<p>Extracellular matrix (ECM) creates high-resolution chemical patterns, by assembling simple molecules with nm-scale features (e.g., carbohydrates, nucleotides, amino acids) into complex structures up to micrometers and extending to even larger scales across tissues (e.g., glycans, DNA, proteins), capable of carrying out the diverse and complex cellular functions. Mimicking the complexity of such biological systems requires precise control over the chemical patterning on substrates that exhibit physiochemical properties similar to biological systems (such as hydrogels). Although hydrogels provide tunable physiochemical properties suitable for biological applications; it is a porous material where pore sizes can range from 30 nm to greater than 1000 nm. Due to this structural heterogeneity, chemical patterning below the length scale of this heterogeneity is very challenging.</p> <p>Here, we demonstrate a new assembly system for generating a nanostructured presentation of carbohydrates on the hydrogel surface. This approach is based on the striped phases assembly of functional alkanes where 1-nm resolution functional patterns are readily assembled on substrates such as highly ordered pyrolytic graphite (HOPG). In this assembly, molecules are stabilized by noncovalent interactions, including alkyl-pi interactions underlying the HOPG, van der Waals interaction between the adjacent alkyl chains, and hydrogen bonding between polar head groups. Topochemical polymerization converts internal diynes into conjugated polydiacetylenes (PDAs). PDAs can also be utilized to covalently attach the striped pattern to polyacrylamide hydrogels through free radical chemistry.</p> <p>Here, we synthesize new amphiphiles with carbohydrate headgroups (N-acetyl-D-glucosamine (GlcNAc), and D-glucuronic acid (GlcA)), assembled into striped phases on HOPG and covalently transfer to polyacrylamide hydrogels. GlcNAc binds to wheat germ agglutinin (WGA), a lectin that binds specifically in a multivalent fashion (dissociation constant KD in nm range) to GlcNAc. We show that GlcNAc striped phases generate highly selective interactions with wheat germ agglutinin (WGA) but do not induce specific binding with concanavalin A (another lectin molecule that does not target GlcNAc). We further demonstrate that WGA binding affinity can be modulated by shifting the position of diacetylenes that bring the polymer backbone closer to the GlcNAc, increasing the effecting local concentration of carbohydrates.</p> <p>We investigated the possibility of using sPDA for secondary functionalization with complex biological molecules (such as biotin and cRGD) to mimic the ECM composition closely. The unusual reactivity of the sPDA backbones during the covalent transfer of the striped phase monolayer to hydrogels illustrates the potential of sPDA reactivity azides. In this work, we show that the addition of substituted azide molecules to sPDA-functionalized hydrogels produces a decrease in the fluorescence of the sPDA monolayer. Since these reactions are occurring on porous hydrogel surfaces characterization using techniques such as IR or NMR is difficult. We carried out further solution-phase reactions using a soluble PDA where PDA UV-vis absorption spectra red-shift after the reaction between the PDA backbone and azide. These experiments support the hypothesis of sPDA and azide click reaction.</p>