New High Performance Magnet Structures for Bead Based Molecular Separation David HumphriesLawrence Berkeley National Laboratory, D.O.E. Joint Genome Institute Abstract High performance Hybrid magnetic separation technology is under continuing development at the D.O.E. Joint Genome Institute and Lawrence Berkeley National Laboratory for general laboratory and high throughput automated applications. This technology has broad applicability for molecular separation in genomics, proteomics and other areas. It s applicability ranges from large and small scale microtiter plate and flow separation processes to single molecule DNA manipulation. It is currently an enabling purification technology for very high throughput production sequencing at the D.O.E. Joint Genome Institute. This technology incorporates hybrid magnetic structures that combine linear permanent magnet material and ferromagnetic material to produce significantly higher fields and gradients than those of currently available commercial devices. These structures incorporate ferromagnetic poles that can be easily shaped to produce complex field distributions for specialized applications. The higher maximum fields and strong gradients of the hybrid structures result in greater holding forces on magnetized targets that are being processed as well as faster extraction. Current development versions of these magnet plates have exhibited fields in excess of 1.0 tesla and gradients approaching 1000.0 tesla/meter. Second generation Hybrid magnet plates have now been developed for both 384 and 96-well applications. This technology is currently being made available to industry through the Tech Transfer Department at Lawrence Berkeley National Laboratory.This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program and the by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-6SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36.

We have developed an automated purification method for terminator sequencing products based on a magnetic bead technology. This 384-well protocol generates labeled DNA fragments that are essentially free of contaminates for less than $0.005 per reaction. In comparison to laborious ethanol precipitation protocols, this method increases the phred20 read length by forty bases with various DNA templates such as PCR fragments, Plasmids, Cosmids and RCA products. Our method eliminates centrifugation and is compatible with both the MegaBACE 1000 and ABI Prism 3700 capillary instruments. As of September 2001, this method has produced over 1.6 million samples with 93 percent averaging 620 phred20 bases as part of Joint Genome Institutes Production Process.

A new class of magnet plates for biological and industrial applications has recently been developed at the D.O.E. Joint Genome Institute and Lawrence Berkeley National Laboratory (JGI/LBNL). These devices utilize hybrid technology that combines linear permanent magnet material and ferromagnetic material to produce significantly higher fields and gradients than currently available commercial magnet plates. These hybrid structures incorporate ferromagnetic poles that can be easily shaped to produce complex field distributions for specialized applications. The higher maximum fields and strong gradients of the hybrid structures result in greater holding forces on magnetized targets that are being processed as well as faster draw-down. Current development versions of these magnet plates have exhibited maximum fields in excess of 9000.0 Gauss. The design of these structures is easily scalable to allow for field increases to significantly above 1.0 tesla (10000.0 gauss). Author's note: 11000.0 Gauss peak fields have been achieved as of January 2005.