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Eco-evolutionary significance of domesticated retroelements in microbial genomes. 微生物基因组中驯化的逆位基因的生态进化意义。
IF 4.7 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2022-02-23 DOI: 10.1186/s13100-022-00262-6
Blair G Paul, A Murat Eren

Since the first discovery of reverse transcriptase in bacteria, and later in archaea, bacterial and archaeal retroelements have been defined by their common enzyme that coordinates diverse functions. Yet, evolutionary refinement has produced distinct retroelements across the tree of microbial life that are perhaps best described in terms of their programmed RNA-a compact sequence that preserves core information for a sophisticated mechanism. From this perspective, reverse transcriptase has been selected as the modular tool for carrying out nature's instructions in various RNA templates. Beneficial retroelements-those that can provide a fitness advantage to their host-evolved to their extant forms in a wide array of microorganisms and their viruses, spanning nearly all habitats. Within each specialized retroelement class, several universal features seem to be shared across diverse taxa, while specific functional and mechanistic insights are based on only a few model retroelement systems from clinical isolates. Currently, little is known about the diversity of cellular functions and ecological significance of retroelements across different biomes. With increasing availability of isolate, metagenome-assembled, and single-amplified genomes, the taxonomic and functional breadth of prokaryotic retroelements is coming into clearer view. This review explores the recently characterized classes of beneficial, yet accessory retroelements of bacteria and archaea. We describe how these specialized mechanisms exploit a form of fixed mobility, whereby the retroelements do not appear to proliferate selfishly throughout the genome. Moreover, we discuss computational approaches for systematic identification of retroelements from vast sequence repositories and highlight recent discoveries in terms of their apparent distribution and ecological significance in nature. Lastly, we present a new perspective on the eco-evolutionary significance of these genetic elements in marine bacteria and demonstrate approaches that enable the characterization of their environmental diversity through metagenomics.

自从在细菌和古细菌中首次发现逆转录酶以来,细菌和古细菌的逆转录酶就被定义为协调各种功能的共同酶。然而,进化的不断完善使微生物生命树上的逆转录酶各具特色,这些逆转录酶也许最适合用它们的程序化 RNA 来描述--一种保留了复杂机制核心信息的紧凑序列。从这个角度来看,逆转录酶被选为模块化工具,用于在各种 RNA 模板中执行大自然的指令。有益的逆转录酶--那些能为宿主提供适应优势的逆转录酶--在几乎所有栖息地的各种微生物及其病毒中进化为现存形式。在每一类特化的逆转录酶元中,不同类群似乎都有一些共同的特征,而具体的功能和机理则仅基于少数来自临床分离物的模型逆转录酶元系统。目前,人们对逆转录酶在不同生物群落中的细胞功能多样性和生态意义知之甚少。随着分离基因组、元基因组组装基因组和单体扩增基因组的不断增加,原核生物逆转录酶的分类和功能广度逐渐清晰可见。这篇综述探讨了细菌和古细菌中最近表征的有益而又附属的逆转录酶。我们描述了这些特殊机制如何利用一种固定的流动性,即逆转录子似乎不会在整个基因组中自私地增殖。此外,我们还讨论了从庞大的序列库中系统识别逆源基因的计算方法,并重点介绍了最近在自然界中发现的逆源基因的明显分布和生态意义。最后,我们从一个新的角度阐述了这些遗传因子在海洋细菌中的生态进化意义,并展示了通过元基因组学鉴定其环境多样性的方法。
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引用次数: 0
Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus. 迁徙者中的迁徙者:探索帝王斑蝶的转座元件动态。
IF 4.7 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2022-02-16 DOI: 10.1186/s13100-022-00263-5
Tobias Baril, Alexander Hayward

Background: Lepidoptera (butterflies and moths) are an important model system in ecology and evolution. A high-quality chromosomal genome assembly is available for the monarch butterfly (Danaus plexippus), but it lacks an in-depth transposable element (TE) annotation, presenting an opportunity to explore monarch TE dynamics and the impact of TEs on shaping the monarch genome.

Results: We find 6.21% of the monarch genome is comprised of TEs, a reduction of 6.85% compared to the original TE annotation performed on the draft genome assembly. Monarch TE content is low compared to two closely related species with available genomes, Danaus chrysippus (33.97% TE) and Danaus melanippus (11.87% TE). The biggest TE contributions to genome size in the monarch are LINEs and Penelope-like elements, and three newly identified families, r2-hero_dPle (LINE), penelope-1_dPle (Penelope-like), and hase2-1_dPle (SINE), collectively contribute 34.92% of total TE content. We find evidence of recent TE activity, with two novel Tc1 families rapidly expanding over recent timescales (tc1-1_dPle, tc1-2_dPle). LINE fragments show signatures of genomic deletions indicating a high rate of TE turnover. We investigate associations between TEs and wing colouration and immune genes and identify a three-fold increase in TE content around immune genes compared to other host genes.

Conclusions: We provide a detailed TE annotation and analysis for the monarch genome, revealing a considerably smaller TE contribution to genome content compared to two closely related Danaus species with available genome assemblies. We identify highly successful novel DNA TE families rapidly expanding over recent timescales, and ongoing signatures of both TE expansion and removal highlight the dynamic nature of repeat content in the monarch genome. Our findings also suggest that insect immune genes are promising candidates for future interrogation of TE-mediated host adaptation.

背景:鳞翅目昆虫(蝴蝶和飞蛾)是生态学和进化中的重要模式系统。帝王斑蝶(Danaus plexippus)有一个高质量的染色体基因组,但缺乏深入的转座元件(TE)注释,这为探索帝王斑蝶 TE 的动态以及 TE 对帝王斑蝶基因组形成的影响提供了机会:结果:我们发现帝王斑蝶基因组中有 6.21% 由 TE 组成,与对基因组组装草案进行的原始 TE 注释相比减少了 6.85%。与Danaus chrysippus(33.97% TE)和Danaus melanippus(11.87% TE)这两个有可用基因组的近缘物种相比,帝王斑蝶的TE含量较低。帝王斑中对基因组大小贡献最大的 TE 是 LINEs 和 Penelope-like 元素,三个新发现的家族:r2-hero_dPle(LINE)、penelope-1_dPle(Penelope-like)和 hase2-1_dPle(SINE)总共贡献了总 TE 含量的 34.92%。我们发现了近期 TE 活动的证据,两个新的 Tc1 家族(tc1-1_dPle、tc1-2_dPle)在近期迅速扩展。LINE 片段显示出基因组缺失的特征,表明 TE 更替速度很快。我们研究了TE与翅膀着色和免疫基因之间的关联,发现与其他宿主基因相比,免疫基因周围的TE含量增加了三倍:我们对帝王斑鸠基因组进行了详细的 TE 注释和分析,发现与两个有基因组组装的近缘 Danaus 种类相比,TE 对基因组内容的贡献要小得多。我们发现了非常成功的新型 DNA TE 家族,它们在最近的时间尺度内迅速扩展,TE 扩展和移除的持续特征凸显了帝王斑蝶基因组中重复内容的动态性质。我们的发现还表明,昆虫免疫基因是未来研究 TE 介导的宿主适应性的有希望的候选基因。
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引用次数: 0
Correction: Characterization of transposable elements within the Bemisia tabaci species complex 更正:烟粉虱物种复合体内转座因子的表征
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-02-02 DOI: 10.21203/rs.3.rs-1312818/v1
Juan Paolo A. Sicat, Paul Visendi, Steven O. Sewe, S. Bouvaine, S. Seal
Background Whiteflies are agricultural pests that have caused worldwide negative impacts that have led to severe financial losses. The Bemisia tabaci whitefly species complex is the most damaging in terms of their broad crop host range and its ability to serve as vector for over 300 plant viruses. Whitefly genomes of the species complex provide valuable genomic data; however, transposable elements (TEs) within the species complex remain unexplored. This study provides the first accurate exploration of TE content within the B. tabaci species complex.Results This study identified an average of 40.61% of the genomes of three whitefly species (MEAM1, MEDQ, and SSA-ECA) consists of TEs. Majority of the TEs identified were DNA transposons (22.85% average) while SINEs (0.14% average) were the least represented. This study also compared the TE content the three whitefly genomes with three other hemipteran genomes and found a significant difference in the presence of DNA transposons and LINEs. A total of 63 TE superfamilies were identified to be present across the three whitefly species (39 DNA transposons, six LTR, 16 LINE, and two SINE) of which 11 TE superfamilies were identified to not be present in the three other hemipteran genomes (nine DNA transposon, and two LINE). This study is the first to characterize TEs found within different B. tabaci species and has created a standardized annotation workflow that could be used to analyze future whitefly genomes.Conclusion This study is the first to characterize the landscape of TEs within the B. tabaci species complex. The characterization of these elements within the three whitefly genomes shows that TEs occupy a significant portion of the whitefly genome, majority of which are DNA transposons. This study also identified TE superfamilies of note and provides a framework for future TE studies within the species complex.
背景白蝇是一种农业害虫,已在全球范围内造成负面影响,并导致严重的经济损失。烟粉虱(Bemisia tabaci whitefly)物种复合体具有广泛的作物宿主范围和作为300多种植物病毒载体的能力,是最具破坏性的。该物种复合体的白蝇基因组提供了有价值的基因组数据;然而,物种复合体中的转座元件(TE)仍未被探索。本研究首次对烟粉虱物种复合体中的TE含量进行了准确的探索。结果本研究确定三种粉虱(MEAM1、MEDQ和SSA-ECA)的基因组中平均40.61%由TE组成。鉴定的大多数TE是DNA转座子(平均22.85%),而SINE(平均0.14%)的代表性最低。这项研究还将三个粉蝶基因组的TE含量与其他三个半翅目基因组进行了比较,发现DNA转座子和LINE的存在存在存在显著差异。共有63个TE超家族被鉴定存在于三个粉蝶物种中(39个DNA转座子、6个LTR、16个LINE和2个SINE),其中11个TE超家庭被鉴定不存在于其他三个半翅目基因组中(9个DNA转座子和2个LINE)。这项研究首次对不同烟粉虱物种中发现的TE进行了表征,并创建了一个标准化的注释工作流程,可用于分析未来的粉虱基因组。结论本研究首次对烟粉虱群落中的TE景观进行了表征。三个粉虱基因组中这些元素的特征表明,TE占据了粉虱基因组的重要部分,其中大多数是DNA转座子。这项研究还确定了值得注意的TE超家族,并为未来在物种复合体中进行TE研究提供了框架。
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引用次数: 0
KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences. KRAB 锌指蛋白 ZNF676 控制着 LTR12 相关内源性逆转录病毒序列的转录影响。
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-01-18 DOI: 10.1186/s13100-021-00260-0
Alexandra Iouranova, Delphine Grun, Tamara Rossy, Julien Duc, Alexandre Coudray, Michael Imbeault, Jonas de Tribolet-Hardy, Priscilla Turelli, Alexandre Persat, Didier Trono

Background: Transposable element-embedded regulatory sequences (TEeRS) and their KRAB-containing zinc finger protein (KZFP) controllers are increasingly recognized as modulators of gene expression. We aim to characterize the contribution of this system to gene regulation in early human development and germ cells.

Results: Here, after studying genes driven by the long terminal repeat (LTR) of endogenous retroviruses, we identify the ape-restricted ZNF676 as the sequence-specific repressor of a subset of contemporary LTR12 integrants responsible for a large fraction of transpochimeric gene transcripts (TcGTs) generated during human early embryogenesis. We go on to reveal that the binding of this KZFP correlates with the epigenetic marking of these TEeRS in the germline, and is crucial to the control of genes involved in ciliogenesis/flagellogenesis, a biological process that dates back to the last common ancestor of eukaryotes.

Conclusion: These results illustrate how KZFPs and their TE targets contribute to the evolutionary turnover of transcription networks and participate in the transgenerational inheritance of epigenetic traits.

背景:可转座元件嵌入调控序列(TEeRS)及其含KRAB锌指蛋白(KZFP)的调控因子越来越被认为是基因表达的调控因子。我们的目的是描述这一系统对人类早期发育和生殖细胞中基因调控的贡献:结果:在对内源性逆转录病毒长末端重复序列(LTR)驱动的基因进行研究后,我们发现猿限制性 ZNF676 是当代 LTR12 整合子集的序列特异性抑制因子,它负责人类早期胚胎发育过程中产生的大部分跨单体基因转录本(TcGTs)。我们接着揭示了这种 KZFP 的结合与这些 TEeRS 在生殖系中的表观遗传标记相关,并且对控制参与纤毛生成/鞭毛生成的基因至关重要,这一生物过程可追溯到真核生物的最后一个共同祖先:这些结果说明了 KZFPs 及其 TE 靶标是如何促进转录网络的进化更替并参与表观遗传特征的跨代遗传的。
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引用次数: 0
The fifth Japanese meeting on biological function and evolution through interactions between hosts and transposable elements. 第五届日本生物功能和进化会议通过宿主和转座因子之间的相互作用。
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-01-13 DOI: 10.1186/s13100-022-00261-7
Kenji Ichiyanagi, Kuniaki Saito

The fifth Japanese meeting on host-transposon interactions, titled "Biological Function and Evolution through Interactions between Hosts and Transposable Elements (TEs)," was held online on August 26-27, 2021. The meeting was supported by National Institute of Genetics and aimed to bring together researchers studying the diverse roles of TEs in genome function and evolution, as well as host defense systems against TE mobility by chromatin and RNA modifications and protein-protein interactions. Here, we present the highlights of the talks.

日本第五届宿主-转座子相互作用会议于2021年8月26日至27日在线举行,题为“宿主与转座子元件(te)相互作用的生物功能和进化”。会议由美国国家遗传研究所支持,旨在汇集研究TE在基因组功能和进化中的不同作用,以及通过染色质和RNA修饰以及蛋白质-蛋白质相互作用抵御TE迁移的宿主防御系统的研究人员。在此,我们为您介绍会谈要点。
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引用次数: 0
Comment on "the IS6 family, a clinically important group of insertion sequences including IS26" by Varani and co-authors. Varani及其合作者对“IS6家族,包括IS26在内的临床重要插入序列组”的评论。
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-01-03 DOI: 10.1186/s13100-021-00257-9
Ruth M Hall

The insertion sequence IS26 has long been known to play a major role in the recruitment of antibiotic resistance genes into the mobile resistance gene pool of Gram-negative bacteria and IS26 also plays a major role in their subsequent broad dissemination. Related IS, IS431/257 and IS1216 are important in the same roles in Gram positive bacteria. However, until recently the properties of IS26 movement that could potentially explain this ability had not been explored. A much needed insight has come from our recent demonstration that IS26 uses a novel targeted mechanism that is conservative. The targeted conservative mechanism is much more efficient than the known replicative mechanism, which is now more accurately called copy-in. A recent review "The IS6 family, a clinically important group of insertion sequences including IS26" by Varani, He, Siguier, Ross and Chandler published in Mobile DNA has substantially misrepresented the recent studies on the targeted conservative mechanism and at the same time incorrectly implied that any mechanism established for IS26 can be assumed to apply to a range of IS that are at best very distantly related. A few of the most important issues are examined in this comment. Readers are advised to consult the original literature to check facts before drawing firm conclusions.

长期以来,人们都知道插入序列IS26在将抗生素耐药基因招募到革兰氏阴性菌的移动耐药基因库中起着重要作用,IS26在其随后的广泛传播中也起着重要作用。相关IS, IS431/257和IS1216在革兰氏阳性菌中发挥同样重要的作用。然而,直到最近,IS26运动的特性才有可能解释这种能力。我们最近的演示表明,IS26使用了一种新颖的靶向机制,这种机制是保守的。目标保守机制比已知的复制机制更有效,复制机制现在更准确地称为复制-in。最近由Varani, He, Siguier, Ross和Chandler发表在Mobile DNA上的一篇综述“IS6 family, A clinical important group of insertion sequences包括IS26”在很大程度上歪曲了最近关于靶向保守机制的研究,同时错误地暗示为IS26建立的任何机制都可以被认为适用于最多是非常远亲的一系列IS。本文探讨了几个最重要的问题。建议读者在得出确切的结论之前查阅原始文献以核实事实。
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引用次数: 1
Response from Varani et al. to "Comment on 'the IS6 family, a clinically important group of insertion sequences including IS26' by Ruth M. Hall". Varani等人对“评论Ruth M. Hall的‘IS6家族,包括IS26在内的临床重要插入序列组’”的回应。
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-01-03 DOI: 10.1186/s13100-021-00258-8
Alessandro Varani, Susu He, Patricia Siguier, Karen Ross, Michael Chandler

The IS6 family of insertion sequences is a large but coherent group which was originally named to avoid confusion between a number of identical or nearly identical IS that were identified at about the same time and given different names (IS15D, IS26, IS46, IS140, IS160, IS176). The underlying common mechanistic feature of all IS6 family members which have been investigated is that they appear to transpose by replicative transposition and form pseudo compound transposons with the flanking IS in direct repeat and in which associated genes are simply transferred to the target replicon and lost from the donor.In the accompanying letter Hall raises a number of very serious and wide-ranging criticisms of our recent review article concerning the IS6 family of insertion sequences. She clearly feels that we have undervalued her work and that we question or ignore certain of her in vivo results. This impression is almost certainly the result of the standard of proof we generally apply to mechanistic aspects of transposition where we think it important to identify transposition intermediates including the types of synaptic, strand cleavage and strand transfer complexes involved.

IS6家族插入序列是一个庞大但连贯的群体,最初命名是为了避免在大约同一时间发现的许多相同或几乎相同的is之间混淆,并给出不同的名称(IS15D, IS26, IS46, IS140, IS160, IS176)。已研究的所有IS6家族成员的潜在共同机制特征是,它们似乎通过复制转座而转座,并与侧面的is形成直接重复的伪复合转座子,其中相关基因简单地转移到目标复制子上,并从供体中丢失。在随附的信中,Hall对我们最近关于IS6插入序列家族的评论文章提出了一些非常严肃和广泛的批评。她显然觉得我们低估了她的工作,我们质疑或忽视了她的某些体内实验结果。这种印象几乎肯定是我们通常应用于转位机制方面的证明标准的结果,我们认为重要的是确定转位中间体,包括突触,链切割和链转移复合物的类型。
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引用次数: 0
Exploring Material Design Space with a Deep-Learning Guided Genetic Algorithm 用深度学习引导遗传算法探索材料设计空间
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-01-01 DOI: 10.4230/LIPIcs.DNA.28.4
Kuan-Lin Chen, Rebecca Schulman
Designing complex, dynamic yet multi-functional materials and devices is challenging because the design spaces for these materials have numerous interdependent and often conflicting constraints. Taking inspiration from advances in artificial intelligence and their applications in material discovery, we propose a computational method for designing metamorphic DNA-co-polymerized hydrogel structures. The method consists of a coarse-grained simulation and a deep learning-guided optimization system for exploring the immense design space of these structures. Here, we develop a simple numeric simulation of DNA-co-polymerized hydrogel shape change and seek to find designs for structured hydrogels that can fold into the shapes of different Arabic numerals in different actuation states. We train a convolutional neural network to classify and score the geometric outputs of the coarse-grained simulation to provide autonomous feedback for design optimization. We then construct a genetic algorithm that generates and selects large batches of material designs that compete with one another to evolve and converge on optimal objective-matching designs. We show that we are able to explore the large design space and learn important parameters and traits. We identify vital relationships between the material scale size and the range of shape change that can be achieved by individual domains and we elucidate trade-offs between different design parameters. Finally, we discover material designs capable of transforming into multiple different digits in different actuation states.
设计复杂、动态但多功能的材料和设备是具有挑战性的,因为这些材料的设计空间有许多相互依存且经常相互冲突的限制。从人工智能的进步及其在材料发现中的应用中获得灵感,我们提出了一种设计变质dna共聚合水凝胶结构的计算方法。该方法由粗粒度模拟和深度学习引导优化系统组成,用于探索这些结构的巨大设计空间。在这里,我们开发了dna共聚合水凝胶形状变化的简单数值模拟,并寻求在不同驱动状态下可以折叠成不同阿拉伯数字形状的结构水凝胶的设计。我们训练卷积神经网络对粗粒度模拟的几何输出进行分类和评分,为设计优化提供自主反馈。然后,我们构建了一个遗传算法,该算法生成并选择大量相互竞争的材料设计,以进化并收敛于最优目标匹配设计。我们表明,我们能够探索更大的设计空间,并学习重要的参数和特征。我们确定了材料尺寸和单个领域可以实现的形状变化范围之间的重要关系,并阐明了不同设计参数之间的权衡。最后,我们发现材料设计能够在不同的驱动状态下转换成多个不同的数字。
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引用次数: 0
Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking 使用概率模型检查的DNA堆叠纳米器件的建模和优化
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-01-01 DOI: 10.4230/LIPIcs.DNA.28.5
Bowen Li, N. Mackenzie, Ben Shirt-Ediss, N. Krasnogor, P. Zuliani
A DNA stack nano-device is a bio-computing system that can read and write molecular signals based on DNA-DNA hybridisation and strand displacement. In vitro implementation of the DNA stack faces a number of challenges affecting the performance of the system. In this work, we apply probabilistic model checking to analyse and optimise the DNA stack system. We develop a model framework based on continuous-time Markov chains to quantitatively describe the system behaviour. We use the PRISM probabilistic model checker to answer two important questions: 1) What is the minimum required incubation time to store a signal? And 2) How can we maximise the yield of the system? The results suggest that the incubation time can be reduced from 30 minutes to 5-15 minutes depending on the stack operation stage. In addition, the optimised model shows a 40% increase in the target stack yield. project “Synthetic Portabolomics: Leading the way at the crossroads of the Digital and the Bio Economies” (EP/N031962/1). Krasnogor was supported by the Royal Academy of Engineering under the Chairs in Emerging Technologies scheme.
DNA堆叠纳米器件是一种基于DNA-DNA杂交和链位移的分子信号读写生物计算系统。DNA堆栈的体外实现面临许多影响系统性能的挑战。在这项工作中,我们应用概率模型检查来分析和优化DNA堆栈系统。我们开发了一个基于连续时间马尔可夫链的模型框架来定量描述系统行为。我们使用PRISM概率模型检查器来回答两个重要问题:1)存储信号所需的最小潜伏期是多少?2)我们如何使系统的收益最大化?结果表明,根据堆垛阶段的不同,孵育时间可从30分钟缩短至5-15分钟。此外,优化后的模型显示目标堆产量提高了40%。项目“合成组合组学:在数字经济和生物经济的十字路口引领道路”(EP/N031962/1)。Krasnogor得到了皇家工程院新兴技术项目主席的支持。
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引用次数: 1
A Coupled Reconfiguration Mechanism for Single-Stranded DNA Strand Displacement Systems 单链DNA链置换系统的耦合重配置机制
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-01-01 DOI: 10.4230/LIPIcs.DNA.28.3
H. Johnson, A. Condon
DNA Strand Displacement (DSD) systems model basic reaction rules, such as toehold-mediated strand displacement and 4-way branch migration, that modify complexes of bound DNA strands. DSD systems have been widely used to design and reason about the correctness of molecular programs, including implementations of logic circuits, neural networks, and Chemical Reaction Networks. Such implementations employ a valuable toolkit of mechanisms – sequences of basic reaction rules – that achieve catalysis, reduce errors (e.g., due to leak), or simulate simple computational units such as logic gates, both in solution and on surfaces. Expanding the DSD toolkit of DSD mechanisms can lead to new and better ways of programming with DNA. Here we introduce a new mechanism, which we call controlled reconfiguration . We describe one example where two single-stranded DSD complexes interact, changing the bonds in both complexes in a way that would not be possible for each independently on its own via the basic reaction rules allowed by the model. We use coupled reconfiguration to refer to instances of controlled reconfiguration in which two reactants change each other in this way. We note that our DSD model disallows pseudoknots and that properties of our coupled reconfiguration construction rely on this restriction of the model. A key feature of our coupled reconfiguration example, which distinguishes it from mechanisms (such as 3-way strand displacement or 4-way branch migration) that are typically used to implement molecular programs, is that the reactants are single-stranded. Leveraging this feature, we show how to use coupled reconfiguration to implement Chemical Reaction Networks (CRNs), with a DSD system that has both single-stranded signals (which represent the species of the CRN) and single-stranded fuels (which drive the CRN reactions). Our implementation also has other desirable properties; for example it is capable of implementing reversible CRNs and uses just two distinct toeholds. We discuss drawbacks of our implementation, particularly the reliance on pseudoknot-freeness for correctness, and suggest directions for future research that can provide further insight on the capabilities and limitations of controlled reconfiguration. computing (DSD) systems. a particularly well-studied abstract model of well-mixed chemical systems, in which many interesting programs can be and have been written [2, 3, 28, 36, 41]. Moreover, arbitrary CRNs can be transformed into DSD systems that implement the original CRN [7, 10, 30, 37, 39].
DNA链位移(DSD)系统模拟了基本的反应规则,如支点介导的链位移和4向分支迁移,这些反应规则修饰了结合DNA链的复合物。DSD系统已被广泛用于设计和推理分子程序的正确性,包括逻辑电路、神经网络和化学反应网络的实现。这样的实现采用了一个有价值的机制工具包——基本反应规则序列——来实现催化,减少错误(例如,由于泄漏),或模拟简单的计算单元,如逻辑门,无论是在溶液中还是在表面上。扩展DSD机制的DSD工具包可以带来新的、更好的DNA编程方法。这里我们引入一种新的机制,我们称之为受控重构。我们描述了一个例子,其中两个单链DSD配合物相互作用,改变了两个配合物中的键,通过模型允许的基本反应规则,每个配合物都不可能独立地改变键。我们使用耦合重构来指两个反应物以这种方式相互改变的受控重构实例。我们注意到我们的DSD模型不允许假结,并且我们的耦合重构结构的性质依赖于模型的这一限制。我们的耦合重构示例的一个关键特征是,反应物是单链的,这与通常用于实现分子程序的机制(如3向链位移或4向分支迁移)不同。利用这一特性,我们展示了如何使用耦合重构来实现化学反应网络(CRN),其中DSD系统同时具有单链信号(代表CRN的种类)和单链燃料(驱动CRN反应)。我们的实现还具有其他理想的属性;例如,它能够实现可逆的crn,并且只使用两个不同的支点。我们讨论了我们实现的缺点,特别是对伪结无性的依赖,并提出了未来研究的方向,可以进一步了解受控重构的能力和局限性。计算机系统。一种对混合良好的化学系统进行了特别深入研究的抽象模型,在这种模型中可以编写出许多有趣的程序[2,3,28,36,41]。此外,任意CRN都可以转化为实现原始CRN的DSD系统[7,10,30,37,39]。
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Mobile DNA
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