DNA Shearing for 454

alanc · 11-07-2008, 02:08 AM

I came across this technology for DNA shearing http://www.kbioscience.co.uk/instrum...ept%202008.pdf. Has anyone got any experience with this technology?

jOn · 11-08-2008, 06:10 AM

I saw this poster being presented at a recent GS-FLX user’s group meeting in London. I got the impression that 454 Branford had primarily implemented this technology in order to scale up their sample throughput.

gilly · 11-27-2008, 02:13 AM

Using the Covaris for shearing DNA has both advantages and disadvantages.

On the plus side you can massively reduce the amount of input DNA, we’ve made shotgun libraries using 500 ng of DNA. On the down side however it’s not as reproducible as using nebulisation.

The attached are screenshots of Agilent traces (without SPRI bead clean up) where the following settings have been used:
Duty cycle = 20%
Intensity = 3
Cycle burst = 200
Time = 45 seconds.

Peak on 1 is at around 640 bp and about 100 bases lover on 2.

Both samples contain 5 ug of DNA in 100 ul of TE. The smaller sized tube was used (max capacity 130 ul) with the fiber in place. It’s also important to use the metal crimped cap as lots of the energy is lost using the plastic ones.

As things stand I wouldn't recommend switching all DNA shearing over to this system but it can be very useful when less starting material is available.

Anthony · 02-26-2009, 03:27 AM

The graphs seem to indicate that there may be a sample viscosity issue and you might want to try some of the following ideas,
-What is the mass of DNA, if it is more than 3ug it is worth trying a "pre-conditioning step"
Simply raise waterbath to 20degC and run a short "blast" 5 secs, (20% duty cycle, level 5 intensity, 200 cycles per burst) prior to the desired fragmentation dose. Up to 20ug/100ul have been run under these conditions.

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11-07-2008, 02:08 AM	#1
alanc Junior Member Location: Netherlands Join Date: Nov 2008 Posts: 3	DNA Shearing for 454 I came across this technology for DNA shearing http://www.kbioscience.co.uk/instrum...ept%202008.pdf. Has anyone got any experience with this technology?

02-26-2009, 03:27 AM	#4
Anthony Junior Member Location: West London Join Date: Feb 2009 Posts: 2	The graphs seem to indicate that there may be a sample viscosity issue and you might want to try some of the following ideas, -What is the mass of DNA, if it is more than 3ug it is worth trying a "pre-conditioning step" Simply raise waterbath to 20degC and run a short "blast" 5 secs, (20% duty cycle, level 5 intensity, 200 cycles per burst) prior to the desired fragmentation dose. Up to 20ug/100ul have been run under these conditions. Last edited by Anthony; 02-26-2009 at 09:15 AM.

11-08-2008, 06:10 AM	#2
jOn Member Location: UK Join Date: Oct 2008 Posts: 19	I saw this poster being presented at a recent GS-FLX user’s group meeting in London. I got the impression that 454 Branford had primarily implemented this technology in order to scale up their sample throughput.

11-27-2008, 02:13 AM	#3
gilly Junior Member Location: East of England Join Date: Nov 2008 Posts: 8	Using the Covaris for shearing DNA has both advantages and disadvantages. On the plus side you can massively reduce the amount of input DNA, we’ve made shotgun libraries using 500 ng of DNA. On the down side however it’s not as reproducible as using nebulisation. The attached are screenshots of Agilent traces (without SPRI bead clean up) where the following settings have been used: Duty cycle = 20% Intensity = 3 Cycle burst = 200 Time = 45 seconds. Peak on 1 is at around 640 bp and about 100 bases lover on 2. Both samples contain 5 ug of DNA in 100 ul of TE. The smaller sized tube was used (max capacity 130 ul) with the fiber in place. It’s also important to use the metal crimped cap as lots of the energy is lost using the plastic ones. As things stand I wouldn't recommend switching all DNA shearing over to this system but it can be very useful when less starting material is available.