DNA计算与DNA密码

DNA在信息科学中的应用,给现代密码学带来了新的挑战和机遇。一方面,DNA计算固有的超大规模并行性给安全性依赖于数学困难问题的现代密码学带来了新的挑战。另一方面, 利用DNA可以实现新的密码技术DNA密码。本文首先介绍了DNA计算,认为在已有的DNA计算模型下,DNA计算不能对现代密码学构成真正的威胁。其次介绍了DNA密码, 并讨论了DNA密码与现代密码学的关系。新生的DNA计算与DNA密码表现出巨大的潜力, 必将会对密码学的未来发展产生深远的影响。     

DNA Mold-Based Fabrication of Palladium Nanostructures

DNA origami molds allow a shape-controlled growth of metallic nanoparticles. So far, this approach is limited to gold and silver. Here, the fabrication of linear palladium nanostructures with controlled lengths and patterns is demonstrated. To obtain nucleation centers for a seeded growth, a synthesis procedure of palladium nanoparticles (PdNPs) using Bis(p-sulfonatophenyl)phenylphosphine (BSPP) both as reductant and stabilizer is developed to establish an efficient functionalization protocol of the particles with single-stranded DNA. Attaching the functionalized particles to complementary DNA strands inside DNA mold cavities supports subsequently a highly specific seeded palladium deposition. This provides rod-like PdNPs with diameters of 20–35 nm of grainy morphology. Using an annealing procedure and a post-reduction step with hydrogen, homogeneous palladium nanostructures can be obtained. With the adaptation of the procedure to palladium the capabilities of the mold-based tool-box are expanded. In the future, this may allow a facile adaptation of the mold approach to less noble metals including magnetic materials such as Ni and Co.     

Identifying DNA methylation in a nanochannel

DNA methylation is a stable epigenetic modification, which is well known to be involved in gene expression regulation. In general, however, analyzing DNA methylation requires rather time consuming processes (24–96 h) via DNA replication and protein modification. Here we demonstrate a methodology to analyze DNA methylation at a single DNA molecule level without any protein modifications by measuring the contracted length and relaxation time of DNA within a nanochannel. Our methodology is based on the fact that methylation makes DNA molecules stiffer, resulting in a longer contracted length and a longer relaxation time (a slower contraction rate). The present methodology offers a promising way to identify DNA methylation without any protein modification at a single DNA molecule level within 2 h.     

Programming Motions of DNA Origami Nanomachines

DNA nanotechnology enables the precise fabrication of DNA‐based machines with nanoscale dimensions. A wide range of DNA nanomachines are designed, which can be activated by specific inputs to perform various movement and functions. The excellent rigidity and unprecedented addressability of DNA origami have made it an excellent platform for manipulating and investigating the motion behaviors of DNA machines at single‐molecule level. In this Concept, power supply, machine actuation, and motion behavior of DNA machines on origami platforms are summarized and classified. The strategies utilized for programming motion behavior of DNA machines on DNA origami are also discussed with representative examples. The challenges and outlook for future development of manipulating DNA nanomachines at the single molecule level are presented and discussed.     

碳纳米管的DNA修饰研究进展

对碳纳米管生物分子修饰的研究引起了科学家极大的兴趣,将碳纳米管应用到生物体系具有重要的价值.首要的是纳入生物体系的碳纳米管具有生物相容性和特殊的识别功能.因此,利用生物分子功能化碳纳米管是将碳纳米管纳入生物体系必须解决的一个关键问题.综述了DNA功能化碳纳米管的最新研究进展,并阐述了DNA功能化碳纳米管在生物传感器、电化学检测等方面的应用.     

结构DNA纳米技术:利用链霉亲和素-生物素相互作用增强DNA纳米结构的稳定性(英文)

实现纳米尺寸物体的合理设计与组装是纳米技术与精密工程的主要目标之一.DNA因其双链相互作用和螺旋几何构型的可预测性而使其成为构建纳米尺度结构的优秀建筑基元.DNA纳米结构在溶液状况改变时易分解.为提高DNA纳米结构的稳定性,一个链霉亲和素-生物素复合单元被引入到该纳米结构中.凝胶测试与熔点测试均证实链霉亲和素-生物素复合有助于提高DNA纳米结构的稳定性.该方法可广泛用于解决结构DNA纳米技术中的类似问题.     

Isothermal Hybridization Kinetics of DNA Assembly of Two‐Dimensional DNA Origami

The Watson–Crick base‐pairing with specificity and predictability makes DNA molecules suitable for building versatile nanoscale structures and devices, and the DNA origami method enables researchers to incorporate more complexities into DNA‐based devices. Thermally controlled atomic force microscopy in combination with nanomechanical spectroscopy with forces controlled in the pico Newton (pN) range as a novel technique is introduced to directly investigate the kinetics of multistrand DNA hybridization events on DNA origami nanopores under defined isothermal conditions. For the synthesis of DNA nanostructures under isothermal conditions at 60 °C, a higher hybridization rate, fewer defects, and a higher stability are achieved compared to room‐temperature studies. By quantifying the assembly times for filling pores in origami structures at several constant temperatures, the fill factors show a consistent exponential increase over time. Furthermore, the local hybridization rate can be accelerated by adding a higher concentration of the staples. The new insight gained on the kinetics of staple‐scaffold hybridization on the synthesis of two dimensional DNA origami structures may open up new routes and ideas for designing DNA assembly systems with increased potential for their application.     

Investigating site-selection mechanisms of retroviral integration in supercoiled DNA braids

We theoretically study the integration of short viral DNA in a DNA braid made up by two entwined double-stranded DNA molecules. We show that the statistics of single integration events substantially differ in the straight and buckled, or plectonemic, phase of the braid and are more likely in the latter. We further discover that integration is most likely close to plectoneme tips, where the larger bending energy helps overcome the associated energy barrier and that successive integration events are spatio-temporally correlated, suggesting a potential mechanistic explanation of clustered integration sites in host genomes. The braid geometry we consider provides a novel experimental set-up to quantify integration in a supercoiled substrate in vitro, and to better understand the role of double-stranded DNA topology during this process.     

Dynamically Programmed Switchable DNA Hydrogels Based on a DNA Circuit Mechanism

Biological stimuli‐responsive DNA hydrogels have attracted much attention in the field of medical engineering owing to their unique phase transitions from gel to sol through cleavage of DNA cross‐linking points in response to specific biomolecular inputs. In this paper, a new class of biological stimuli‐responsive DNA hydrogels with a dynamically programmed DNA system that relies on a DNA circuit system through cascading toehold‐mediated DNA displacement reactions is constructed, allowing the catalytic cleavage of cross‐linking points and main chains in response to an appropriate DNA input. The dynamically programmed DNA hydrogels exhibit a significant sharp phase transition from gel to sol in comparison to another DNA hydrogel showing noncatalytic cleavage of cross‐linking points due to synchronization of the catalytic cleavage of cross‐linking points and the main chains. Further, the sol–gel phase transitions of the DNA hydrogels in response to the DNA input are easily tunable by changing the cross‐linking density. Additionally, with a structure‐switching aptamer, DNA hydrogels encapsulating PEGylated gold nanoparticles can be used as enzyme‐free signal amplifiers for the colorimetric detection of adenosine 5′‐triphosphate (ATP); this detection system provides simplicity and higher sensitivity (limit of detection: 5.6 × 10^?6 m at 30 min) compared to other DNA hydrogel‐based ATP detection systems.     

Vacuum effect on DNA lesion and genetic mutation of cells

DNA topological forms can be changed by environmental factors thus to potentially cause genetic mutation. Vacuum of low pressure is considered to be such a factor. An investigation was carried out to check topological form changes of extracellular plasmid DNA due to lesion in DNA under the vacuum condition. Pumping the experimental stage of biological samples to vacuum may result in three effects on the environment of the sample, namely, low pressure, low temperature and low humidity, all of which may impact DNA. In the experiment, the DNA topological form change and related lesion after plasmid DNA samples were exposed to vacuum with varied time was analyzed with gel electrophoresis and fluorometric assay. The electrophoresis results were quantified to obtain percentages of the supercoiled and relaxed forms but no linear form of DNA. The fluorometer measured concentrations of single strand and double strand DNAs. The results showed that the single strand break was the dominant lesion in DNA. The DNA form change and the lesion were found to depend mainly on the pressure change but not much on the pressure itself. The vacuum-exposed DNA was subsequently transformed into bacteria Escherichia coli (E. coli) for checking mutation occurrence. No observable mutation of the DNA-transformed bacteria was found. This study concluded that certain light lesion in DNA dominated by the single strand break could be induced by vacuum exposure but with negligible risk of genetic mutation.     

Self-Assembly of DNA Nanostructures in Different Cations

The programmable nature of DNA allows the construction of custom-designed static and dynamic nanostructures, and assembly conditions typically require high concentrations of magnesium ions that restricts their applications. In other solution conditions tested for DNA nanostructure assembly, only a limited set of divalent and monovalent ions are used so far (typically Mg²⁺ and Na⁺). Here, we investigate the assembly of DNA nanostructures in a wide variety of ions using nanostructures of different sizes: a double-crossover motif (76 bp), a three-point-star motif (~134 bp), a DNA tetrahedron (534 bp) and a DNA origami triangle (7221 bp). We show successful assembly of a majority of these structures in Ca²⁺, Ba²⁺, Na⁺, K⁺ and Li⁺ and provide quantified assembly yields using gel electrophoresis and visual confirmation of a DNA origami triangle using atomic force microscopy. We further show that structures assembled in monovalent ions (Na⁺, K⁺ and Li⁺) exhibit up to a 10-fold higher nuclease resistance compared to those assembled in divalent ions (Mg²⁺, Ca²⁺ and Ba²⁺). Our work presents new assembly conditions for a wide range of DNA nanostructures with enhanced biostability.     

Abstractions for DNA circuit design

DNA strand displacement techniques have been used to implement a broad range of information processing devices, from logic gates, to chemical reaction networks, to architectures for universal computation. Strand displacement techniques enable computational devices to be implemented in DNA without the need for additional components, allowing computation to be programmed solely in terms of nucleotide sequences. A major challenge in the design of strand displacement devices has been to enable rapid analysis of high-level designs while also supporting detailed simulations that include known forms of interference. Another challenge has been to design devices capable of sustaining precise reaction kinetics over long periods, without relying on complex experimental equipment to continually replenish depleted species over time. In this paper, we present a programming language for designing DNA strand displacement devices, which supports progressively increasing levels of molecular detail. The language allows device designs to be programmed using a common syntax and then analysed at varying levels of detail, with or without interference, without needing to modify the program. This allows a trade-off to be made between the level of molecular detail and the computational cost of analysis. We use the language to design a buffered architecture for DNA devices, capable of maintaining precise reaction kinetics for a potentially unbounded period. We test the effectiveness of buffered gates to support long-running computation by designing a DNA strand displacement system capable of sustained oscillations.     

Design and Analysis of Localized DNA Hybridization Chain Reactions

Theoretical models of localized DNA hybridization reactions on nanoscale substrates indicate potential benefits over conventional DNA hybridization reactions. Recently, a few approaches have been proposed to speed‐up DNA hybridization reactions; however, experimental confirmation and quantification of the acceleration factor have been lacking. Here, a system to investigate localized DNA hybridization reactions on a nanoscale substrate is presented. The system consists of six metastable DNA hairpins that are tethered to a long DNA track. The localized DNA hybridization reaction of the proposed system is triggered by a DNA strand which initiates the subsequent self‐assembly. Fluorescence kinetics indicates that the half‐time completion of a localized DNA hybridization chain reaction is six times faster than the same reaction in the absence of the substrate. The proposed system provides one of the first known quantification of the speed‐up of DNA hybridization reactions due to the locality effect.     

快速一步法（ROSE法）提取DNA应用于RAPD—PCR扩增

对ＲＯＳＥ法的操作程序进行了进一步的简化，“一管一步”即可完成ＤＮＡ提取全过程，系统地与ＣＴＡＢ和ＳＤＳ法进行了比较，其提取过程明显比ＣＴＡＢ法、ＳＤＳ法简单，提取效率分别比ＣＴＡＢ、ＳＤＳ提高４倍和９倍，无污染物产生；与ＣＴＡＢ和ＳＤＳ法比分别节省费用约２００％和７００％。提取的ＤＮＡ能满足ＲＡＰＤ－ＰＣＲ研究的需要。因此，改良后的ＲＯＳＥ法可能是一种适合于ＤＮＡ提取自动化的方法，同时可能成为植