9/5/2003 -- A DNA sequence that acts as a
throttle to control the rate at which an enzyme moves along
the DNA has been observed by researchers at UC Davis. By
controlling the activity of the RecBCD helicase enzyme, the
"Chi" sequence can affect how efficiently genes are
RecBCD unwinds the DNA double helix so that the
genetic code can be read, copied or repaired. This unwinding
is an essential first step in most processes involving
The research findings, which are published in
the September 5 issue of the journal Cell, could explain how
short DNA sequences such as Chi can interact with enzymes and
affect how DNA is copied or repaired. They could also give
insight into how to control the speed of tiny nanomachines
built for various purposes.
The enzyme moves along DNA at a rate of up to
1000 base pairs a second. Using special apparatus to film
single enzymes at work in real time, the UC Davis researchers
found that when RecBCD reaches the eight-letter Chi sequence,
it stops for up to 10 seconds and then carries on at half
The researchers attached DNA molecules labeled
with a fluorescent dye to polystyrene beads one-millionth of a
millimeter in size. Under the microscope, the bead looks like
a white sphere with a bright string of DNA attached.
The researchers were postdoctoral scholars Maria
Spies, Piero Bianco, Mark Dillingham and Naofumi Handa with
Stephen Kowalczykowski, professor of microbiology and director
of the UC Davis Center for Genes and Development, and Ronald
Baskin, professor of molecular and cell biology.
They let RecBCD attach to the free end of the
DNA strand, and used laser beams as "optical tweezers" to move
the beads into position under a microscope.
As RecBCD unwinds the DNA strands, the
fluorescent dye is removed, so the bright string of DNA
appears to shorten.
When the researchers put RecBCD onto DNA
molecules carrying the Chi sequence, they found that RecBCD
stops for up to 10 seconds when it reaches the beginning of
the Chi sequence, then continues at a slower rate.
"It's a complete surprise," Kowalczykowski said.
The results would have been impossible to find with a
conventional bulk experiment averaging the activity of many
enzymes and DNA molecules, he said.
RecBCD is a molecular machine made up of three
proteins. Two of these are motor units that propel the enzyme
along the DNA double helix. Kowalczykowski believes that the
change in velocity is due to one of two motor subunits in
RecBCD being switched off by the Chi sequence.
The Chi sequence is known to be associated with
"hotspots" where genes are readily exchanged, or recombined,
Andy Fell, UC Davis News Service, (530)
Source: University of California - Davis