Use of the environmentally sensitive fluorophore 4‐N,N‐dimethylamino‐1,8‐naphthalimide to study peptoid helix structures

Abstract Peptoids, oligomers of N ‐substituted glycine, have been valuable targets for study and diverse application as peptidomimetics and as nanomaterials. Their conformational heterogeneity has made the study of peptoid structures using high‐resolution analyses challenging, limiting our understanding of the physiochemical features that mediate peptoid folding. Here, we introduce a new method for the study of peptoid structure that relies on the environmentally sensitive fluorescence properties of 4‐ N,N ‐dimethylamino‐1,8‐naphthalimide (4‐DMN). We have prepared a 4‐DMN‐functionalized primary amine that is compatible with the traditional submonomer peptoid synthesis methods and incorporated it sequence‐specifically into 11 of 13 new peptoids. When included as a peptoid side chain modification, the fluorescence emission intensity of 4‐DMN correlates with predictions of the fluorophore's local polarity within a putative structure. 4‐DMN fluorescence is maximized when the fluorophore is placed in the middle of the hydrophobic face of an amphiphilic helical peptoid. When the fluorophore is placed near the peptoid terminus or on a polar face of an amphiphilic sequence, 4‐DMN fluorescence is diminished. Disruption of the peptoid secondary structure or amphiphilicity also modulates 4‐DMN fluorescence. The peptoids' helical secondary structures are moderately disrupted by inclusion of a 4‐DMN‐modified side chain as evaluated by changes in the peptoids' CD spectral features. This new method for peptoid structure evaluation should be a valuable complement to existing peptoid structural analysis tools. © 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 96: 627–638, 2011.