discovery is reported in an advanced online publication
of the journal Nature --Oct. 1.
within its double-helix structure, DNA contains the chemical
blueprint that guides all the processes that take place
within the cell and are essential for life. Therefore,
repairing damage and maintaining the integrity of its
DNA is one of the cells highest priorities.
at Vanderbilt University, Pennsylvania State University
and the University of Pittsburgh have discovered a fundamentally
new way that DNA-repair enzymes detect and fix damage to
the chemical bases that form the letters in the genetic
is a general belief that DNA is rock solid extremely
stable" says Brandt Eichman, associate
professor of biological sciences at Vanderbilt,
who directed the project. "Actually DNA
is highly reactive."
a good day about one million bases in the DNA
in a human cell are damaged. These lesions are
caused by a combination of normal chemical activity
within the cell and exposure to radiation and
toxins coming from environmental sources including
cigarette smoke, grilled foods and industrial
protein-DNA interactions at the atomic level
is important because it provides a clear starting
point for designing drugs that enhance or disrupt
these interactions in very specific ways,"says
Eichman. "So it could lead to improved
treatments for a variety of diseases, including
newly discovered mechanism detects and repairs
a common form of DNA damage called alkylation.
A number of environmental toxins and chemotherapy
drugs are alkylation agents that can attack
a DNA base becomes alkylated, it forms a lesion
that distorts the shape of the molecule enough
to prevent successful replication. If the lesion
occurs within a gene, the gene may stop functioning.
To make matters worse, there are dozens of different
types of alkylated DNA bases, each of which
has a different effect on replication.
method to repair such damage that all organisms
have evolved is called base excision repair.
In BER, special enzymes known as DNA glycosylases
travel down the DNA molecule scanning for these
lesions. When they encounter one, they break
the base pair bond and flip the deformed base
out of the DNA double helix. The enzyme contains
a specially shaped pocket that holds the deformed
base in place while detaching it without damaging
the backbone. This leaves a gap (called an "abasic
site") in the DNA that is repaired by another
set of enzymes.
cells contain a single glycosylase, named AAG,
that repairs alkylated bases. It is specialized
to detect and delete ethenoadenine bases, which
have been deformed by combining with highly
reactive, oxidized lipids in the body. AAG also
handles many other forms of akylation damage.
Many bacteria, however, have several types of
glycosylases that handle different types of
hard to figure out how glycosylases recognize
different types of alkylation damage from studying
AAG since it recognizes so many," says
Eichman. "So we have been studying bacterial
glycosylases to get additional insights into
the detection and repair process".
is how they discovered the bacterial glycosylase
AlkD with its unique detection and deletion
scheme. All the known glycosylases work in basically
the same fashion: They flip out the deformed
base and hold it in a special pocket while they
excise it. AlkD, by contrast, forces both the
deformed base and the base it is paired with
to flip to the outside of the double helix.
This appears to work because the enzyme only
operates on deformed bases that have picked
up an excess positive charge, making these bases
very unstable. If left alone, the deformed base
will detach spontaneously. But AlkD speeds up
the process by about 100 times. Eichman speculates
that the enzyme might also remain at the location
and attract additional repair enzymes to the
has a molecular structure that is considerably
different from that of other known DNA-binding
proteins or enzymes. However, its structure
may be similar to that of another class of enzymes
called DNA-dependent kinases. These are very
large molecules that possess a small active
site that plays a role in regulating the cells’
response to DNA damage. AlkD uses several rod-like
helical structures called HEAT repeats to grab
hold of DNA. Similar structures have been found
in the portion of DNA-dependent kinases with
no known function, raising the possibility that
they play an additional, unrecognized role in
new repair mechanism may also prove to be the
key to understanding the differences in the
way that the repair enzymes identify and repair
toxic and mutagenic lesions. That is important
because mutagenic lesions that the repair mechanisms
miss are copied to daughter cells and so can
spread whereas the deleterious effects of toxic
lesions are limited to the original cell.
these differences could lead to more effective
chemotherapy agents, Eichman points out. These
drugs are strong alkylating agents designed
to induce lesions in a cancer patient's DNA.
Because cancer cells are reproducing more rapidly
than the bodys normal cells, the agent kills
them preferentially. However, in addition to
toxic lesions that kill the cell, the agent
also produces lesions that cause mutations,
which can lead to additional complications.
Additionally, the efficacy of these drugs is
low because they are working against the body's
repair mechanisms. If it were possible to design
a chemo drug that predominantly creates toxic
lesions, however, it should be more effective
and have fewer harmful side effects. Alternatively,
if we understood how glycosylases recognize
alkylation damage, it may be possible to design
a drug that specifically inhibits repair of
toxic, but not mutagenic, lesions.
graduate student Emily H. Rubinson, A.S. Prakasha
Gowda and Thomas E. Spratt from Pennsylvania
State University College of Medicine and Barry
Gold from the University of Pittsburgh contributed
to the study, which was supported by grants
from the American Cancer Society, National Institutes
of Health and U.S. Department of Energy.
David Salisbury, (615) 322-NEWS