Topographies, anchoring

The analysis of biomolecules by AFM is sometimes [3] referred to as surface biology, as opposed to the so-called test-tube biology, because the immobilisation of oligonucleotides on sohd surfaces is central to the design, fabrication and operation of DNA-based microdevices, such as biosensors, DNA micro- and nanoarrays, microPCR and lab-on-a-chip devices. As the analysed biomolecules are in close contact and very often in intimate interaction with the surface, sample preparation for the AFM analysis of surface-immobihsed biomolecules is both critical and dehcate. The biomolecules need to be firmly anchored on the substrate, which has to have a sufficiently minimal or easily discriminated topography [1]. The Kleinschmidt method [6] for the DNA... 

P7 We will begin with a study of the topography of an n-alkanethiol self-assembled monolayer (SAM) anchored to a Au(lll) substrate. Alkanethiols will be attached to a Au(lll) substate by published methods. The SAM will be imaged by atomic force microscopy (AFM) to assure that the known structure is observed. (From Spain, 1997)... 

The sialyltransferases are membrane-bound proteins located in the endoplasmic reticulum (ER) and in the Golgi apparatus. Information about their sequence homology is limited, but they do appear to share a common topography [35]. A catalytic domain resides at the C-terminus followed by an N-terminal segment that anchors the enzyme into the ER or Golgi membrane. Soluble, catalytically active sialyltransferases that lack the anchor segment have been isolated from milk, serum, and other body fluids, suggesting that this N-terminal anchor is not necessary for the enzyme to retain catalytic activity. However, the ability to obtain from natural sources quantities of most sialyltransferases that would be needed for synthesis applications is hampered by low tissue concentrations and difficult purifications. 

Figures 6.7(a) and (b) show the topographies of films cast from maleate-stabilized latex, before and after rinsing, respectively. The film before rinsing showed hills , indicative of surfactant aggregates at the surface. After the film was rinsed with water, holes appeared in a regular pattern. This is indicative of removal of surfactant from the surface. The situation is much improved compared to the appearance of the films from the SDS-based latex but, evidently, even with the reactive maleate surfactant, a substantial portion is not anchored to the latex particle. Chemical analysis showed that about 1/3 of the surfactant was not chemically incorporated into the film.

Micro topography On smooth surfaces, the cells are able to spread, perhaps forming greater number of hemi-desmosomes as anchors to the substrate. In contrast, on rougher surfaces, the cells appear to form local contacts that allow the cells to span across the space between surfaces [21]. 

Figure 4. The three main substrate classes (a) smooth surfaces on which surface molecules have a definite orientational distribution (represented surface obtained on a rubbed polyimide film [52]) (b) interpenetrable surfaces of dangling chains (c) topographies (represented grooved surface) with a favorable (left) and unfavorable director field R. In all cases, a is the macroscopic anchoring direction.

Holes are next cut all the way through the first oxide layer (ANCHORl) to anchor structures defined in Polyl to the substrate after the PSG sacrificial spacer layer has been etched. An example is shown in Figure 1.8 [7]. Note that the polysilicon is a conformal coating, so that topographic features, such as the anchor holes, are replicated in the layers deposited on top of them. This replication of topography can give rise to mechanical interferences for features defined in the overlayers. 

Figure 8.6 Effect of OXIDEl anchor width on Polyl and Poly2 topographies with decreasing spacing. Starting from the top figure, the OXIDEl anchor width decreases from 5 pm, 3 pm, and 2 pm down to 1.5 pm (bottom). (Used with permission from Raji Krishnamoorthy Mali, Thomas Bifano, and David Koester, A design-based approach to planarization in multilayer surface micromachining, J. Micromechanical Microengineering 9, pp. 294-299 [1999].) [17].

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