Facilitating the Chemistry of Fluorosequencing

促进荧光测序的化学发展

• 批准号: 10623602
• 负责人: Eric V. Anslyn
• 金额: $ 38.44万
• 依托单位: UNIVERSITY OF TEXAS AT AUSTIN
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-05-01 至 2028-02-29
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10623602
• 关键词: Amino Acids; BODIPY; C-terminal; Chemicals; Chemistry; Collaborations; Databases; Diagnostic; Disease; Dyes; Fluorescence Resonance Energy Transfer; Generations; Genomics; Health; Individual; Label; Lysine; Methods; Methylation; Microscope; N-terminal; Nucleic acid sequencing; Peptide Sequence Determination; Peptides; Positioning Attribute; Post-Translational Protein Processing; Protein Analysis; Proteins; Proteomics; Reporting; Running; Sampling; Series; Techniques; Technology; Time; Ubiquitination; Work; base; design; fluorophore; imaging modality; improved; nanopore; protein aminoacid sequence; sequencing platform; single molecule

ABSTRACT While advances in nucleic acid sequencing to achieve parallel and single molecule analysis have been astounding, analogous techniques for peptide/protein sequencing are lacking. Tandem mass-spec analysis still requires millions of copies of a protein and is inherently serial rather than parallel. Thus, the current approaches being applied to parallel and single molecule protein analysis primarily focus on the use of modified nanopores. But their ability to differentiate subtle differences between individual amino acids (AAs), or strings of AAs, only works in isolated cases. To create a parallel single molecule sequencing platform for peptides/proteins, in collaboration with the Marcotte group, we devised a technique called fluorosequencing. In this technique, we label AAs with fluorophores, and on a TIRF 4-channel microscope the N-terminal AAs are removed using classic Edman degradation. As fluorophore labelled AAs are iteratively removed, both their identity and position are revealed, generating a partial-sequence. The partial-sequences are compared to a genomic database of all possible proteins, thereby revealing the proteins in the sample. Mixtures of millions of peptides are analyzed in parallel; single molecules at a time. Albeit the method is functional, there are several aspects that require improvement to generate a mature technology. One obstacle that we will overcome is the general lack of approaches that allow sequential and selectively labelling of multiple amino acids on the same peptide/protein with different tags, as well as differentiating the N-terminal and C-terminal residues from lysine and Glu/Asp AAs, respectively. We will also explore labeling four AA within the following set: Cys, Lys, Tyr, Typ, His, Ser, Thr, Glu/Asp, Arg, PSer, PThr, PTyr (P = phospho). Moreover, we feel that fluorosequencing can be readily extended to post-translational modifications (PTMs) such as mono, di, and trimethylated Lys, as well as ubiquitination. The sequential and selective labelling of four AAs and/or PTMs will involve conjugation handles carrying “click” partners within a set of what we refer to as “click:clack” pairs, wherein the “clack” partner will carry one of a set of four fluorophores appropriate for the four channels of our TIRF microscope. In some previous sequencing runs we have discovered efficient donor/acceptor FRET between the fluorophores, thereby making the donor intensity either weak or entirely invisible. To solve this problem, we will explore the use of designed fluorophores whose emission can be turned on and off by intramolecular conjugate additions which are controlled by varying the pH. In addition, because a series of common fluorophores, such as Cy and BODIPY dyes, do not survive the TFA treatment used in Edman degradation, we are developing a base-induced method for N-terminal chain-end sequencing. Importantly, while each thrust is focused upon use in fluorosequencing, the advances thereof are broadly applicable to other proteomic approaches (mass spec and nanopore), imaging methods, as well as the general chemical manipulations of peptides and proteins.

抽象的 虽然核酸测序在实现平行和单分子分析方面取得了进展 目前还缺乏令人震惊的类似肽/蛋白质测序技术。串联质谱分析仍然 需要数百万个蛋白质拷贝，并且本质上是串行而不是并行。因此，目前的方法 应用于平行和单分子蛋白质分析主要集中于修饰纳米孔的使用。 但它们区分单个氨基酸 (AA) 或 AA 串之间细微差异的能力仅 在孤立的情况下起作用。为了创建肽/蛋白质的并行单分子测序平台， 通过与 Marcotte 小组的合作，我们设计了一种称为荧光测序的技术。在这项技术中，我们 用荧光团标记 AA，并在 TIRF 4 通道显微镜上使用经典方法去除 N 端 AA 埃德曼退化。随着荧光团标记的 AA 被反复去除，它们的身份和位置都被改变。 显示，生成部分序列。将部分序列与所有基因组数据库进行比较 可能的蛋白质，从而揭示样品中的蛋白质。分析了数百万种肽的混合物 平行线;一次单个分子。尽管该方法是实用的，但有几个方面需要 改进以产生成熟的技术。我们要克服的一个障碍是普遍缺乏 允许在同一肽/蛋白质上顺序且选择性地标记多个氨基酸的方法 具有不同的标签，以及区分赖氨酸和 Glu/Asp AA 的 N 端和 C 端残基， 分别。我们还将探索标记以下组中的四种 AA：Cys、Lys、Tyr、Typ、His、Ser、Thr、 Glu/Asp、Arg、PSer、PThr、PTyr（P = 磷酸）。此外，我们认为荧光测序可以很容易地扩展 翻译后修饰 (PTM)，例如单甲基化、二甲基化和三甲基化赖氨酸，以及泛素化。这 四个 AA 和/或 PTM 的顺序和选择性标记将涉及带有“click”的缀合手柄 一组我们称之为“click:clack”对的伙伴，其中“clack”伙伴将携带一组中的一个 适合我们 TIRF 显微镜四个通道的四种荧光团。在之前的一些排序中 运行中我们发现了荧光团之间有效的供体/受体 FRET，从而使供体 强度微弱或完全看不见。为了解决这个问题，我们将探索使用设计的荧光团 其发射可以通过分子内共轭加成来打开和关闭，分子内共轭加成通过改变来控制 pH值。此外，由于一系列常见的荧光团，例如 Cy 和 BODIPY 染料，无法在高温下存活。 TFA处理用于Edman降解，我们正在开发一种N端链端碱诱导方法 测序。重要的是，虽然每个推动力都集中在荧光测序中的使用，但其进展是 广泛适用于其他蛋白质组学方法（质谱和纳米孔）、成像方法以及 肽和蛋白质的一般化学操作。