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{at}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{at}curie.fr and
Jean-Louis Viovy, Jean-Louis.Viovy{at}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{at}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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