INSIGHTS | PERSPECTIVES
380 25 JULY 2014 • VOL 345 ISSUE 6195
sciencemag.org SCIENCE
Polymers are ubiquitous and occur in many diverse forms, including cross- linked synthetic polymers (e.g., rub- ber and plastic) and biopolymers such as DNA and proteins. DNA has long been used as a model system for polymer science because long, chemically well-defined DNA chains can be prepared using
its ability to self-replicate, and because it
can be analyzed at the single-molecule level.
For instance, the relaxation dynamics of a
distorted DNA molecule eventually reverting to its lowest-energy configuration have
been investigated extensively (1). There has
been growing interest in understanding the
relaxation of spatially confined polymers.
How biopolymers such as DNA and proteins
behave under high spatial confinement is
important because they often experience
such conditions—for example, when DNA
passes through a narrow pore during viral
packaging or bacterial conjugation. With the
advent of nanotechnology (DNA is 2 nm in
diameter), it has now become possible to
study the relaxation dynamics of DNA confined in one (2) and two (3) dimensions.
Berndsen et al. (4) have undertaken the first
characterization of DNA relaxation under
extreme confinement in three dimensions.
Remarkably, they find that DNA relaxation
under such circumstances is slowed by a factor of more than 60,000, presenting a daunting challenge for the biological machines
that need to compact DNA reliably into tight
spaces.
Extreme confinement of DNA can be
achieved in viruses and bacteriophages (i.e.,
viruses that infect bacteria). They package
their genome to near-crystalline densities
in the smallest volume possible—a protein
shell called the capsid typically only 50
to 100 nm in its largest dimension. Most
double-stranded DNA bacteriophages and
many eukaryotic viruses (notably, the her-
pes virus) use powerful molecular motors
to reel in newly replicated viral DNA into
empty, preformed capsids. Using the energy
of adenosine triphosphate (ATP) hydrolysis,
this motor must work against tremendous
pressure as high as 2 to 6 megapascals (5,
6). These pressures are believed eventually
to drive DNA ejection into new host cells
for infection.
Recent single-molecule measurements
(7) have provided important new insights
into the mechanism of viral DNA packaging. Smith et al. (5) used optical traps to
pull on an individual DNA molecule as it
is packaged into a single φ29 phage. Their
work established that packaging slows down
as DNA fills the capsid because of the buildup of internal pressure within the capsid.
Berndsen et al. (4) used this assay to inves-
tigate the dynamics of the confined DNA
inside the capsid. During the reaction, they
stalled packaging complexes with a non-
hydrolyzable ATP analog, then restarted
them with ATP after a variable wait ranging
from 1 to >10 min. Surprisingly, packaging
became faster upon restarting if the φ29
capsids were nearly filled to capacity when
they were stalled; this finding suggests
that densely packed DNA can
become kinetically trapped in
nonequilibrium conformations
that jam the motor. Stalling the
motor allows DNA time to relax
to its lowest-energy state and
to present a lower resistance to
packaging, leading to an acceler-
ation of the packaging reaction.
The fact that the effect was more
pronounced after stalls longer
than 10 min indicates that the
relaxation time scales must be
longer than those of unconfined
DNA of the same length by a fac-
tor of 60,000 (1).
In addition, 1- to 10-s pauses
that had been observed during
the late stages of packaging became all but eliminated by stalling and restarting of the motor,
The ultraslow dynamics have a number of
implications for the viral packaging mechanism. Because the relaxation time scales in
φ29 exceed the duration of the entire packaging reaction, the motor must overcome
large fluctuations in resistance because of
ultraslow DNA dynamics. On the other
hand, because cell infection occurs much
later in the viral life cycle, presumably allowing more time for the viral DNA to relax to
its lowest-energy conformation, the forces
Ultraslow relaxation of confined DNA
A tight fit. During packaging of the viral genome into its capsid, DNA
can become kinetically trapped in nonequilibrium conformations,
generating high resistances against the packaging motor. Relaxation to
the lowest-energy state is extremely slow.
By Yann R. Chemla1 and Taekjip Ha1,2
DNA dynamics in tight spaces challenge nature’s nanomachines
BIOPHYSICS
1Department of Physics, Center for the Physics of Living
Cells, and Center for Biophysics and Computational Biology,
Institute for Genomic Biology, University of Illinois at Urbana–
Champaign, Urbana, IL 61820, USA. 2Howard Hughes Medical
Institute, University of Illinois at Urbana–Champaign, Urbana,
IL 61820, USA. E-mail: ychemla@illinois.edu; tjha@illinois.edu I L L U S T
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