基于DNA折纸订书钉链折叠的信息加密策略

侯晓玲; 田卓立; 王建榜; 王丽华; 李江; 张继超; 柳华杰

doi:10.11999/JEIT231434

基于DNA折纸订书钉链折叠的信息加密策略

doi: 10.11999/JEIT231434

侯晓玲^{1, 2},
田卓立^{1, 2},
王建榜³,
王丽华^{1, 2, 4},
李江^{1, 2, 4},
张继超^{1, 5},
柳华杰^3, ,

1.
中国科学院上海应用物理研究所中国科学院微观界面物理与探测重点实验室上海 201800
2.
中国科学院大学北京 100049
3.
同济大学化学科学与工程学院上海 200092
4.
上海大学理学院材料生物学研究所上海 200444
5.
中国科学院上海高等研究院上海同步辐射光源上海 201210

基金项目: 国家重点研发计划(2020YFA0908900)，上海市基础研究特区计划

详细信息

作者简介:
侯晓玲：女，博士生，研究方向为DNA计算和DNA自组装

田卓立：女，硕士生，研究方向为DNA器件和DNA自组装

王建榜：男，研究员，研究方向为DNA器件和DNA自组装

王丽华：女，研究员，研究方向为生物传感和DNA自组装

李江：男，研究员，研究方向为DNA分子机器和DNA自组装

张继超：男，副研究员，研究方向为同步辐射X射线成像

柳华杰：男，教授，研究方向为DNA计算和DNA自组装

通讯作者:
柳华杰　liuhuajie@tongji.edu.cn

中图分类号: TP301
计量
- 文章访问数: 206
- HTML全文浏览量: 73
- PDF下载量: 23
- 被引次数: 0
出版历程
- 收稿日期: 2023-12-28
- 修回日期: 2024-07-16
- 网络出版日期: 2024-07-24
- 刊出日期: 2024-09-26

A DNA Origami Cryptography Scheme Based on Staple Folding

HOU Xiaoling^{1, 2},
TIAN Zhuoli^{1, 2},
WANG Jianbang³,
WANG Lihua^{1, 2, 4},
LI Jiang^{1, 2, 4},
ZHANG Jichao^{1, 5},
LIU Huajie^{3
, ,}

1.
CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
2.
University of Chinese Academy of Sciences, Beijing 100049, China
3.
School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China
4.
Institute of Materiobiology, College of Science, Shanghai University, Shanghai 200444, China
5.
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China

Funds: The National Key R&D Program of China (2020YFA0908900), Shanghai Pilot Program for Basic Research

摘要

摘要: DNA折纸结构是蕴含复杂序列折叠信息的纳米结构，为发展具有超大密钥空间的信息加密技术提供了新思路。该文设计了一种能够充分发挥DNA折纸结构信息特征的信息加密策略，与先前利用DNA折纸骨架链折叠的思路不同，该文基于订书钉链集合的非线性组合特征，提出通过探索其更为广阔的折叠多样性来实现更大的密钥空间。该策略的密钥空间计算模型分解为订书钉链的结合域模式、协同折叠以及独立性3个因素，分别考虑了订书钉链的链内区段分布性、链间排布多样性以及序列特异性。以上3种因素的组合，使单位几何空间内DNA折纸的折叠多样性更有效地转化为密钥空间。该策略是一种基于生物分子热力学的加密方式，为扩展信息安全的应用场景提供了新的可能。
- DNA折纸 /
- DNA纳米结构 /
- 信息加密 /
- 密钥空间 /
- 自组装
Abstract: The DNA origami nanostructure encapsulates intricate sequence-folding information, presenting a novel avenue for exploiting cryptography with a vast key space. This paper introduces an encryption strategy that fully realizes the structure-based potential of DNA origami. In contrast to previous approach centered on the folding of DNA origami scaffold, an alternative methodology is introduced based on the nonlinear combination characteristics of staple ensembles. This approach aims to achieve a larger key space by exploring the inherent extensive folding diversity of staple. The key space computational model is delineated into three factors: the binding domain mode, cooperative folding, and independence of staples. These three factors respectively account for the intra-chain distribution, inter-chain arrangement diversity, and sequence specificity of staples. The combination of these factors effectively converts the folding diversity of DNA origami in per unit of geometric space into key space. This strategy represents a cryptography rooted in the principles of biomolecular thermodynamics, offering new possibilities for extending the application scenarios of information security.
- DNA origami /
- DNA nanostructure /
- Information encryption /
- Key space /
- Self-assembly

HTML全文

图 1 DNA折纸的信息编码方式

下载: 全尺寸图片幻灯片

图 2 发送方使用骨架链密钥进行加密

下载: 全尺寸图片幻灯片

图 3 分别使用正确及错误的骨架链密钥进行解密

下载: 全尺寸图片幻灯片

图 4 订书钉链的结合模式

下载: 全尺寸图片幻灯片

图 5 订书钉链的协同折叠

下载: 全尺寸图片幻灯片

图 6 订书钉链的序列独立性

下载: 全尺寸图片幻灯片

参考文献(39)

[1]	ZHIRNOV V, ZADEGAN R M, SANDHU G S, et al. Nucleic acid memory[J]. Nature Materials, 2016, 15(4): 366–370. doi: 10.1038/nmat4594.
[2]	CEZE L, NIVALA J, and STRAUSS K. Molecular digital data storage using DNA[J]. Nature Reviews Genetics, 2019, 20(8): 456–466. doi: 10.1038/s41576-019-0125-3.
[3]	BENENSON Y, PAZ-ELIZUR T, ADAR R, et al. Programmable and autonomous computing machine made of biomolecules[J]. Nature, 2001, 414(6862): 430–434. doi: 10.1038/35106533.
[4]	王君珂, 印珏, 牛人杰, 等. DNA计算与DNA纳米技术[J]. 电子与信息学报, 2020, 42(6): 1313–1325. doi: 10.11999/JEIT190826. WANG Junke, YIN Jue, NIU Renjie, et al. DNA computing and DNA nanotechnology[J]. Journal of Electronics & Information Technology, 2020, 42(6): 1313–1325. doi: 10.11999/JEIT190826.
[5]	PENCHOVSKY R and BREAKER R R. Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes[J]. Nature Biotechnology, 2005, 23(11): 1424–1433. doi: 10.1038/nbt1155.
[6]	QIAN Lulu and WINFREE E. Scaling up digital circuit computation with DNA strand displacement cascades[J]. Science, 2011, 332(6034): 1196–1201. doi: 10.1126/science.1200520.
[7]	殷志祥, 唐震, 张强, 等. 基于DNA折纸基底的与非门计算模型[J]. 电子与信息学报, 2020, 42(6): 1355–1364. doi: 10.11999/JEIT190825. YIN Zhixiang, TANG Zhen, ZHANG Qiang, et al. NAND gate computational model based on the DNA origami template[J]. Journal of Electronics & Information Technology, 2020, 42(6): 1355–1364. doi: 10.11999/JEIT190825.
[8]	CLELLAND C T, RISCA V, and BANCROFT C. Hiding messages in DNA microdots[J]. Nature, 1999, 399(6736): 533–534. doi: 10.1038/21092.
[9]	JONOSKA N, PĂUN G, and ROZENBERG G. Aspects of Molecular Computing: Essays Dedicated to Tom Head on the Occasion of His 70th Birthday[M]. Berlin: Springer, 2004: 167–188. doi: 10.1007/b94864.
[10]	LEIER A, RICHTER C, BANZHAF W, et al. Cryptography with DNA binary strands[J]. Biosystems, 2000, 57(1): 13–22. doi: 10.1016/S0303-2647(00)00083-6.
[11]	LUSTGARTEN O, MOTIEI L, and MARGULIES D. User authorization at the molecular scale[J]. ChemPhysChem, 2017, 18(13): 1678–1687. doi: 10.1002/cphc.201700506.
[12]	NUMMELIN S, KOMMERI J, KOSTIAINEN M A, et al. Evolution of structural DNA nanotechnology[J]. Advanced Materials, 2018, 30(24): 1703721. doi: 10.1002/adma.201703721.
[13]	SEEMAN N C. Nucleic acid junctions and lattices[J]. Journal of Theoretical Biology, 1982, 99(2): 237–247. doi: 10.1016/0022-5193(82)90002-9.
[14]	FU T J and SEEMAN N C. DNA double-crossover molecules[J]. Biochemistry, 1993, 32(13): 3211–3220. doi: 10.1021/bi00064a003.
[15]	LABEAN T H, YAN Hao, KOPATSCH J, et al. Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes[J]. Journal of the American Chemical Society, 2000, 122(9): 1848–1860. doi: 10.1021/ja993393e.
[16]	REISHUS D, SHAW B, BRUN Y, et al. Self-assembly of DNA double-double crossover complexes into high-density, doubly connected, planar structures[J]. Journal of the American Chemical Society, 2005, 127(50): 17590–17591. doi: 10.1021/ja0557177.
[17]	KE Yonggang, LIU Yan, ZHANG Junping, et al. A study of DNA tube formation mechanisms using 4-, 8-, and 12-Helix DNA nanostructures[J]. Journal of the American Chemical Society, 2006, 128(13): 4414–4421. doi: 10.1021/ja058145z.
[18]	ROTHEMUND P W K. Folding DNA to create nanoscale shapes and patterns[J]. Nature, 2006, 440(7082): 297–302. doi: 10.1038/nature04586.
[19]	OBER M F, BAPTIST A, WASSERMANN L, et al. In situ small-angle X-ray scattering reveals strong condensation of DNA origami during silicification[J]. Nature Communications, 2022, 13(1): 5668. doi: 10.1038/s41467-022-33083-5.
[20]	DAI Xinpei, CHEN Xiaoliang, JING Xinxin, et al. DNA origami-encoded integration of heterostructures[J]. Angewandte Chemie International Edition, 2022, 61(11): e202114190. doi: 10.1002/anie.202114190.
[21]	ZHAO Yumeng, ZHANG Chao, YANG Linlin, et al. Programmable and site-specific patterning on DNA origami templates with heterogeneous condensation of silver and silica[J]. Small, 2021, 17(47): 2103877. doi: 10.1002/smll.202103877.
[22]	HANNEWALD N, WINTERWERBER P, ZECHEL S, et al. DNA origami meets polymers: A powerful tool for the design of defined nanostructures[J]. Angewandte Chemie International Edition, 2021, 60(12): 6218–6229. doi: 10.1002/anie.202005907.
[23]	ARYAL B R, RANASINGHE D R, PANG Chao, et al. Annealing of polymer-encased nanorods on DNA origami forming metal–semiconductor nanowires: Implications for nanoelectronics[J]. ACS Applied Nano Materials, 2021, 4(9): 9094–9103. doi: 10.1021/acsanm.1c01682.
[24]	MADSEN M, BAKKE M R, GUDNASON D A, et al. A single molecule polyphenylene-vinylene photonic wire[J]. ACS Nano, 2021, 15(6): 9404–9411. doi: 10.1021/acsnano.0c10922.
[25]	YANG Yunqi, LU Qinyi, HUANG Chaomin, et al. Programmable site-specific functionalization of DNA origami with polynucleotide brushes[J]. Angewandte Chemie International Edition, 2021, 60(43): 23241–23247. doi: 10.1002/anie.202107829.
[26]	KAHN J S, XIONG Yan, HUANG J, et al. Cascaded enzyme reactions over a three-dimensional, wireframe DNA origami scaffold[J]. JACS Au, 2022, 2(2): 357–366. doi: 10.1021/jacsau.1c00387.
[27]	WANG S T, MINEVICH B, LIU Jianfang, et al. Designed and biologically active protein lattices[J]. Nature Communications, 2021, 12(1): 3702. doi: 10.1038/s41467-021-23966-4.
[28]	ZHAO Shuai, TIAN Run, WU Jun, et al. A DNA origami-based aptamer nanoarray for potent and reversible anticoagulation in hemodialysis[J]. Nature Communications, 2021, 12(1): 358. doi: 10.1038/s41467-020-20638-7.
[29]	孙彤, 刘文静, 张萍, 等. 基于DNA折纸的单个链霉亲和素分子的原子力显微术高分辨成像[J]. 核技术, 2019, 42(4): 040501. doi: 10.11889/j.0253-3219.2019.hjs.42.040501. SUN Tong, LIU Wenjing, ZHANG Ping, et al. High-resolution imaging of single-molecule streptavidin using atomic force microscopy based on DNA origami[J]. Nuclear Techniques, 2019, 42(4): 040501. doi: 10.11889/j.0253-3219.2019.hjs.42.040501.
[30]	YE Jingjing, AFTENIEVA O, BAYRAK T, et al. Complex metal nanostructures with programmable shapes from simple DNA building blocks[J]. Advanced Materials, 2021, 33(29): 2100381. doi: 10.1002/adma.202100381.
[31]	RYSSY J, NATARAJAN A K, WANG Jinhua, et al. Light-responsive dynamic DNA-origami-based plasmonic assemblies[J]. Angewandte Chemie, 2021, 133(11): 5923–5927. doi: 10.1002/ange.202014963.
[32]	MA Yuxuan, LU Zhangwei, JIA Bin, et al. DNA origami as a nanomedicine for targeted rheumatoid arthritis therapy through reactive oxygen species and nitric oxide scavenging[J]. ACS Nano, 2022, 16(8): 12520–12531. doi: 10.1021/acsnano.2c03991.
[33]	COMBERLATO A, KOGA M M, NÜSSING S, et al. Spatially controlled activation of toll-like receptor 9 with DNA-based nanomaterials[J]. Nano Letters, 2022, 22(6): 2506–2513. doi: 10.1021/acs.nanolett.2c00275.
[34]	KNAPPE G A, WAMHOFF E C, READ B J, et al. In situ covalent functionalization of DNA origami virus-like particles[J]. ACS Nano, 2021, 15(9): 14316–14322. doi: 10.1021/acsnano.1c03158.
[35]	CHATTERJEE G, DALCHAU N, MUSCAT R A, et al. A spatially localized architecture for fast and modular DNA computing[J]. Nature Nanotechnology, 2017, 12(9): 920–927. doi: 10.1038/nnano.2017.127.
[36]	THUBAGERE A J, LI Wei, JOHNSON R F, et al. A cargo-sorting DNA robot[J]. Science, 2017, 357(6356): eaan6558. doi: 10.1126/science.aan6558.
[37]	LIU Fengsong, LI Na, SHANG Yingxu, et al. A DNA-based plasmonic nanodevice for cascade signal amplification[J]. Angewandte Chemie International Edition, 2022, 61(22): e202114706. doi: 10.1002/anie.202114706.
[38]	ZHANG Yinan, WANG Fei, CHAO Jie, et al. DNA origami cryptography for secure communication[J]. Nature Communications, 2019, 10(1): 5469. doi: 10.1038/s41467-019-13517-3.
[39]	STALLINGS W. The advanced encryption standard[J]. Cryptologia, 2002, 26(3): 165–188. doi: 10.1080/0161-110291890876.