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Skriven 2005-01-11 22:08:27 av Herman Trivilino (1:106/2000.7)
Ärende: PNU 715
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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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 * Origin: Big Bang (1:106/2000.7)