Although AFM cannot easily detect short stubby branches it is possible to visualise larger branched polysaccharide structures. In order to detect branches the molecules have to be deposited onto substrates in an extended form. Height measurements allow branching to be distinguished from overlapping molecules.
The starch polysaccharide amylose is known to contain a small fraction of branched molecules. By forming soluble helical complexes it is possible to deposit amylose as extended molecules. The majority of the molecules are semi-flexible chains. When the molecule loops back and crosses itself the height doubles marking the junction point with a bright spot. The small fraction of branched molecules shows no change in height at the junction point. Different types of branched structures can be visualised and characterised.
For some cell-wall polysaccharides (arabinoxylans and pectins) it has been possible to observe previously unsuspected branching of the polysaccharides through the use of AFM.
In the case of sugar beet pectin about 17% of the pectin molecules were found to be branched. Similar studies on water-soluble wheat pentosans showed that about 15% of the arabinoxylan molecules were found to be branched structures.
Present evidence suggests that the images represent branched backbones rather than extended neutral sugar side-chains.
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