SHF: Collaborative Research: Biocompatible I/O Interfaces for Robust Bioorthogonal Molecular Computing

糖分子可以以两种形式存在，这两种形式互为镜像，但在其他方面难以区分，比如左分子和右分子。自然界中所有的DNA分子都含有右糖，这使得它们呈现出众所周知的双螺旋形状，并带有右旋。自然界中细胞中的蛋白质识别右旋DNA以执行有用的细胞功能，其中之一就是破坏单链DNA。在过去的十年里，DNA已经被用于传感、计算和诊断病原体和疾病的合成设备中。然而，当这些装置被引入细胞时，它们很容易被这些蛋白质破坏。该项目将开发使用左手DNA的设备，这种DNA在自然界中是不存在的，并且可以抵抗这种形式的降解。特别是，该项目将开发(1)输入接口，用于从感兴趣的目标(如小分子或天然DNA （D-DNA）向左旋DNA （L-DNA）发送信号；(2)输出接口，用于从左旋DNA向相关的自然分子途径（如DNA翻译和转录）发送信号。这一发展将使未来的设备能够感知细胞状态（健康或患病）的多个标记，然后使用DNA计算整合传感器，最后对细胞起作用，例如在细胞患病时摧毁它，但设备本身将主要由左旋DNA组成，因此在细胞中是健壮的。该项目将涉及研究生和本科生。它将是跨学科的，涉及计算机科学和生物医学工程，并将在新墨西哥大学和哥伦比亚大学进行。该项目的第一个目标是研究L-DNA（左旋DNA）分子逻辑器件与自然分子之间的结合相互作用。这项研究将产生一个基本技术工具箱，用于实现可以检测自然发生的目标分子的输入接口，反过来，可以将这些结合事件翻译为生物正交L-DNA逻辑电路中的信息处理。这将通过描述由纯D-DNA输入链驱动的混合L-DNA/D-DNA分子计算组件来完成。该项目的第二个目标是开发输出接口，使L-DNA系统能够根据其编程的分子计算结果对环境产生某种影响（即进行某种形式的驱动）。具体来说，该项目将侧重于从L-DNA分子逻辑电路产生有用输出信号的一种特殊机制，即通过L-DNA分子电路对隔离的反义d核酸的变抗“激活”来敲低基因。总之，这些将为L-DNA分子逻辑电路提供一种机制，通过控制基因表达来驱动。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Sugar molecules can exist in two forms that are the mirror image of each other but otherwise indistinguishable, like the left and right hand. All DNA molecules in nature contain right-hand sugars that cause them to assume the well-known double-helix shape with a right-handed twist. Proteins in cells in nature recognize the right-handed DNA in order to perform useful cellular functions, one of which is destroying single-stranded DNA. Over the last decade, DNA has come to be used in synthetic devices for sensing, computing, and diagnosing pathogens and disease. However, when these devices are introduced into a cell, they are prone to being destroyed by these proteins. This project will develop devices using left-handed DNA, which is not found in nature and is resistant to this form of degradation. In particular, the project will develop (1) input interfaces, for signaling from targets of interest, such as small molecules or natural DNA (D-DNA), to left-handed DNA (L-DNA), and (2) output interfaces, for signaling from left-handed DNA back into a relevant natural molecular pathway (such as DNA translation and transcription). This development will enable future devices that can sense multiple markers of the state of a cell (healthy or diseased), then integrate the sensors using DNA computing, and finally act on the cell, for example to destroy it if diseased, but the device itself will consist mainly of left-handed DNA and will therefore be robust in the cell. The project will involve both graduate and undergraduate students. It will be interdisciplinary, involving computer science and biomedical engineering, and will be carried out at the University of New Mexico and Columbia University.The first aim of the project is to study the binding interactions between L-DNA (left-handed DNA) molecular logic devices and naturally occurring molecules. This study will produce a toolbox of basic techniques for implementing input interfaces that can detect naturally occurring target molecules, which in turn, can translate those binding events for information processing within a bio-orthogonal L-DNA logic circuit. This will be done by characterizing the actuation of hybrid L-DNA/D-DNA molecular computing components by pure D-DNA input strands. The second aim of the project is developing output interfaces that will enable L-DNA systems to produce some effect on the environment (i.e., carry out some form of actuation) as a result of their programmed molecular computations. Specifically, the project will focus on one particular mechanism for generating a useful output signal from an L-DNA molecular logic circuit, namely, gene knockdown by the allosteric "activation" of sequestered antisense D-nucleic acids by an L-DNA molecular circuit. Together, these will provide a mechanism for L-DNA molecular logic circuits to actuate via control of gene expression.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.