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SINGLE MOLECULE BIOLOGY: ONE, TWO, THREE & FOUR
[Taekjip Ha]
Professor, Physics
Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Howard Hughes Medical Institute
I call myself an accidental biophysicist. My Physics Ph.D work began in semiconductor physics and through a series of accidents I ended
up developing methods to detect single fluorescence molecules. It turned out that the single molecule fluorescence methods could be
applied to many biological systems and gradually my research topics shifted to biological questions, and although I teach physics in a
physics department, all of the questions that we are addressing are biological in nature.
Why would a physicist want to study biology? First, minimal functional units in biology are molecules and they can range between 1
and 100 nm, the scale of current and future electronics. Second, biomolecules have been optimized through billions of years of evolution
and often biological sensor reach the physical limits of sensitivity. A deep understanding of biological systems may ultimately lead
to development of man-made nanomachines through reverse engineering. But is the population notion that biological molecules, for
example proteins are nanomachines justified? For example, do the nanomachine have what man-made machines have such as engines
and springs?
The answer is a definitive yes for molecular motors that convert chemical energy stored in ATP or another high energy molecules into
mechanical energy. A great example is myosin V which takes a 37 nm step along its track every time it consumes an ATP molecule as
the fuel (Figure 1a). There was, however, a controversy as to whether myosin V walks on the track like a person (two feet alternating in
position) or it crawls like a baby (one foot stays ahead of the other). Single molecule imaging and localization down to 1.5 nm precision
led to a definitive proof that myosin V walks (1). This is an example of using detection of single fluorescent molecule to answer fundamental
questions in biology (‘One’ in the title of this article).
We recently made an exciting discovery that a protein can store elastic energy through multiple cycles of chemical energy release and
that this stored energy can be released in a single burst (Gwangrog Lee et al., submitted). In this work, an enzyme that can digest RNA
strand one base at a time even in the presence of basepaired structures was studied using another single molecule method called single
molecule fluorescence resonance energy transfer (FRET). FRET measures the interaction between two dye molecules attached to a
biological molecule and because FRET is a strong function of distance, it can report on even minute distance changes during biological
reactions. In this particular work, we attached the dyes to the RNA so that FRET would increase during RNA unwinding by the enzyme
(Figure 1b). The surprise was that the enzyme unwound RNA in large steps about 4 base pairs even though the motion is powered
by RNA digestion in single base steps, strong suggesting the enzyme/RNA complex can be viewed as a spring. ‘Two’ in the title of this
article refers to FRET and my laboratory has been fortunate to make several interesting discoveries on enzymes that work on DNA and
RNA using the method.
Figure 1. Protein as a nanomachine (a) A nanoengine.
(b) A nano-spring.
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KSEA LETTERS Vol. 40 No. 3 April 2012