Silica
passivating agents have shown great success in minimizing
nonspecific protein binding to glass surfaces for imaging and microscopy
applications. Amine-derivatized surfaces are commonly used in conjugation
with amide coupling agents to immobilize peptides/proteins through
C-terminal or side-chain carboxylic acids. In the case of the single-molecule
fluorosequencing of peptides, attachment occurs via the C-terminus
and nonspecific surface binding has previously been a source of error
in peptide identification. Here, we employ fluorosequencing as a high-throughput,
single-molecule sensitivity assay to identify and quantify the extent
of nonspecific binding of peptides to amine-derivatized surfaces.
We show that there is little improvement when using common passivating
agents in combination with the surface derivatizing agent 3-aminopropyl-triethoxysilane
(APTES) to couple the peptides to the modified surface. Furthermore,
many xanthene fluorophores have carboxylic acids in the appended phenyl
ring at positions ortho and meta or ortho and para, and the literature
shows that conjugation through the ortho position is not favored.
Because xanthene-derived fluorophores are commonly used for single-molecule
applications, we devised a novel assay to probe the conjugation of
peptides via their fluorophores relative to their C-termini on silane-derivatized
surfaces. We find significant attachment to the ortho position, which
is a warning to those attempting to immobilize fluorophore-labeled
peptides to silica surfaces via amide coupling agents. However, eliminating
all amines on the surface by switching to 3-azidopropyl-triethoxysilane
(AzTES) for coupling via copper-catalyzed azide–alkyne cycloaddition
(CuAAC) and omitting additional passivation agents allowed us to achieve
a high level of C-terminally bound peptides relative to nonspecifically
or ortho-phenyl-bound, fluorophore-labeled peptides. This strategy
substantially improves the specificity of peptide immobilization for
single-molecule fluorosequencing experiments.