Designing active DNA-based constructs as protein-inspired transmembrane structures

Lead Research Organisation: University of Cambridge
Department Name: Physics

Abstract

Phospholipid membrane envelopes every cell, and is an important signaling platform for all organisms. Embedded within it, transmembrane proteins are molecular machines responsible for membrane's properties. Their relatively complex structure allows for a high level of control over bilayer shape and lipid composition. Such degree of control makes protein-inspired transmembrane structures a desirable tool, and the development of these a vibrant field of study.
One of the materials currently explored as a prospective protein-mimicking building block is DNA, due to the ease with which it may be modified, designed and assembled using complementary base pairing. Starting with a synthetic DNA-origami membrane channel, a whole variety of structures was developed, all designed to insert into the membrane via hydrophobic anchors.
This project aims to lay foundation under the smart design of these DNA-based transmembrane structures. It focuses particularly on the problems listed below:
1. Due to its strong charge, membrane-spanning DNA rearranges lipids within the pore. The project aims to create a protein-inspired structure exhibiting control over this lipid arrangement.
2. In biological environment ionic concentration is very finely tuned. However, the current DNA structures require high amounts of cations in order to fold properly. The project will explore the dependency of DNA-lipid interactions on cations.
3. The insertion efficiency of current DNA structures is relatively low. The project aims to assess the effects of surfactants on the insertion, as well as explore basic design principles that will facilitate DNA-lipid interactions.
This project is based on an experimental research. The aforementioned structures will be designed and folded, then tested on model cell membranes. Optical techniques as well as single-molecule measurements will be the foundation of the work.

Studentship Projects

Project Reference Relationship Related To Start End Student Name
EP/N509620/1 01/10/2016 30/09/2021
1948702 Studentship EP/N509620/1 01/10/2017 30/09/2020 Diana Sobota
 
Description Different versions of a transmembrane DNA-based synthetic enzyme were designed and produced. The differences between them allow studying:
- membrane insertion efficiency: insertion was optimized with respect to modification placement and surfactant addition
- DNA-lipid interactions (DNA-induced lipid flipping activity can be controlled)
- membrane interactions with respect to the ionic concentration of divalent cations and lipid phase
Exploitation Route The findings are crucial for building ANY transmembrane structure - we show how lipids arrange around membrane-spanning domains, and were able to control it.
The studies on DNA-lipids attachement mediated by ions is of huge importance to DNA-based synthetic structures, but also any DNA-related molecular biology work.
Sectors Pharmaceuticals and Medical Biotechnology