Isaac Gállego

DNA assembly under control: From DNA nanotechnology to the self-replication of nucleic acids

ZNN Ground Floor Seminarraum

22.06.2015, 10:00


Assembly of nucleic acids in vitro has always been carried out in aqueous solution, because DNA naturally functions inside the aqueous environment of living cells. Reduced water activity typically results in alteration of DNA helical structure or even the loss of base pairing. Previously, our laboratory demonstrated that DNA duplex formation is stable and reversible in reline[1] a water-free, deep eutectic solvent (DES).[2] Here we will discuss the use of DES for the control of DNA assembly with two examples. First, we have reported the first assembly of a DNA nanostructure in a DES composed of glycerol and choline chloride in a 4:1 molar ratio (glycholine) in isothermal conditions.[3] The assembled nanostructures can be transferred between aqueous solution and the DES, providing the ability to tune the solvent properties and to control the assembly process. Glycholine and its hydrated mixtures facilitate DNA folding by alleviating kinetic traps that are often encountered during the folding of DNA structures in aqueous solvent. Second, the non-enzymatic template-directed synthesis of nucleic acids is limited by a bottleneck known as strand inhibition[4] —upon cooling, the rate of duplex reformation is sufficiently fast to inhibit the binding of mononomer/oligomers on the template strands. We show that the high viscosity of DES can be used to slow the annealing kinetics of a long template duplex after heating and cooling. Meanwhile, short oligomers can diffuse faster and bind to their complementary targets on the templates. Subsequent ligation of the short oligonucleotides allow template information transfer, an important and unsolved problem in the origins of life field. These two examples illustrate the use of alternative solvents for the control of the kinetics and thermodynamics of DNA assembly. We anticipate that DES will provide tunable, DNA compatible milieu with properties that can be optimized for a range of applications and the formation of nanodevices.

 

[1]            I. Mamajanov, A. E. Engelhart, H. D. Bean, N. V. Hud, Angew. Chem. Int. Ed. 2010, 49, 6310.

[2]            A. P. Abbott, G. Capper, D. L. Davies, R. K. Rasheed, V. Tambyrajah, Chem. Commun. 2003, 70.

[3]            I. Gallego, M. A. Grover, N. V. Hud, Angew. Chem. Int. Ed. 2015, 54, 6765.

[4]            J. W. Szostak, J. Syst. Chem. 2012, 3, 2.