AF: Medium: Collaborative Research: Top-down algorithmic design of structured nucleic acid assemblies

AF:中:协作研究:结构化核酸组装体的自上而下的算法设计

基本信息

  • 批准号:
    1563799
  • 负责人:
  • 金额:
    $ 56.08万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
    Continuing Grant
  • 财政年份:
    2016
  • 资助国家:
    美国
  • 起止时间:
    2016-04-01 至 2021-03-31
  • 项目状态:
    已结题

项目摘要

The past decade has witnessed dramatic growth in ability to "print" complex nanometer-scale structures and patterns using self-assembling nucleic acids. These structures can be used as templates to synthesize inorganic materials on the 1-100 nanometer-scale, or employed directly in applications such as DNA-based memory storage, therapeutic delivery, single-molecule structure-determination, and nanoscale excitonic materials. While various computational strategies are available to forward design these complex 3D structures manually from underlying DNA or RNA sequence and topology, the inverse problem of autonomously generating linear nucleic acid sequences from target geometry alone remains an unsolved computational challenge. In this project, fully automatic, top-down computer-aided design (CAD) algorithms are explored to generate topological sequence designs for broad classes of programmed DNA and RNA assemblies in an autonomous manner using target geometry alone. These assemblies can be "printed" via self-assembly in vitro or in vivo to form target nanoscale geometries using either synthetic or transcribed nucleic acids. The approach will offer a broadly accessible, high-level programming language to realize sequence-based programming of arbitrary 1D/2D/3D nanoscale structured materials based on nucleic acids with diverse applications in basic science and nanotechnology.The proposed computational algorithms will be distributed freely online as open source software as well as integrated into a variety of software packages to broadly enable the top-down design of DNA and RNA assemblies. These algorithms and software will provide the broader scientific and industrial communities with easy-to-use, high-level design strategies that will accelerate the broad participation of groups in the use of nucleic acid nanotechnology for diverse applications in biomolecular and materials science and technology. The tools will open up opportunities for high school students and undergraduates to gain hands-on experience in nucleic acid nanostructure design. Curriculum developments at ASU and MIT will employ the use of this sequence design software for participation by undergraduate and graduate students in its use and application to basic questions in computer science and nanotechnology research.Foundational aspects of the design of nanoscale structured materials using DNA and RNA will be explored. Algorithmic approaches to rendering diverse CAD-based geometric primitives using DNA and RNA will be investigated, including wireframe lattices in 2D and 3D, single-layer surfaces that may contain arbitrary curvatures, as well as 3D solid objects. Meshing algorithms will be used to discretize geometric objects in 1D, 2D, and 3D, and topological routing and sequence design will be applied to position nucleic acid strands within CAD objects. Continuous and discontinuous single stranded nucleic acids will be routed through duplexes using anti-parallel and parallel crossover configurations to exploit distinct modes of programmed self-assembly. Sequence design and routing will be validated experimentally to explore principles for obtaining optimal folding, self-assembly, and positioning of specific base pairs in 3D space. Self-assembly of nanostructures from RNA will additionally be explored, utilizing staple-free designs from single long continuous scaffold strands. Close interaction between experiment and computation will help to distill fundamental yet practical approaches to programming structured nucleic acid assemblies.
过去十年,使用自组装核酸“打印”复杂纳米级结构和图案的能力急剧增长。这些结构可以用作模板来合成1-100纳米尺度的无机材料,或者直接用于诸如基于DNA的存储器存储、治疗递送、单分子结构确定和纳米级激子材料等应用中。虽然各种计算策略可用于从底层DNA或RNA序列和拓扑结构手动正向设计这些复杂的3D结构,但仅从靶几何形状自主生成线性核酸序列的逆问题仍然是未解决的计算挑战。在这个项目中,全自动的,自上而下的计算机辅助设计(CAD)算法进行了探索,以产生拓扑序列设计的广泛类别的编程DNA和RNA组件在一个自主的方式,单独使用目标的几何形状。这些组装体可以通过体外或体内自组装进行“打印”,以使用合成或转录的核酸形成目标纳米级几何形状。该方法将提供一个广泛使用的,高级编程语言,实现基于核酸的任意1D/2D/3D纳米结构材料的基于序列的编程,在基础科学和纳米技术中具有不同的应用。所提出的计算算法将作为开源软件在网上免费发布,并集成到各种软件包中,以广泛地实现最高-DNA和RNA组装的向下设计。这些算法和软件将为更广泛的科学和工业界提供易于使用的高水平设计策略,这将加速群体广泛参与核酸纳米技术在生物分子和材料科学技术中的各种应用。这些工具将为高中生和大学生提供机会,获得核酸纳米结构设计的实践经验。亚利桑那州立大学和麻省理工学院的课程开发将使用这种序列设计软件,让本科生和研究生参与其在计算机科学和纳米技术研究中的基本问题的使用和应用。将探索使用DNA和RNA设计纳米结构材料的基础方面。将研究使用DNA和RNA绘制各种基于CAD的几何图元的数学方法,包括2D和3D中的线框网格,可能包含任意曲率的单层表面以及3D固体对象。网格算法将用于离散化1D、2D和3D中的几何对象,拓扑路由和序列设计将用于在CAD对象内定位核酸链。连续和不连续的单链核酸将使用反平行和平行交叉构型通过双链体路由,以利用不同的程序化自组装模式。序列设计和路由将通过实验验证,以探索在3D空间中获得最佳折叠,自组装和特定碱基对定位的原理。此外,还将探索RNA纳米结构的自组装,利用来自单个长的连续支架链的无钉设计。实验和计算之间的密切互动将有助于提炼出基本而实用的方法来编程结构化核酸组装。

项目成果

期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)

数据更新时间:{{ journalArticles.updateTime }}

{{ item.title }}
{{ item.translation_title }}
  • DOI:
    {{ item.doi }}
  • 发表时间:
    {{ item.publish_year }}
  • 期刊:
  • 影响因子:
    {{ item.factor }}
  • 作者:
    {{ item.authors }}
  • 通讯作者:
    {{ item.author }}

数据更新时间:{{ journalArticles.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ monograph.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ sciAawards.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ conferencePapers.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ patent.updateTime }}

Hao Yan其他文献

Refined assessment of size-fractioned particulate matter (PM2.5/PM10/PMtotal) emissions from coal-fired power plants in China
中国燃煤电厂粒度分级颗粒物(PM2.5/PM10/PMtotal)排放的精细化评估
  • DOI:
    10.1016/j.scitotenv.2019.135735
  • 发表时间:
    2020
  • 期刊:
  • 影响因子:
    9.8
  • 作者:
    Wu Bobo;Tian Hezhong;Hao Yan;Liu Shuhan;Sun Yujiao;Bai Xiaoxuan;Liu Wei;Lin Shumin;Zhu Chuanyong;Hao Jiming;Luo Lining;Zhao Shuang;Guo Zhihui
  • 通讯作者:
    Guo Zhihui
Establishment and pathogenesis of mouse peanut allergy model: Establishment and pathogenesis of mouse peanut allergy model
小鼠花生过敏模型的建立及发病机制: 小鼠花生过敏模型的建立及发病机制
  • DOI:
  • 发表时间:
    2012
  • 期刊:
  • 影响因子:
    0
  • 作者:
    Zhi;Chenghui Yang;Hao Yan;Xiaoyu Liu;L. Xia;Li Li
  • 通讯作者:
    Li Li
Regulation of the phytotoxic response of Arabidopsis thaliana to the Fusarium mycotoxin deoxynivalenol
拟南芥对镰刀菌毒素脱氧雪腐镰刀菌烯醇植物毒性反应的调节
  • DOI:
    10.1016/s2095-3119(19)62741-3
  • 发表时间:
    2020-03
  • 期刊:
  • 影响因子:
    4.8
  • 作者:
    Yan Wang;Hao Yan;Qi Wang;Ran Zheng;Kai Xia;Yang Liu
  • 通讯作者:
    Yang Liu
A high-resolution emission inventory of anthropogenic trace elements in Beijing-Tianjin-Hebei (BTH) region of China
中国京津冀(BTH)地区人为微量元素高分辨率排放清单
  • DOI:
    10.1016/j.atmosenv.2018.08.035
  • 发表时间:
    2018
  • 期刊:
  • 影响因子:
    5
  • 作者:
    Zhu Chuanyong;Tian Hezhong;Hao Yan;Gao Jiajia;Hao Jiming;Wang Yong;Hua Shenbing;Wang Kun;Liu Huanjia
  • 通讯作者:
    Liu Huanjia
Urban energy-water nexus: Spatial and inter-sectoral analysis in a multi-scale economy
城市能源与水的关系:多规模经济中的空间和部门间分析
  • DOI:
    10.1016/j.ecolmodel.2019.04.020
  • 发表时间:
    2019-07
  • 期刊:
  • 影响因子:
    3.1
  • 作者:
    Nawab Asim;Liu Gengyuan;Meng Fanxin;Hao Yan;Zhang Yan
  • 通讯作者:
    Zhang Yan

Hao Yan的其他文献

{{ item.title }}
{{ item.translation_title }}
  • DOI:
    {{ item.doi }}
  • 发表时间:
    {{ item.publish_year }}
  • 期刊:
  • 影响因子:
    {{ item.factor }}
  • 作者:
    {{ item.authors }}
  • 通讯作者:
    {{ item.author }}

{{ truncateString('Hao Yan', 18)}}的其他基金

Collaborative Research: Multi-Agent Adaptive Data Collection for Automated Post-Disaster Rapid Damage Assessment
协作研究:用于灾后自动化快速损害评估的多智能体自适应数据收集
  • 批准号:
    2316654
  • 财政年份:
    2023
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Standard Grant
Self-assembled DNA crystals as scaffolds for macromolecules
自组装 DNA 晶体作为大分子支架
  • 批准号:
    2324944
  • 财政年份:
    2023
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Standard Grant
SemiSynBio-III: DNA Templated Chiral Metamaterials for Information Storage
SemiSynBio-III:用于信息存储的 DNA 模板手性超材料
  • 批准号:
    2227650
  • 财政年份:
    2022
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Standard Grant
Rational design of self-assembled, three-dimensional DNA crystals
自组装三维DNA晶体的合理设计
  • 批准号:
    2004250
  • 财政年份:
    2020
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Standard Grant
SemiSynBio-II: DNA-Based Memory for High-Density Information Storage and Molecular Cryptography with Fast Readout Methods
SemiSynBio-II:基于 DNA 的存储器,用于高密度信息存储和具有快速读出方法的分子密码学
  • 批准号:
    2027215
  • 财政年份:
    2020
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Standard Grant
ATD: Collaborative Research: Adaptive and Rapid Spatial-Temporal Threat Detection over Networks
ATD:协作研究:网络上的自适应快速时空威胁检测
  • 批准号:
    1830363
  • 财政年份:
    2018
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Continuing Grant
Student and Postdoc Travel Support for International Workshop on Future trends in DNA-based nanotechnology
基于 DNA 的纳米技术未来趋势国际研讨会的学生和博士后旅行支持
  • 批准号:
    1707491
  • 财政年份:
    2017
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Standard Grant
Bilateral NSF/BIO-BBSRC: Synthetic DNA Nanopores for Selective Transmembrane Transport
双边 NSF/BIO-BBSRC:用于选择性跨膜运输的合成 DNA 纳米孔
  • 批准号:
    1644745
  • 财政年份:
    2016
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Standard Grant
EAGER: Collaborative Research: Algorithmic design principles for programmed DNA nanocages
EAGER:协作研究:编程 DNA 纳米笼的算法设计原理
  • 批准号:
    1547962
  • 财政年份:
    2015
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Standard Grant
Self-assembling Quasi-crystals from DNA Tiles
DNA 瓦片自组装准晶体
  • 批准号:
    1360635
  • 财政年份:
    2014
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Continuing Grant

相似海外基金

Collaborative Research: AF: Medium: The Communication Cost of Distributed Computation
合作研究:AF:媒介:分布式计算的通信成本
  • 批准号:
    2402836
  • 财政年份:
    2024
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Continuing Grant
Collaborative Research: AF: Medium: Foundations of Oblivious Reconfigurable Networks
合作研究:AF:媒介:遗忘可重构网络的基础
  • 批准号:
    2402851
  • 财政年份:
    2024
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Continuing Grant
Collaborative Research: AF: Medium: Algorithms Meet Machine Learning: Mitigating Uncertainty in Optimization
协作研究:AF:媒介:算法遇见机器学习:减轻优化中的不确定性
  • 批准号:
    2422926
  • 财政年份:
    2024
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Continuing Grant
Collaborative Research: AF: Medium: Fast Combinatorial Algorithms for (Dynamic) Matchings and Shortest Paths
合作研究:AF:中:(动态)匹配和最短路径的快速组合算法
  • 批准号:
    2402283
  • 财政年份:
    2024
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Continuing Grant
Collaborative Research: AF: Medium: Foundations of Oblivious Reconfigurable Networks
合作研究:AF:媒介:遗忘可重构网络的基础
  • 批准号:
    2402852
  • 财政年份:
    2024
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Continuing Grant
Collaborative Research: AF: Medium: Fast Combinatorial Algorithms for (Dynamic) Matchings and Shortest Paths
合作研究:AF:中:(动态)匹配和最短路径的快速组合算法
  • 批准号:
    2402284
  • 财政年份:
    2024
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Continuing Grant
Collaborative Research: AF: Medium: The Communication Cost of Distributed Computation
合作研究:AF:媒介:分布式计算的通信成本
  • 批准号:
    2402837
  • 财政年份:
    2024
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Continuing Grant
Collaborative Research: AF: Medium: The Communication Cost of Distributed Computation
合作研究:AF:媒介:分布式计算的通信成本
  • 批准号:
    2402835
  • 财政年份:
    2024
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Continuing Grant
Collaborative Research: AF: Medium: Adventures in Flatland: Algorithms for Modern Memories
合作研究:AF:媒介:平地历险记:现代记忆算法
  • 批准号:
    2423105
  • 财政年份:
    2024
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Continuing Grant
Collaborative Research: AF: Medium: Sketching for privacy and privacy for sketching
合作研究:AF:中:为隐私而素描和为素描而隐私
  • 批准号:
    2311649
  • 财政年份:
    2023
  • 资助金额:
    $ 56.08万
  • 项目类别:
    Continuing Grant
{{ showInfoDetail.title }}

作者:{{ showInfoDetail.author }}

知道了