Biomedical Engineering Reference
In-Depth Information
overall charge and hydrophobicity, but also a heterogeneous distribution of
these, depending on the types and distributions of surface-exposed groups.
The biomolecules of interest can be broadly grouped into nucleic acids
(DNA, RNA, PNA), proteins (antibodies, enzymes, receptors, a
bodies),
small molecules (e.g. peptides, metabolites) and other biomolecules (e.g. car-
bohydrates, lipids), of which the first two classes have been by far the most
studied with respect to microarray applications. Figures 2.1 and 2.2 depict
the distribution of charges and hydrophobicity on a single stranded oligonu-
cleotide and a protein (lysozyme), respectively. The oligonucleotide shows
more ordered and predictable patterns, with regularly-spaced negatively-
charged phosphate groups in the backbone region, and hydrophobic base pair-
ing regions. In contrast, proteins are characterized by both heterogeneous and
irregular regions of positive charge, negative charge, and hydrophobicity. As
we will see in the next section, the relative structural simplicity of DNA, as
compared to protein, results in more predictable and controllable patterns of
surface attachment.
Fig. 2.1.
Structure of a single stranded oligonucleotide (
left
) and the 3D map of
the electrostatic potential (darker patches = negative charges)
