Week 5 L2: RECOMBINATION- Holiday Junction Flashcards
What is the Holliday Junction?
A four-way intermediate
central intermediate in genetic recombination
-four-way connection between 4 DNA helices
How are the 4 stands connected?
by their continuity
What are the 2 possible conformations of the Holliday Junction?
extended: 4 strands pointing to different corners
Stacked X structure, tightly bound.
What induces the Stacked X-structure?
ion-induced folding
e.g. Mg+
How do we get from the extended to stacked structure?
1) Pairwise coaxial staking e.g. 1 & 4, 2&3
2) rotation of axis to a scissor shape. 2&4 forwards 3&1 back
What is the issue of the first step in Holliday stacking?
helixes are side-by-side, axial to one another.
A lot of clash between the backbones and a lot of electrostatic repulsion. etc.
How do we overcome the issue of axial clashing?
rotate axis like a pair of scissors II –> X shape
What happens to symmetry from extended to stacked structure?
4-fold (4 equivalent strands)–> 2-fold (2 equivalent strands)
What 2 kinds of strand are in stacked structure?
continuous and exchanging
antiparallel structure.
What are the continuous strands?
from front view it is the ends which are both facing towards you.
run from one end to the other or a coaxial helices.
Are there alternative conformers in stacking?
yes
How can we observe the different confomers?
spectroscopic method: fluorescence resonance energy transfer
How is FRET carried out?
attach 2 different flurophores, one called donor, one called acceptor.
What are the 2 different flurophores?
donor and acceptor
What happens when the 2 diff flurophores are close together?
High FRET
enhances flurensence
