Zipper-Based Devices and Future Directions

Abstract

A strand displacement-based system has been developed that substitutes inosine for guanosine in DNA sequences called “zippers”. Each zipper sequence employs traditional adenosine-thymine bonding as well as non-traditional inosine-cytidine bonding. The I-C bond consists of only 2 hydrogen bonds as opposed to the typical 3 hydrogen bonds found in G-C bonds. A zipper helix consists of one strand with A and C and a second strand with complementary I and T nucleotides. The second strand is displaced by the introduction of a strand with G and T nucleotides complementary to the first strand. These zippers can be introduced as an active element in larger DNA devices and be designed to be used in different situations. The first example is of zippers incorporated into single and double “spring” systems. The springs incorporate in such a manner that allow them be repeatedly extended and reset. Multiple springs can be incorporated into larger 2D and 3D DNA structures, allowing them to change between conformations on demand. Zippers can also be incorporated into a gating system for ion channels such as hemolysin and DNA tethered to a larger nanoparticle and passing through the hemolysin channel. Zippers at the end of such a strand could lock the DNA strand in place, effectively allowing the nanoparticle to block the channel on the other side. Finally DNA zippers have not been properly characterized by quantitative measurements yet. AFM or optical trap studies can be performed to study the binding energy of a zipper sequence.