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Molecular Motors Synthetic DNA-Based Walkers Inspired by Kinesin.

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Molecular Motors
Molecular Motors: Synthetic DNA-Based Walkers
Inspired by Kinesin**
T. Ross Kelly*
bioorganic chemistry · DNA ·
molecular devices · nanotechnology
field of molecular devices has
stimulated much research during the
last two decades.[1] Over the past several
years, increasing attention has focused
on the construction of synthetic molecular motors, and both rotary and linear
motors have been observed with “organic”[2–9] and DNA-based[10–16] systems.
Biology is rich with molecular motors
(flagella, muscles, cilia, etc.),[17] and until
2004 only biology provided examples of
processive molecular motors in which a
motor molecule moves across a surface.
Kinesin is the prototypical processive
biological motor,[18] although others
such as DNA polymerases also exist.
Fueled by ATP, kinesin “walks” along a
microtubule as illustrated by the cartoons in Figure 1. A key feature of the
kinesin system is that the direction of
movement is controlled. The challenge
of controlling directionality is perhaps
best illustrated by considering the situation halfway between Figure 1 b and
1 c: If the kinesin is attached by only the
turquoise-colored foot, and the nearest
binding sites for a pink foot are identical
(one to the left, to give Figure 1 a, and
one to the right, to give Figure 1 d), how
is unidirectional movement accomplished? Nature has clearly found a solution
with kinesin, but to solve the issue of
directionality in a synthetic device is
probably the most challenging part of
[*] Prof. T. R. Kelly
Department of Chemistry
Merkert Chemistry Center
Boston College
Chestnut Hill, MA 02467 (USA)
Fax: (+ 1) 617-552-2705
[**] We thank the National Institutes of Health
(grant GM56262) for support of our work
on molecular motors.
base-pairing and double-helix formation, while the
fourth is impelled primarily
by the energetics of ATP
Progress in this area of
molecular motors was first
reported by Sherman and
Seeman.[19] Their concept is
illustrated in Figure 2 and
consists of several all-DNA
components including a
“footpath” (dark blue), two
“legs” (brown, connected to
each other by three flexible
linkers) that bear singlestranded “feet” (foot 1 (F1)
pink, foot 2 (F2) orange),
and “footholds” (FH) A
(turquoise) and B (green).
Both movement and standing
still are achieved by using
two families of single-strandFigure 1. Schematic representation of kinesin (carrying
ed DNA fuel strands desigcargo) “walking” along a microtubule.
nated as “unset” and “set”
strands. Set strands join single-stranded segments by hythe problem. Four papers published in bridizing with them, but can be removed
2004[19–22] provide the first steps toward by the addition of unset strands for
meeting this challenge. All of these use which they have greater affinity. A foot
attaches to a foothold when a set strand
DNA-based systems.
The specifics of the four reports vary, that is complementary to both is added
but in essence the association/dissocia- to the solution. Complementary strand
tion processes are driven by the hybrid- sections are shown in Figure 2 with the
ization of complementary single strands same color. Thus, when the pink and
of DNA to form double helices, some- turquoise set strand labeled “SS 1A” is
times with the simultaneous cleavage of present as in Figure 2 a, it connects
a second double helix. The second law of foot 1 of the biped to foothold A as
thermodynamics requires the expendi- shown.
Each set strand has an eight-base
ture of energy to achieve unidirectional
motion.[23] All four systems utilize chem- overhang or “toehold” that is not comical energy to accomplish movement; plementary to any of the feet or footthe first three are powered by the free holds (it is colored gray in Figure 2 a).
energy released during the course of The toehold allows the set strand to be
2005 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
DOI: 10.1002/anie.200500568
Angew. Chem. Int. Ed. 2005, 44, 4124 –4127
Figure 2. Conceptual representation of the operation of the Sherman–Seeman[19] biped walking
device (see text for details). Matching colors indicate complementary sequences between
strands; SS = set strand, USS = unset strand, F = foot, and FH = foothold. Panels (b) and (c)
depict unset strand 2B first attaching to the toehold section of set strand 2B (drawn in gray)
and then removing it to set foot 2 free. The set/unset complex in panel (c) can, if desired, then
be removed by complexing the biotin group (depicted as a light blue circle) with streptavidincoated magnetic beads. (Reproduced with permission of the authors.)
removed by the unset strand (Figure 2 b,
c). The sequences of each foot, foothold,
and toehold are represented in the
cartoons by unique colors. Detailed
sequences are provided in Figure 3.
Figure 2 a shows state 1A,2B of the
system: In this state, foot 1 is set to
foothold A, and foot 2 is set to foothold B. The biped is initially prepared in
this state. For the biped to take a step,
foot 2 first needs to be released from
foothold B, as shown in Figure 2 b and c.
To start, unset strand 2B is introduced
into the solution. It binds to the toehold
of set strand 2B (Figure 2 b) and subsequent branch migration results in the
complete hybridization of set strand 2B
with unset strand 2B. The resulting state
shown in Figure 2 c leaves foot 2 connected to the footpath only indirectly
through the flexible linkers to foot 1 and
set strand 1A. Once foot 2 has been
freed from foothold B, it is free to be
set back down either on foothold B,
which would return the system to state
1A,2B, or on foothold C, which would
move the system to state 1A,2C, as
shown in Figure 2 d. Note that the flexible linkers need to extend across foothold B to reach from foothold A to
foothold C. Starting with state 1A,2C
(Figure 2 d) similar unset and set operations can be used to move foot 1 from
foothold A to foothold B to bring the
system to state 1B,2C, as shown in
Figure 2 f. The total distance traveled
by the biped relative to the footpath
during this step is approximately the 2nm width of one DNA helical domain.
At present the range of the Sherman–Seeman walker is limited to one or
two steps. Notably, it moves in a socalled inchworm fashion, with one foot
always trailing the other. Until recently,
it was not known if kinesin itself locomotes by an inchworm or hand-overhand (foot-over-foot) mode. The inchworm motif has now been disproven[18] for kinesin (but not for inchworms).
Shin and Pierce[20] have taken Sherman and Seemans work a step further
by demonstrating a processive bipedal
DNA nanomotor that moves by advancing the trailing foot to the lead at each
step, as shown in Figure 4. As noted in
the introduction, directionality is a crucial issue and especially difficult if only
two feet and two kinds of footholds are
used. The Shin–Pierce system uses two
Figure 3. DNA base sequence corresponding to Figure 2 a rotated 908 counterclockwise relative to Figure 2 a, with SS = set strand, F = foot, and
FH = foothold. (Reproduced with permission of the authors.)
Angew. Chem. Int. Ed. 2005, 44, 4124 –4127
2005 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Figure 5. Rolling around a circle (or two meshed gears) following
the design of Tian and Mao.[21] L = linker (set) strands, R = removal
(unset) strands. (Figure courtesy of C. Mao.)
Figure 4. Schematic of the locomotion of the Shin–Pierce walker[20]
(see text for details). The diagrams depict a) unbound walker, b) walker attached to branch 1, c) walker attached to branches 1 and 2, and
d) walker released from branch 1 to yield DNA duplex waste. A and D
denote attachment (set, SS) and detachment (unset, USS) strands,
respectively. (Reproduced with permission of the authors.)
feet and four footholds and succeeds in
efficiently achieving directionality.
Their system comprises four components: a walker, a track, attachment fuel
(i.e. “set”) strands (A), and detachment
(i.e. “unset”) strands (D). The walker
consists of two partially complementary
oligonucleotides, with two single-stranded legs (feet) joined by a double-stranded helix. The track, which is constructed
of six oligonucleotides, has four protruding single-stranded branches (footholds)
separated by 15-base-pair scaffold helices. Neighboring branches run in opposite directions, so spacings of 1.5 helical
turns place all branches on the same side
of the track at approximately 5 nm apart
(Figure 4 a).
As shown in Figure 4, the walker
strides along a track under the external
control of A and D strands. An A set
strand (yellow in the first instance)
specifically anchors the orange leg of
the walker to the green branch (foothold) by forming double helices with the
corresponding leg and foothold. Singlestranded hinges adjacent to either end of
these helices provide flexibility for
adopting different conformations that
depend on the fuel species that are
present. When both legs are bound to
the track, the trailing
leg is released (Figure 4, c!d) by using
a D unset strand that
nucleates with the
complementary A1 strand
at a 10-base overhang
(toehold) and then
undergoes a stranddisplacement reaction to produce duplex waste and to free
the walker leg for the
next step. Although
Figure 4 does not Figure 6.[22]Operation of the device by Yan, Turberfield, Reif, and coworkers (see text for details). The green and pink arrows indicate
show it, by appropri- the sites of restriction; the purple \/[ symbols show where ligation
ate additions of A occurs. (Reproduced with permission of the authors.)
and D strands, the
walker is able to traverse the track from one end to the six-nucleotide fragment colored red and
other and back, with full directional indicated by * in Figure 6, moves along a
DNA track, but it is more like a bucket
A conceptually similar approach, being passed along a bucket brigade (or
except that movement is around a a crowd surfer being transported across
circular track, was reported by Tian a mosh pit). Here too, the process is
and Mao[21] and is summarized in Fig- unidirectional, but instead of using set
and unset strands, T4 ligase accomplishure 5.
A third strategy was recently de- es the set function and creates, at the
scribed by Yan, Turberfield, Reif, and same time, a recognition site for restricco-workers.[22] In this case, the walker, a tion endonucleases (PflM I, BstAP I)
2005 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Angew. Chem. Int. Ed. 2005, 44, 4124 –4127
that subsequently operate in place of
unset strands.
As shown in Figure 6, the self-assembled track contains three anchorages at which the walker (the red sixnucleotide fragment) can be bound.
Each anchorage consists of a doublestranded segment with a three-nucleotide single-strand overhang (“sticky
end”). At each step the ligand is ligated
(e.g. 0!1) to the next anchorage, then
cut (1!2) from the previous one by the
restriction endonuclease. Each ligation
creates a new restriction site, and each
cut destroys the previous restriction site.
The motion of the walker is unidirectional: the product of ligation between
two neighboring anchorages can only be
cleaved such that the walker moves onto
the downstream anchorage (A*B and
B*C can only be cut such that the walker
is left attached to B and C, respectively).
In effect, the system burns its bridges
behind it as the six-nucleotide bundle
tumbles down the track. Two idling steps
are possible: B* can be religated to A
and regenerated by restriction with
PflM I; similarly, C* can be religated to
B and regenerated with BstAP I. However, these idling steps neither reverse
nor block the overall unidirectional
motion of the walker. Once B* has been
ligated to C, the walker can never return
to A. It should be possible to extend the
motion of the walker beyond three
The sequence of events in Figure 6,
unlike those discussed in the context of
Figures 2–5, is said to be “autonomous,”
because once the walker (A*), the track
(with its anchorages), and the three
enzymes (T4 ligase and the restriction
endonucleases PflM I and BstAP I) are
mixed at the beginning, all the events
(0!4) in Figure 6 occur without further
external intervention.
The four papers highlighted above
offer ingenious responses to a challenging design problem. Much remains to be
done before a practical synthetic solution to transporting cargo across surfaces is achieved. But, as Confucius reputedly said, a journey of a thousand
miles begins with a single step. With the
walkers described above, the journey
has begun.
Published online: June 2, 2005
Angew. Chem. Int. Ed. 2005, 44, 4124 –4127
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base, synthetic, motor, inspire, molecular, walker, dna, kinesin
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