Functional DNA-based assemblies

Deoxyribonucleic acid, or DNA, is a long polymer made up of repeating units called nucleotides. Each nucleotide consists of three components: sugar, phosphate and base. There are four possible bases that can be attached to the sugar-phosphate backbone, thymine (T), adenine (A), guanine (G) and cytosine (C). A specific base sequence along the chain enables DNA to encode a set of unique instructions for the synthesis of various biological components of the cell, for example a particular protein. DNA can adopt different conformations and structures in solution but the most common one is called B-DNA, where two polymer strands combine (hybridise) through base-pairing to form a right-handed double helix (or duplex).Due to its crucial role in initiating cell division (i.e. growth of an organism), DNA has long been a target for drugs, in particular anti-cancer compounds. However more recently, chemists have become interested in ways of chemically modifying DNA by attaching other groups (or tags) to the polymer chain. Part of this interest has stemmed from a need to sense DNA, in particular specific base sequences that could signify a genetic disease. We have shown that by attaching fluorescent groups to a DNA probe strand, a selective sensor can be designed that enables two target strands, 15 bases long, that differ only in the identity of one of their bases (G instead of A), to be told apart. This is a result of the two duplexes (each formed from the target strand binding to the probe strand) giving different different emission profiles (colour intensities) upon hybridisation. In this fellowship, we wish to explore and rationalise these findings in more detail and work with end users so that the viability of this new approach to detecting these so-called single nucleotide polymorphisms (or SNPs, pronounced 'snips') in DNA can be assessed.We also wish to extend the chemical modification of DNA further by introducing groups that give DNA even more functionality. One particular aspect concerns so-called photochromic groups that undergo a reversible structural change upon their exposure to light. If these groups are attached to DNA, then the structure of DNA should also change upon photo-irradation, which in turn should control its biological function.Using a similar approach, we will also attach groups to DNA that respond to an oxidising potential rather than light. These so-called redox-active groups can be oxidised which, if attached to DNA, allow DNA to be sensed electrochemically through the flow of current. We wish to use redox-active groups that are not only tagged to DNA but also interact with the structure itself through a process called intercalation, where a group inserts itself between the base pairs of duplex DNA. Through this approach, we expect that electrochemical DNA sensing can be made more effective and sensitive. Finally, we wish to incorporate the redox-active group ferrocene into the actual backbone of DNA through its replacement of a sugar-phosphate-sugar motif to create synthetic mimics of DNA. If such a process is successful, then oxidation of the ferrocene groups could change the stability of the DNA duplex in an unprecedented manner, allowing redox processes to control various DNA functions.