Biomolecular Machines - Bionanoelectronics: Bioinquiring and Bioinspired Devices - page 173

Chapter 6
Biomolecular Machines
Abstract This chapter presents several devices, such as actuators and switches,
based on conformational changes in biomolecules, as well as biomolecular walkers
and motors, which change their spatial position and can also carry cargoes from one
point to another.
The biomolecular machines described in this chapter are based either on con-
formation changes of a biological molecule or on its motility. Reviews on DNA
nanomachines that address the problems of the different driven mechanisms and
waste products can be found in Liu and Liu ( 2009 ), Simmel and Dittmer ( 2005 ),
and Dragoman and Dragoman ( 2009 ).
In the vast majority of cases, the conformation change is due to hybridization
of DNA, which changes its state from the nonstiff ssDNA to much stiffer dsDNA,
although different conformations of dsDNA can also be involved in these devices.
Not all conformation changes result in modifications of the dimensions of a
molecule. For example, the transition between right-handed to left-handed DNA
and RNA, known respectively as the B-Z and A-Z transitions, do not change the
dimensions of the molecules but influence the fluorescent signal of aminopurine,
attached to DNA or RNA; the fluorescence is high in the left-handed form and
low in the right-handed form ( Tashiro and Sugiyama 2005 ). These transitions are
controlled by salt concentration or temperature: the left-handed state of DNA is
stable at lower temperatures, while for RNA, the thermal response is different, i.e.,
the left-handed state is favored at high temperatures. We are interest here only in the
conformation changes related to modifications of biomolecule dimensions.
Motile biological molecules are called motors because they convert one form of
energy, generally chemical, into mechanical energy. Biological motors, perfected
in millions of years of evolution, are in many ways superior to man-made motors
because they are smaller (have nanometer to micrometer sizes), highly specialized,
and, generally, convert other forms of energy into mechanical energy with better
efficiency. Nature had perfected a number of biomolecular motors. There are linear
motors, which are protein machines that step along protein tracks in the cytoplasm