Number 715, January 11, 2005
by Phil Schewe and 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 (Tlustyet 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. (Dorfmanet 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 prior 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. (Shortet al., Physical Review Letters, 14 January 2005)
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