Hi,
Thank you very much for your question. I had a very interesting time
researching the information for you. DNA replication with 100%
fidelity is a nice feature to keep offspring in just the genetic
background of the species. But to get there, or to evolve further,
requires genetical changes, one of which results from recombination of
(near) homologous parts of DNA.
"The nature of structural changes in DNA neccessary to result in
homologous genetic recombination were layed out by Holliday in 1964,
and in subsequent years the crossover-structures were visualized by
electron microscopy. The actual conformation of a DNA crossover was
speculated to be a four-way-junction with separate DNA helices, or
with stacked helices in either a parallel or an antiparallel
orientation of the helices. The models had to allow for branch
migration, else no exchange of genetic material would happen.
Homologous genetic recombination is a highly dynamic process, in
contrast to X-ray crystallography relaying on static structures. So it
took to the end of the previous millenium to get an atomic detail view
of relevant structures..."
http://www.biologie.uni-hamburg.de/lehre/bza/holliday/4wjdna.htm
Brief Backgroud of the Holliday Junction:
Scientists, by the year 1999 were finally seeing the four-way DNA
junction proposed by Robin Holliday in 1964. The Holliday junction as
it is now known is a model that explains recombination of genes and
DNA repair events.This model of recombination was first proposed by
Robin Holliday and re-established by David Dressler and Huntington
Potter in 1976 who demonstrated that the proposed physical
intermediates existed. They published the results of a series of
experiments that demonstrated the validity of the Holliday model of
recombination.They used E. coli cells containing the colicin E1
derived plasmid, pMB9. This plasmid was one of the very earliest
plasmids developed for cloning in Herbert Boyer's laboratory.
"By 1988 David Lilley, professor of biochemistry at the University of
Dundee, United Kingdom, solved the structure in solution, but it took
another 10 years to solve the actual crystal structure. "People have
tried to design their molecules cleverly, but none of it has worked.
The curious thing is, two crystal structures [have been determined] in
the past several months, and both were obtained completely by
accident," says Lilley. Gerald Joyce , professor of biochemistry at
The Scripps Research Institute, was trying to crystallize a DNA enzyme
complex with an RNA substrate when it dimerized, forming a four-way
junction of two DNA strands and two RNA strands. Recently Miquel Coll,
from the Institut de Biologia Molecular de Barcelona, Spain,
crystallized a true Holliday junction when studying a DNA duplex
containing central consecutive adenine-guanine mismatches The
structures found by both groups support the Holliday junction model
formed over the years. Joyce comments, "We were stunned by how closely
[our structure] matches up with the proposals." Technically, the
molecule from the Joyce lab is not a Holliday junction, since it is
formed of RNA and DNA strands"
Sources for the above information and further details on background:
1)J. Nowakowski et al., "Crystal structure of an 82-nucleotide RNA-DNA
complex formed by the 10-23 DNA enzyme," Nature Structural Biology,
6:151-6, February 1999
2)M. Ortiz-Lombardia et al., "Crystal structure of a DNA Holliday
junction," Nature Structural Biology, 6:913-7, October 1999
These journals should be available in an good library.
Structural Formation:
A number of models have been put forth over the years to explain how
DNA recombination occurs. The basis of these models lies in what has
been learned of recombination from yeast and other fungi.Recombination
plays an important role in many aspects.For example, the process of
introducing genetic variation by allowing genes to be reassorted into
different combinations.Genetic recombination results in the exchange
of genes between paired homologous chromosomes during meiosis.
The Original Model that was proposed:
1) Single-stranded nicks are introduced at the same position on both
parental DNA molecules.
2) Each nicked strand then invades the other DNA molecule by
complementary base pairing
3) Ligation produces a crossed-strand intermediate called a Holliday
junction
4) Once a Holliday junction is formed, it can be resolved by nicking
and rejoining of the crossed strands to yield recombinant or
nonrecombinant heteroduplexes.
1975 revision of Holliday model:
"Recombination is initiated by one nick only (more likely!). The
nicked strand is then displaced, and invades the other homologous DNA
molecule by homologous base pairing. This process produces a displaced
loop of single-stranded DNA, which can then be cleaved and joined to
the other parental molecule. The result is a crossed-strand Holliday
junction as before, resolved as before into recombinant or
nonrecombinant heteroduplex molecules..."
http://bioweb.wku.edu/courses/biol22000/16Recombination/Text.html
When strand exchange occurs between two DNA duplexes, they become
linked by a structure known as a Holliday junction.
There are basically two models involved in the study of the Holliday
Junction in today's DNA Research:
1) A Simple ( basic) model
2) A More Realistic Model
In the Simple Model the basic steps involved are:
a) two homologous DNA molecules are initially aligned suitably for the
process to occur.
b) The DNA is nicked at the same place on the two molecules. (This
must happen in strands with the same polarity.)
c) no the strands and ligate are exchanged and thus an intermediate is
formed. (The intermediate that is formed is called a Holliday
intermediate or Holliday structure. The shape of this intermediate is
pretty similar to that of the greek letter chi, hence this is also
called a chi form.)
d) Structure Resolvation. There are two ways in which this can happen:
(i) If the same strands are cleaved a second time then the original
two DNA molecules are generated:
(ii) If the other strands are cleaved, then
recombinant molecules are generated.
You can see a more graphic description of the above process including
the Realistic Model here:
"Step by Step explanation of the The Holliday Model of Genetic
Recombination - Two Models"
http://www.mun.ca/biochem/courses/3107/Lectures/Topics/Recombination_holliday.html
I have also found a beautiful animated description of the entire
process created at the University of Wisconsin(Madison), I think you
will love this:
http://engels.genetics.wisc.edu/Holliday/index.html
Another excellent representation. This animated website that has very
clear pictures with a nice, easy-to-understand format:
http://engels.genetics.wisc.edu/Holliday/holliday3D.html
The functional aspects of the Holliday Junction will become clear from
these links. I have also looked at various other resources for
information on the participation of this junction in recombination. I
have listed these resources below for your reference.
Additional Link for further reference:
"Structure of the Recombination Protein RuvA and a model for its
Binding to Holliday Junction"
http://www.sdsc.edu/journals/mbb/ruva.html
"Different Structural Steps involved in the Holliday Junction"
http://www.web-books.com/MoBio/Free/Ch8D2.htm
Resource material for Genetics and biology:
http://www.cmb.uab.edu/courses/2002/CMBII/Higgins101102/higgins.pdf
"Holliday Junction Parallelogram DNA Arrays"
http://seemanlab4.chem.nyu.edu/HJ.arrays.html
"Animation model of recombination - Holliday junction"
http://genetics.hannam.ac.kr/lecture/rec-anim.htm
http://www.biology.ucsc.edu/classes/bio115/Lectures/lecture%2015/Holliday%20animation/Holliday/
Search Strategy:
"Holliday Junction"
"Holliday Junction" DNA
recombination "Holliday Junction"
robin holliday DNA
I hope my research provides you with a clear understanding of the DNA
Holliday Junction. Thank you once again for the very interesting
question.
Warm Regards and Season's greetings,
Shiv Reddy |
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