Page Two

DNA STRAND SEPARATION

The seperation of DNA strands takes place as a result of the translocation of a helicase along the dsDNA. As the helicase moves down a DNA strand, it forces the two strands apart. This translocation is powered by the hydrolysis of NTPs.
(These two images depict the divergence of the strands. The green helix is the DNA binding domain.)

As learned in the DNA Binding section, the DNA is bound and unbound by the hydrolysis of NTPs and conformational changes associated with it. These conformational changes also serve as the mechanical force behind the translocation of the helicase. Exactly how the system of ssDNA catch and release moves the helicase is unknown, but some models have been proposed.

The two most popular models are the “inchworm” mechanism and the active rolling mechanism. The “inchworm” mechanism involves two DNA binding sites working in tandem. With one site bound to the DNA, the second site “inches” forward along the strand to bind a new section. The lagging site then releases the DNA strand and moves forward to repeat the process.

The active rolling mechanism also takes advantage of the multiple binding sites within the central channel of the helicase. In this model, with one site bound to the DNA, one of the neighboring sites (for example, the site on the right) would then bind further down the strand. As the first site releases the strand, the third site in succession rolls up and binds downstream of the second. This process continues with sites binding and releasing in turn.

The distance between any two binding sites on the helicase is not very large considering the central channel is only about 35 angstroms across. Regardless of what type of mechanism the helicase uses for translocation, the step size of the movement is about 4-5 bases or 1/2 turn of the DNA double helix. This means that the helicase binds to every 4th or 5th base on the strand. Even with such short “steps”, helicase speeds have recently been measured at 132 bases per second per hexamer at the sub-optimal temperature of 18 C^o. The helicase attains this speed by hydrolyzing NTP’s at a rate of 49+ per second per hexamer. This speed is necessary for DNA replication to occur in seconds instead of hours.

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	The seperation of DNA strands takes place as a result of the translocation of a helicase along the dsDNA. As the helicase moves down a DNA strand, it forces the two strands apart. This translocation is powered by the hydrolysis of NTPs. (These two images depict the divergence of the strands. The green helix is the DNA binding domain.)
	As learned in the DNA Binding section, the DNA is bound and unbound by the hydrolysis of NTPs and conformational changes associated with it. These conformational changes also serve as the mechanical force behind the translocation of the helicase. Exactly how the system of ssDNA catch and release moves the helicase is unknown, but some models have been proposed.
	The two most popular models are the “inchworm” mechanism and the active rolling mechanism. The “inchworm” mechanism involves two DNA binding sites working in tandem. With one site bound to the DNA, the second site “inches” forward along the strand to bind a new section. The lagging site then releases the DNA strand and moves forward to repeat the process.
	The active rolling mechanism also takes advantage of the multiple binding sites within the central channel of the helicase. In this model, with one site bound to the DNA, one of the neighboring sites (for example, the site on the right) would then bind further down the strand. As the first site releases the strand, the third site in succession rolls up and binds downstream of the second. This process continues with sites binding and releasing in turn.
	The distance between any two binding sites on the helicase is not very large considering the central channel is only about 35 angstroms across. Regardless of what type of mechanism the helicase uses for translocation, the step size of the movement is about 4-5 bases or 1/2 turn of the DNA double helix. This means that the helicase binds to every 4th or 5th base on the strand. Even with such short “steps”, helicase speeds have recently been measured at 132 bases per second per hexamer at the sub-optimal temperature of 18 C^o. The helicase attains this speed by hydrolyzing NTP’s at a rate of 49+ per second per hexamer. This speed is necessary for DNA replication to occur in seconds instead of hours.