Modifying nucleic acid nanostructures using triplex formation

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In addition to its natural role in the storage of genetic information DNA is also an excellent material for constructing precise three-dimensional objects and assemblies on the nano-scale. By using the well-known base pairing of G with C and A with T, sequences of DNA can be easily designed so that they assemble into these structures forming precise shapes. In some cases it is possible to achieve nearly 100% yield by simply heating the sequences together in salty water and allowing the solution to cool back to room temperature. As a construction material DNA is also relatively easy and cheap to make, as well as being biodegradable and non-toxic. DNA has been used to construct containers capable of holding drugs and other biological molecules as well as devices capable of responding to different molecular signals. The next step is to develop a method of introducing different chemical or biological molecules within these DNA nano-structures. This would be useful, for example, in positioning different components within a DNA assembly to generate tiny 'nano' or 'bio' chips or to introduce a molecule onto a DNA cage capable of targeting it to a specific cell type, where it could then dispense its cargo. In this work we will develop such a method by exploiting the capacity of DNA to form three-stranded structures. These triplex structures are simply formed by adding a third strand of DNA to an existing double-stranded structure, where it attaches to the normal base pairs using specific triplet combinations. As the majority of DNA nano-structures are constructed from double-stranded segments it is possible to recognise these regions using a third strand of DNA, by generating a such three-stranded structure. Triplex formation is exquisitely specific and the third strand can therefore be designed to recognise a single region within a nanostructure. By attaching other molecules to this 'extra' strand it will be possible to position these at precise locations. The strategy can also be used to join nano-structures together, or to increase the rigidity of an existing structure. These complexes can also be easily disassembled by changing the conditions (i.e. increasing the pH). Our approach will offer a new general platform for producing many nanometer-scale structures and devices and will enable the design and synthesis of new supramolecular structures and materials.