (1989), 414–420. doi:10.1080/01621459.1989.10478785.

12.

D.C.

Jupiter, DNA watermarking of infectious agents: Progress and prospects, PLOS Pathogens 6(6) (2010), e1000950. doi:10.1371/journal.ppat.1000950.

13.

D.M.

Kar,

Ray,

Gallegos and

Peccoud, Digital signatures to ensure the authenticity and integrity of synthetic DNA molecules, in: Proceedings of the New Security Paradigms Workshop, Windsor, UK, ACM, 2018.

14.

V.I.

Levenshtein, Binary codes capable of correcting deletions, insertions, and reversals, Soviet Physics Doklady 10(8) (1966), 707–710.

15.

Liss, Embedding permanent watermarks in synthetic genes, PLOS ONE 7(8) (2012), e42465. doi:10.1371/journal.pone.0042465.

16.

Nakamoto, Bitcoin: A peer-to-peer electronic cash system, Bitcoin.org Working Paper, 2008.

17.

National Academies of Sciences, Engineering, and Medicine, Biodefense in the Age of Synthetic Biology, The National Academies Press, Washington, DC, 2018. doi:10.17226/24890.

18.

Ney,

Koscher,

Organick,

Ceze and

Kohno, Computer security, privacy, and DNA sequencing: Compromising computers with synthesized DNA, privacy leaks, and more, in: Proceedings of the 26th USENIX Security Symposium, Vancouver, Canada, 2017.

19.

A.A.

Nielsen and

C.A.

Voigt, Deep learning to predict the lab-of-origin of engineered DNA, Nature Communications 9(1) (2018), 3135. doi:10.1038/s41467-018-05378-z.

20.

K.G.

Paterson, ID-based signatures from pairings on elliptic curves, Electronics Letters 38(18) (2002), 1025–1026. doi:10.1049/el:20020682.

21.

Peccoud,

J.E.

Gallegos,

Murch,

W.G.

Buchholz and

Raman, Cyberbiosecurity: From naive trust to risk awareness, Trends in Biotechnology 36(1) (2018), 4–7. doi:10.1016/j.tibtech.2017.10.012.

22.

J.S.

Plank, A tutorial on Reed–Solomon coding for fault-tolerance in RAID-like systems, Software Practice and Experience 27(9) (1997), 995–1012. doi:10.1002/(SICI)1097-024X(199709)27:9<995::AID-SPE111>3.0.CO;2-6.

23.

I.S.

Reed and

Solomon, Polynomial codes over certain finite fields, Journal of the Society for Industrial and Applied Mathematics 8(2) (1960), 300–304. doi:10.1137/0108018.

24.

S.M.

Richardson,

L.A.

Mitchell,

Stracquadanio,

Yang,

J.S.

Dymond,

J.E.

DiCarlo,

Lee,

C.L.V.

Huang,

Chandrasegaran,

Cai,

J.D.

Boeke and

J.S.

Bader, Design of a synthetic yeast genome, Science 355(6329) (2017), 1040–1044. doi:10.1126/science.aaf4557.

25.

Sakai and

Kasahara, ID based cryptosystems with pairing on elliptic curve, IACR Cryptology ePrint Archive, 2003.

26.

Sakai,

Ohgishi and

Kasahara, Cryptosystems based on pairing, in: Proceedings of the 2000 Symposium on Cryptography and Information Security, Okinawa, Japan, 2000.

27.

Shamir, Identity-based cryptosystems and signature schemes, in: Advances in Cryptology – CRYPTO 1984,

G.R.

Blakley and

Chaum, eds, Lecture Notes in Computer Science, Vol. 196, Springer, Berlin, 1984, pp. 47–53.

28.

Wood

et al., Ethereum: A secure decentralised generalised transaction ledger, Ethereum Project Yellow Paper 151 (2014), 1–32.

29.

Yi, An identity-based signature scheme from the Weil pairing, IEEE Communications Letters 7(2) (2003), 76–78. doi:10.1109/LCOMM.2002.808397.

30.

Zhao and

Sahni, String correction using the Damerau–Levenshtein distance, BMC Bioinformatics 20 (2019), 277. doi:10.1186/s12859-019-2819-0.

Synthesizing DNA molecules with identity-based digital signatures to prevent malicious tampering and enabling source attribution

Abstract

Keywords

Get full access to this article

References