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

糖分子可以以两种形式存在，它们是彼此的镜像，但在其他方面无法区分，就像左手和右手一样。自然界中所有DNA分子都含有右旋糖，这使它们呈现出众所周知的右旋扭转的双螺旋形状。自然界细胞中的蛋白质识别右手DNA，以执行有用的细胞功能，其中之一是破坏单链DNA。在过去的十年中，DNA已被用于传感，计算和诊断病原体和疾病的合成设备。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，这种设备在自然界中找不到，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，用于从感兴趣的靶点（如小分子或天然DNA（D-DNA））到左手DNA（L-DNA）的信号传递，以及（2）输出接口，用于从左手DNA到相关天然分子途径（如DNA翻译和转录）的信号传递。这一发展将使未来的设备能够感测细胞状态（健康或患病）的多个标记，然后使用DNA计算集成传感器，并最终作用于细胞，例如在患病时将其摧毁，但设备本身将主要由左手DNA组成，因此在细胞中具有鲁棒性。该项目将涉及研究生和本科生。这是一个跨学科的项目，涉及计算机科学和生物医学工程，将在新墨西哥州和哥伦比亚大学进行，该项目的第一个目标是研究L-DNA（左手DNA）分子逻辑器件与自然存在的分子之间的结合相互作用。这项研究将产生一个工具箱的基本技术，用于实现输入接口，可以检测自然发生的目标分子，这反过来，可以翻译这些结合事件的信息处理内的生物正交L-DNA逻辑电路。这将通过表征纯D-DNA输入链对混合L-DNA/D-DNA分子计算组件的致动来完成。该项目的第二个目标是开发输出接口，使L-DNA系统能够对环境产生某种影响（即，执行某种形式的致动）作为其编程分子计算的结果。具体而言，该项目将集中在一个特定的机制，产生一个有用的输出信号从L-DNA分子逻辑电路，即基因敲低的变构“激活”的隔离反义D-核酸的L-DNA分子电路。这两项研究将共同为L-DNA分子逻辑电路提供一种通过控制基因表达来启动的机制。该奖项反映了NSF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.