Science > Physics > PHYSICS NEWS UPDATE -- Number 715 January 11, 2005 by Phillip F.Schewe, Ben Stein
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PHYSICS NEWS UPDATE -- Number 715 January 11, 2005 by Phillip F.Schewe, Ben Stein |
PHYSICS NEWS UPDATE
The American Institute of Physics Bulletin of Physics News
Number 715 January 11, 2005 by Phillip F. Schewe, Ben Stein
UNCOVERING NEW SECRETS IN A DNA HELPER. The protein RecA performs
some profoundly important functions in bacteria. Two independent
papers shed light on how the bacterial protein helps (1) identify
and (2) replace damaged DNA while making few mistakes.
Error-correction mechanisms keep DNA fidelity during replication to
within an average of one error per billion "letters" or base pairs.
This research may provide insight on how damage to existing DNA from
processes such as UV radiation can be detected and repaired
efficiently in living organisms, including humans, who carry
evolutionary cousins of RecA. By polymerizing (bonding) onto
damaged DNA, RecA is able to detect DNA damage and send out an "SOS"
message to the rest of the cell. When the double-helix DNA is
seriously damaged, single-stranded DNA is exposed and RecA
polymerizes onto it, activating a biochemical SOS signal. To do
this, Tsvi Tlusty and his colleagues at the Weizmann Institute and
Rockefeller University (Tsvi.Tlusty@weizmann.ac.il) suggest that
RecA performs "kinetic proofreading" in which RecA can precisely
identify a damaged strand and its length by using ATP (the
energy-delivering molecule in cells) to inspect (proofread) the
DNA's binding energy and to detach after a certain time delay (the
"kinetic" part) if the DNA has the "wrong" binding energy. (For
more on kinetic proofreading, see American Scientist, March-April
1978). The researchers argue that the RecA performs the precise
binding and unbinding actions that are necessary for kinetic
proofreading through "assembly fluctuations," a protein's structural
changes brought about by constant bonding and dissociation of RecA
from its target. According to the authors, this is the first known
biological process in which kinetic proofreading and assembly
fluctuations are combined (Tlusty et al., Physical Review Letters,
17 December 2004).
Meanwhile, researchers at L'Institut Curie in France (Kevin Dorfman,
Kevin.Dorfman@curie.fr and Jean-Louis Viovy,
Jean-Louis.Viovy@curie.fr) have studied how RecA exchanges a damaged
strand with a similar copy. In bacteria, RecA protein catalyzes
this process by binding to a healthy single DNA strand to form a
filament that "searches" for damaged double-stranded DNA (dsDNA). At
odds with the conventional view, they propose that the dsDNA which
needs to be repaired is the more active partner in this mutual
search. Unbound, it first diffuses towards the more rigid and thus
less mobile filament. In a second step, local fluctuations in the
structure of the dsDNA, caused only by thermal motion, allow the
base pairs of the filament to align and pair with the strand of
replacement DNA. (Dorfman et al, Phys. Rev. Lett., 31 December 2004)
STALACTITE: GEOMETRY AS DESTINY. Scientists at the University of
Arizona, bringing together ideas and observational techniques from
the physics and geophysics disciplines, have derived a mathematical
theory to explain the morphology of cave formations such as
stalactites (the carrot-like shapes hanging down from the roof) and
stalagmites (growing up from the
floor). The precipitative growth of speleotherms (the collective
name for cave shapes) is important since features of weather from
thousands of years ago can be unfolded from the layering in these
underground repositories, much as tree rings or ice core samples
render up clues to ancient climate. Stalactites are composed of
calcium carbonate precipitated from water entering the cave after
percolating through CO2-rich soil and rock Treating stalactite
growth as a "free boundary problem" (meaning that no a priori
assumptions were made as to the evolving shape of the speleothem),
the researchers linked the fluid dynamics and precipitative growth
to obtain a law for surface growth which produces a unique
"attractor" in the space of shapes (that is, a recurrent favored
shape or trajectory in the abstract space of possible morphologies),
one which closely matches observed shapes. Raymond Goldstein
(520-621-1065, gold@physics.arizona.edu) suggests that the new
theory should be applicable to other speleothem formations, and
highlights interesting related problems such as the growth of
hydrothermal vents, chemical gardens, and mollusk shells. (Short et
al., Physical Review Letters, 14 January 2005).
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PHYSICS NEWS UPDATE is a digest of physics news items arising
from physics meetings, physics journals, newspapers and
magazines, and other news sources. It is provided free of charge
as a way of broadly disseminating information about physics and
physicists. For that reason, you are free to post it, if you like,
where others can read it, providing only that you credit AIP.
Physics News Update appears approximately once a week.
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