IDBR (EAGER): An AFM-Based Instrument for Monitoring DNA Synthesis in Real-Time

IDBR (EAGER):基于 AFM 的实时监测 DNA 合成的仪器

基本信息

  • 批准号:
    1225720
  • 负责人:
  • 金额:
    $ 20万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
    Standard Grant
  • 财政年份:
    2012
  • 资助国家:
    美国
  • 起止时间:
    2012-05-01 至 2015-04-30
  • 项目状态:
    已结题

项目摘要

AbstractThis NSF award supports development of an instrument that is capable of sequencing human and other genomes with unprecedented low cost, long read sections, and high speed and accuracy. To achieve this goal, the probe of an atomic force microscope (AFM) will be functionalized with a DNA polymerase, and the conformational perturbations of the polymerase during DNA synthesis will be monitored by the AFM in real-time. Because different nucleotides cause different conformational perturbations of the enzyme, the sequence of the template DNA will be read out directly from the order of unique conformational perturbations as it travels through the polymerase. Using instruments currently on the market, genome sequencing is highly expensive, which hampers many applications such as personalized medicine. With these instruments, only short read segments can be obtained, which results in high computational efforts in post-sequencing genome assembly. The short reads also cause problems for sequencing genomes that have long repeats. Existing methods require sample amplification by polymerase chain reaction (PCR). Because of inaccuracies introduced during sample amplification, the genome sequences are not accurate enough for applications such as disease diagnosis. During traditional sequencing, information on epigenetic DNA base modifications, which is linked to many important biological processes, is lost. The proposed AFM-based instrument is expected to overcome these problems. Because the new instrument uses single-molecular sequencing, the costs for DNA sample preparation and amplification in existing technologies will be minimized. In many known sequencing technologies, expensive reagents are required. The new technology may only need natural nucleotides, which will further reduce costs. The sample DNAs used for sequencing with the proposed instrument will not need amplification by PCR, thus the inaccuracies introduced during sample preparation in existing sequencing methods will be avoided. Because the sequences of DNAs are read out directly and continuously during DNA synthesis, the sequencing speed and read length will far exceed those of technologies currently on the market. Because original sample DNAs are used for sequencing and epigenetically modified nucleobases are predicted to cause different conformational fluctuations of polymerase from unmodified ones, the new instrument is expected to sequence genomes without losing any epigenetic base modification information.The instrument will have a broad impact on many research areas such as human health, food, energy, environment, and national security, all of which demand sequencing the genomes of human, animals, plants, bacteria, viruses or other organisms. Besides sequencing, the instrument will also find application in DNA polymerase conformational dynamic studies giving data that cannot be obtained directly using known techniques. Similar instruments for studying other enzymes can also be readily made using the technologies developed in this project. These instruments will help to answer important fundamental questions on enzyme catalysis. Initially, the new sequencing service will be provided to biological research labs through collaborations. Later, the service and the instrument will be made commercially available to medical, academic, and commercial labs. The project is highly multidisciplinary. Three research groups that have expertise in biology, chemistry, and engineering will work together to develop the instrument. During this process, two postdoctoral researchers and at least two PhD students will gain extensive research experiences in these fields. In addition, three or more undergraduate students will also be trained. Some of these next generation scientists are expected to help the commercialization of the instrument and sequencing technology.
美国国家科学基金会的这一奖项支持开发一种能够以前所未有的低成本、长读段、高速度和准确性对人类和其他基因组进行测序的仪器。为了实现这一目标,原子力显微镜(AFM)的探针将与DNA聚合酶功能化,和DNA合成过程中的聚合酶的构象扰动将由AFM实时监测。因为不同的核苷酸引起酶的不同构象扰动,模板DNA的序列将在其穿过聚合酶时从独特构象扰动的顺序直接读出。使用目前市场上的仪器,基因组测序是非常昂贵的,这阻碍了许多应用,如个性化医疗。使用这些仪器,只能获得短的读段,这导致测序后基因组组装中的高计算工作量。短读段也会给具有长重复序列的基因组测序带来问题。现有方法需要通过聚合酶链式反应(PCR)进行样品扩增。由于在样品扩增期间引入的不准确性,基因组序列对于诸如疾病诊断的应用不够准确。在传统的测序过程中,与许多重要的生物过程相关的表观遗传DNA碱基修饰的信息丢失了。基于AFM的仪器有望克服这些问题。由于新仪器使用单分子测序,现有技术中DNA样品制备和扩增的成本将最小化。在许多已知的测序技术中,需要昂贵的试剂。新技术可能只需要天然核苷酸,这将进一步降低成本。用于使用所提出的仪器进行测序的样品DNA将不需要通过PCR扩增,因此将避免现有测序方法中样品制备期间引入的不准确性。由于DNA的序列在DNA合成过程中直接连续读出,测序速度和读取长度将远远超过目前市场上的技术。由于测序使用的是原始样本DNA,而且表观遗传修饰的核碱基预计会引起聚合酶与未修饰的核碱基不同的构象波动,因此新仪器有望在不丢失任何表观遗传碱基修饰信息的情况下进行基因组测序,该仪器将对人类健康、食品、能源、环境和国家安全等多个研究领域产生广泛影响,所有这些都需要对人类、动物、植物、细菌、病毒或其他生物体的基因组进行测序。除了测序之外,该仪器还将应用于DNA聚合酶构象动态研究,提供无法使用已知技术直接获得的数据。利用本项目开发的技术,也可以很容易地制造用于研究其他酶的类似仪器。这些仪器将有助于回答酶催化的重要基本问题。最初,新的测序服务将通过合作提供给生物研究实验室。随后,该服务和仪器将向医疗、学术和商业实验室提供商业服务。该项目是高度多学科的。拥有生物学、化学和工程专业知识的三个研究小组将共同开发该仪器。在此过程中,两名博士后研究人员和至少两名博士生将在这些领域获得广泛的研究经验。此外,还将培养三名或三名以上的本科生。这些下一代科学家中的一些人有望帮助仪器和测序技术的商业化。

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 }}

Shiyue Fang其他文献

Reversible Biotinylation of the 5′‐Terminus of Oligodeoxyribonucleotides and its Application in Affinity Purification
寡脱氧核糖核苷酸5′端的可逆生物素化及其在亲和纯化中的应用
Simple and Efficient Synthesis of 4,7‐Dimethoxy‐1(H)‐indene
4,7-二甲氧基-1(H)-茚的简单高效合成
  • DOI:
    10.1080/00397910701319189
  • 发表时间:
    2007
  • 期刊:
  • 影响因子:
    2.1
  • 作者:
    X. Zhang;M. Thimmaiah;Shiyue Fang
  • 通讯作者:
    Shiyue Fang
Synthesis of 3-Amino-2,2-dimethyl-8-thia-1-azaspiro[4.5]decane
3-氨基-2,2-二甲基-8-硫杂-1-氮杂螺[4.5]癸烷的合成
  • DOI:
    10.1080/00397910903289255
  • 发表时间:
    2010
  • 期刊:
  • 影响因子:
    2.1
  • 作者:
    W. Mai;S. Green;D. K. Bates;Shiyue Fang
  • 通讯作者:
    Shiyue Fang
Efficient palladium-catalyzed Suzuki-Miyaura coupling of aryl chlorides with arylboronic acids using benzoferrocenyl phosphines as supporting ligands
使用苯并二茂铁基膦作为支持配体,实现芳基氯与芳基硼酸的高效钯催化 Suzuki-Miyaura 偶联
  • DOI:
    10.1016/j.tet.2007.04.057
  • 发表时间:
    2007
  • 期刊:
  • 影响因子:
    2.1
  • 作者:
    M. Thimmaiah;Shiyue Fang
  • 通讯作者:
    Shiyue Fang
Purification of Synthetic Oligonucleotides via Catching by Polymerization
通过聚合捕获纯化合成寡核苷酸

Shiyue Fang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('Shiyue Fang', 18)}}的其他基金

CAS: Long Oligodeoxynucleotides Directly from Automated De Novo Synthesis
CAS:直接来自自动化从头合成的长寡脱氧核苷酸
  • 批准号:
    1954041
  • 财政年份:
    2020
  • 资助金额:
    $ 20万
  • 项目类别:
    Standard Grant
PFI-TT: Affordable and High-Quality Polyethylene Glycols for Nanomedicine and Other Applications
PFI-TT:用于纳米医学和其他应用的经济实惠的高质量聚乙二醇
  • 批准号:
    1918585
  • 财政年份:
    2019
  • 资助金额:
    $ 20万
  • 项目类别:
    Standard Grant
I-Corps: Monodisperse Polyethylene Glycol Synthesis Technologies
I-Corps:单分散聚乙二醇合成技术
  • 批准号:
    1754235
  • 财政年份:
    2017
  • 资助金额:
    $ 20万
  • 项目类别:
    Standard Grant
Purification of Synthetic Peptides Using a Catching by Polymerization Approach
使用聚合捕获法纯化合成肽
  • 批准号:
    1111192
  • 财政年份:
    2011
  • 资助金额:
    $ 20万
  • 项目类别:
    Standard Grant
Simple Methods for Oligonucleotide Purification
寡核苷酸纯化的简单方法
  • 批准号:
    0647129
  • 财政年份:
    2007
  • 资助金额:
    $ 20万
  • 项目类别:
    Standard Grant

相似海外基金

Collaborative Research: EAGER: The next crisis for coral reefs is how to study vanishing coral species; AUVs equipped with AI may be the only tool for the job
合作研究:EAGER:珊瑚礁的下一个危机是如何研究正在消失的珊瑚物种;
  • 批准号:
    2333604
  • 财政年份:
    2024
  • 资助金额:
    $ 20万
  • 项目类别:
    Standard Grant
EAGER/Collaborative Research: An LLM-Powered Framework for G-Code Comprehension and Retrieval
EAGER/协作研究:LLM 支持的 G 代码理解和检索框架
  • 批准号:
    2347624
  • 财政年份:
    2024
  • 资助金额:
    $ 20万
  • 项目类别:
    Standard Grant
EAGER: Innovation in Society Study Group
EAGER:社会创新研究小组
  • 批准号:
    2348836
  • 财政年份:
    2024
  • 资助金额:
    $ 20万
  • 项目类别:
    Standard Grant
EAGER: Artificial Intelligence to Understand Engineering Cultural Norms
EAGER:人工智能理解工程文化规范
  • 批准号:
    2342384
  • 财政年份:
    2024
  • 资助金额:
    $ 20万
  • 项目类别:
    Standard Grant
EAGER/Collaborative Research: Revealing the Physical Mechanisms Underlying the Extraordinary Stability of Flying Insects
EAGER/合作研究:揭示飞行昆虫非凡稳定性的物理机制
  • 批准号:
    2344215
  • 财政年份:
    2024
  • 资助金额:
    $ 20万
  • 项目类别:
    Standard Grant
Collaborative Research: EAGER: Designing Nanomaterials to Reveal the Mechanism of Single Nanoparticle Photoemission Intermittency
合作研究:EAGER:设计纳米材料揭示单纳米粒子光电发射间歇性机制
  • 批准号:
    2345581
  • 财政年份:
    2024
  • 资助金额:
    $ 20万
  • 项目类别:
    Standard Grant
Collaborative Research: EAGER: Designing Nanomaterials to Reveal the Mechanism of Single Nanoparticle Photoemission Intermittency
合作研究:EAGER:设计纳米材料揭示单纳米粒子光电发射间歇性机制
  • 批准号:
    2345582
  • 财政年份:
    2024
  • 资助金额:
    $ 20万
  • 项目类别:
    Standard Grant
Collaborative Research: EAGER: Designing Nanomaterials to Reveal the Mechanism of Single Nanoparticle Photoemission Intermittency
合作研究:EAGER:设计纳米材料揭示单纳米粒子光电发射间歇性机制
  • 批准号:
    2345583
  • 财政年份:
    2024
  • 资助金额:
    $ 20万
  • 项目类别:
    Standard Grant
EAGER: Accelerating decarbonization by representing catalysts with natural language
EAGER:通过用自然语言表示催化剂来加速脱碳
  • 批准号:
    2345734
  • 财政年份:
    2024
  • 资助金额:
    $ 20万
  • 项目类别:
    Standard Grant
EAGER: Search-Accelerated Markov Chain Monte Carlo Algorithms for Bayesian Neural Networks and Trillion-Dimensional Problems
EAGER:贝叶斯神经网络和万亿维问题的搜索加速马尔可夫链蒙特卡罗算法
  • 批准号:
    2404989
  • 财政年份:
    2024
  • 资助金额:
    $ 20万
  • 项目类别:
    Standard Grant
{{ showInfoDetail.title }}

作者:{{ showInfoDetail.author }}

知道了