DNA unwinding and SSBinding protein.txt

The hexamer at the unwiding junction interacts with one DNA strand through its central channel. The excluded strand and duplex DNA do not interact tightly. The force producing unidirectional translocation leads to separation of duplex base pairs .

The helicase interacts tightly with both the separated strands. The rotation of one strand with respect to the other results in unwinding of duplex DNA.

The hexamer interacs with one of the separated strands in the central channel, and also it interacts with the dsDNA on the outer parts of the hexamer. Helicases encounter a region of double helix they continue to move along their strand prying apart the double helix. The duplex region is melted by the helicase, and the helicase translocates unidirectionally along the DNA in the central channel.

• There are three different models of DNA unwinding:
• 1. The wedge model
• 2. The torsional model
• 3. The helix destabilizing model.

SSBP (single stranded binding proteins) are homotetramers that bind to exposed ssDNA strands without covering the bases.

• 1. Protect ssDNA from degradation.
• 2. Control what proteins have access to the ssDNA.
• 3. Aid helicases by stabilizing the unwound ssDNA.
• 4. ssDNA can bond to itself forming hairpin helices. SSB prevent formation of the hairpin helices that impede synthesis by DNA polymerase. They exhibit cooperative binding on the ss-lagging strand of the DNA.
• Model of Chi-DNA binding to SSB-proteins
• Unwinding of the Chi-DNA sequence is almost completely dependent on the SSB-proteins.
• Refer to MODEL

DNA sequences in E. coli that attenuate the nuclease activity of helicases

• 1) Add AB helicase advances along the DNA and unwinds the duplex to expose ssDNA for potential binding by SSB protein.
• 2) At low or 0 SSB concentrations the ssDNA rapidly reforms the duplex (pathway i) whereas at high SSB concentrations the ssDNA is stabilized by SSB (pathway ii).
• 3) Upon further ATP hydrolysis AddAB continues to translocate through the duplex and reannealing or unwinding continues.
• 4) AddAB continues to translocate but remains bound to Chi on the 3’ terminated strand.
• 5) This generates a ssDNA loop downstream of Chi which both prevents degradation of the 3’terminated strand and suppresses reannealing activating unwinding in pathway i.