DNA sequencing arrays and Magnetotactic Bacteria

Prof McIntyre

Prof Teizer

 

McIntyre’s group has developed a novel architecture for integrating arrays of DNA probes on nanoscale porous silicon substrates.[i] His group is developing the arrays for applications in expression analysis, mutation detection, DNA fingerprinting, and DNA screening. The architecture, shown in Figure 1, offers several important advantages over current DNA probe array technologies:

§         it achieves rapid attachment of probes (complete in 30 seconds ® manufacturability)

§         it achieves rapid hybridization (complete in 2 minutes ® fast processing)

§         it detects low levels of expression (all sample presented to all probes ® sensitivity)

§         it enables sequential hybridization to a second probe set (reject single-base mismatch noise)

Nanolithographic technology brings the same benefits to DNA sequencing that is brings to microelectronics: uniform response, reduction in size of expensive probes, and manufacturability (many applications project the need for ~1 Mio. chips/year at a cost of <$10/chip). The TAMU nanoscale array uses advanced nano-fluidic techniques to achieve these improvements.  Anodic etching is used to produce an array of cells, each containing a dense pattern of columnar pores, each 3 mm diameter, extending all the way through the device to create a flowthrough geometry.


We use soft-gel lithography to fabricate “smart gaskets” that seal to both faces of the array and channel fluid flow so that all single-strand DNA (ssDNA) from the sample can be exposed to all probe sequences.  The efficient use of sample DNA yields a 100-fold improvement of sensitivity to low levels of expression without the need for polymerized chain reaction amplification, which is expensive and time consuming.

 

 

 

 

 


 

Figure 1.  ODE seed pits and anodically etched pores in DNA sequencing array.

In a separate project, McIntyre’s group is beginning the development of concepts to fabricate regular surface arrays of single-domain magnetite crystalites, ~100 nm scale.  Remarkably such crystals are synthesized in the gut of magnetotactic bacteria (to be found in ordinary pond water!).  Each bacterium synthesizes an ordered string of such crystallites, as shown in Figure 2.  The group is investigating ways to separate the crystallites from the bacteria after digestion, and to separate the crystallites from one another in each string. By applying nanolithography, Teizer and McIntyre intend to devise a self-assembling strategy for attachment of the separated crystallites on the sites of a high-density porous array etched in aluminum on site spacings of ~200 nm. Such arrays might be used for high-density memory, and for creating the trapping fields for atom chips.


 

 

 

 

 

 

 

Figure 2.  SEM micrograph of single-domain magnetite crystallites taken from magnetotactic bacteria.[ii]


 

[i] K.L.  Beattie et al., “Advances in Genosensor Research”, Clin. Chem. 41, 700-706 (1995).

[ii] I.F. Snowball, “Bacterial magnetite and the magnetic properties of sediments in a Swedish lake”, Earth and Planetary Sci. 126, 129-142 (1994).