Enrichment of DNA/RNA Sequences based on Pre-equilibrium Hybridization Kinetics

基于预平衡杂交动力学的 DNA/RNA 序列富集

基本信息

批准号：
10112940
负责人：
Omid Veiseh
金额：
$ 46.78万
依托单位：
RICE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-03-15 至 2022-02-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10112940
关键词：
Acids Algorithms Arts Base Sequence Behavior Binding Bioinformatics Biological Blood Buffers Chemistry Clinical Complex Copy Number Polymorphism Custom DNA DNA Sequence DNA sequencing Data Disease Early Diagnosis Equilibrium Gene Expression Human Human Genome Hybrids Inherited Kinetics Knowledge Measurement Measures Methods Modeling Molecular Nucleic Acid Hybridization Nucleic Acids Nucleotides Oligonucleotides Organism Pathway interactions Process Protocols documentation RNA RNA Sequences Reagent Research Running Sampling Sequence Analysis Side Silent Mutation Specificity Speed Surface System Techniques Technology Temperature Thermodynamics Time Variant base biophysical analysis biophysical model design disease diagnosis falls human DNA instrument intercellular communication interest kinetic model magnetic beads melting milliliter models and simulation next generation sequencing novel public health relevance reference genome scale up tool

项目摘要

DESCRIPTION (provided by applicant): The sequences and concentrations of nucleic acid molecules within a sample hold vast amounts of scientific as well as clinical information that can be used to understand pathways and inform treatment. However, our current tools for nucleic acid sequence analysis fall orders of magnitude short of analyzing all 1017 nucleotides of DNA within a typical 1 mL sample of human blood. Enrichment, i.e. the selective capture/retention of desired DNA loci or sequences, is crucial to effective and rapid next-generation sequencing (NGS) of DNA and RNA samples. Current enrichment techniques (predominantly multiplexed PCR, hybrid capture, and molecular inversion probes) all suffer from limited uniformity of capture and limited capture specificity. Th first limitation results in poor quantitation of sequences relative to one another (e.g. copy number variations), and the second limitation results downstream in wasted NGS reads. Due to the high multiplexing requirement of most enrichment applications, it is generally difficult to systematically optimize either rationally or empirically, due to the large number of potential interactions between probes and target sequences. The PI proposes to develop novel hybridization probes and systems to allow multiplexed capture and enrichment of DNA and RNA sequences. Unlike previous hybrid capture techniques, the PI's approach focuses on probes with custom designable kinetics of hybridization to different sequences, and seeks to utilize precise predictive understanding to design probes that produce desired sequence capture behavior at particular points in time. By using differential hybridization kinetics, the research team will be able to achieve complex pre-equilibrium enrichment distributions that cannot be achieved at equilibrium. The research team will use a uniquely knowledge-driven design process, based on biophysical models of nucleic acids, and use only minimal empirical optimization. To further enhance the predictability of new capture probe set design, the team will also use novel methods to quickly and more accurately measure nucleic acid thermodynamics and kinetics at native conditions.

描述（由申请人提供）：样品中核酸分子的序列和浓度具有大量的科学和临床信息，可用于了解途径并为治疗提供信息。但是，我们目前用于核酸序列分析的工具下降了分析的数量级，所有1017个DNA的核苷酸在典型的1 ml人体血液样本中。富集，即所需的DNA基因座或序列的选择性捕获/保留，对于有效和快速的下一代测序（NGS）至关重要。DNA和RNA样品至关重要。当前的富集技术（主要是多重PCR，杂种捕获和分子反转问题）均受捕获的均匀性有限和有限的捕获特异性的影响。第一个限制导致序列相对于彼此的定量较差（例如拷贝数变化），而浪费的NGS读数下游的第二个极限结果。由于大多数富集应用的高多路复用要求，由于问题与目标序列之间的大量潜在相互作用，通常很难系统地或紧急地进行系统或紧急地进行优化。 PI的建议是开发新型杂交探针和系统，以允许对DNA和RNA序列的多重捕获和富集。与以前的混合捕获技术不同，PI的方法着重于定制设计的杂交动力学与不同序列的问题，并试图利用精确的预测性理解，以设计在特定时间点产生所需序列捕获行为的设计问题。通过使用差异杂交动力学，研究团队将能够实现在平衡下无法实现的复杂的平衡前富集分布。研究团队将基于核酸的生物物理模型使用独特的知识驱动的设计过程，并仅使用最少的经验优化。为了进一步提高新捕获探针集设计的可预测性，该团队还将使用新颖的方法来快速，更准确地测量天然条件下的核酸热力学和动力学。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Modular probes for enriching and detecting complex nucleic acid sequences.

DOI：
10.1038/nchem.2820
发表时间：
2017-12
期刊：
Nature chemistry
影响因子：
21.8
作者：
Wang JS;Yan YH;Zhang DY
通讯作者：
Zhang DY

Metastable hybridization-based DNA information storage to allow rapid and permanent erasure.

DOI：
10.1038/s41467-020-18842-6
发表时间：
2020-10-06
期刊：
Nature communications
影响因子：
16.6
作者：
Kim J;Bae JH;Baym M;Zhang DY
通讯作者：
Zhang DY

Nucleic Acid Quantitation with Log-Linear Response Hybridization Probe Sets.

DOI：
10.1021/acssensors.0c00052
发表时间：
2020-06-26
期刊：
ACS sensors
影响因子：
8.9
作者：
Wu LR;Fang JZ;Khodakov D;Zhang DY
通讯作者：
Zhang DY

Predicting stability of DNA bulge at mononucleotide microsatellite.

DOI：
10.1093/nar/gkab616
发表时间：
2021-08-20
期刊：
Nucleic acids research
影响因子：
14.9
作者：
Bae JH;Zhang DY
通讯作者：
Zhang DY

A deep learning model for predicting next-generation sequencing depth from DNA sequence.

DOI：
10.1038/s41467-021-24497-8
发表时间：
2021-07-19
期刊：
Nature communications
影响因子：
16.6
作者：
Zhang JX;Yordanov B;Gaunt A;Wang MX;Dai P;Chen YJ;Zhang K;Fang JZ;Dalchau N;Li J;Phillips A;Zhang DY
通讯作者：
Zhang DY