Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

Constructing DNA Based Molecular Machines

Because of its simple and predictable hybridization chemistry, DNA has proven to be a versatile molecule to use in explorations of self-assembly strategies that use molecular recognition. This chemistry has allowed the construction of a variety of DNA based nanostructures. DNA can also serve to power such a nanotechnology. Recently, several animated DNA structures driven by molecular motors, themselves made of DNA and powered by DNA, were constructed. One such structure resembles a pair of tweezers in that it has two arms consisting of double stranded DNA that are connected together by single stranded DNA four bases long. This single stranded region serves as a flexible hinge allowing the two arms to be brought together. Single stranded DNA extensions (overhangs) extending from the arms serve as the motor by which these molecular tweezers are opened and closed. Introducing a strand of DNA whose base sequence has regions that are complementary to the overhangs closes the tweezers. This strand is called the fuel strand. A single stranded extension remains when the fuel strand is hybridized with the overhangs. The tweezers are opened again by introducing a strand that is complementary to the fuel strand. This strand of DNA, called the removal strand, attaches itself to the single stranded overhang of the fuel strand and then wrests the fuel strand from the tweezers through branch migration. This clocked motor is run off of the free energy of hybridization of the fuel strand with the removal strand. We have also shown that by imposing secondary structure, in the form of a loop, on the fuel strands the direct hybridization of the fuel strand with the removal strand can be inhibited. The hybridization rate can be increased again by the catalytic action of a strand of DNA that opens the loop. This mechanism may allow the construction of free-running DNA based molecular motors.

Bernard Yurke

Bell Laboratories, Lucent Technologies, 600 Mountain Avenue, Murray Hill NJ 07974,
E-mail: yurke@lucent.com Phone: (908) 582-4961 Fax: (908) 582-3260