Forced Peptide Synthesis in Nanoscale Confinement under Elastomeric Stamps

Abstract

In solution, only collisions between molecules of sufficient energy to overcome the activation barrier lead to the formation of reaction products. The rate of the reaction is influenced by the temperature, concentration of the reactants, solvent, orientation of the reactants, and structure of the molecules. Catalysts or enzymes lower the activation energy by making available alternative reaction pathways and preorganize the reactant molecules in close proximity, which leads to an increase in the effective concentration of the reactants. [1] Herein, we report the first example in which a reaction (amide-bond formation) is made possible because the reactant molecules are physically pushed together. An elastomeric stamp (as used in microcontact printing [2] ) comes into conformal (van der Waals) contact with a functionalized surface, [3] thus forcing "ink" molecules very close to the surface. We speculate that the nanoscale confinement of the ink at the interface between the stamp and the selfassembled monolayer (SAM), in combination with the preorganization of the reactants in the monolayer, facilitates the formation of covalent bonds.The on-chip synthesis of singlestrand DNA molecules has revolutionized genotyping research. Fodor and co-workers [4,5] developed photolithographic techniques in combination with wet surface chemistry to attain > 99 % yield in coupling steps for the preparation of libraries of peptides or oligonucleotides. Usually, a range of catalysts and activated substrates are required for efficient covalent-bond formation on surfaces. In our research on patterned self-assembled monolayers, we were intrigued by the rapid and efficient formation of SAMs on gold or Si/SiO 2 through the use of microcontact printing (mCP). [2] When an elastomeric stamp inked with trichloroalkyl silanes is placed on a clean Si/SiO 2 surface, the formation of the polysiloxane network is essentially complete within minutes, whereas this process could take hours in solution. Microcontact printing has previously been used to couple molecules to a reactive surface, but in all cases a catalyst or activated substrate was used to induce covalentbond formation. [6][7][8][9] Herein we report the formation of new bonds solely as a result of the nanoscale confinement of molecules between stamp and surface.Amide-bond formation is a suitably challenging test case, as such reactions require catalysts (4-(dimethylamino)pyridine (DMAP), N-hydroxybenzotriazole (HOBT), or dicyclohexylcarbodiimide (DCC)) or elevated temperatures and long reaction times when performed in solution. In a typical reaction (Figure 1), we prepared a clean amine-terminated SAM surface on gold. To ensure all amines were deprotonated, we washed the surface with a saturated solution of K 2 CO 3 . A flat hydrophilic stamp (treated for 30 s with an oxygen plasma and stored under millipore water) was inked with a solution of an appropriate Boc-protected amino acid (1 mm) in ethanol, dried under a stream of nitrogen, and placed on this surface. If necessary the sample w...

Covalent Microcontact Printing of Proteins for Cell Patterning

“…[14] Recently, Huck and co-workers [15] proposed the application of mCP for the in situ synthesis of oligopeptides exclusively in the contact areas between substrate and the poly-(dimethylsiloxane) (PDMS) stamp. The advantage of covalent mCP of peptides is that a chemical bond is formed between the protein and the substrate SAM.…”

“…The FT-IRRAS spectra of SAM 3 (obtained by 1 h of chemisorption of col3a1 from solution) and SAM 3* (obtained by 15 min of mCP with a flat, featureless stamp) are virtually identical, once more confirming the remarkable efficiency of the immobilization reaction in the confinement between stamp and substrate. [15,20] However, the amine band is shifted to higher wavenumbers and also the ratios of amide I to amide II are not equal for SAM 3 and SAM 3*, which could indicate differences in hydration and orientation of the protein layers.…”

Nanoscale Data Storage

“…The results suggested that such nanomemory system can operate at a density of no less than 10 11 bits/cm 2 . To solve the problem of double junctions, the molecule of interest can be controllably deposited onto the desired locations of the nanowire/tube using techniques such as dip-pen nanolithography and stamp-printing method [90,91]. D. Etching hole plus nanotube and Nanopore molecular junctions A silicon/molecule/nanotube approach has been developed as a testbed for fabrication of metalfree molecular junctions, i.e., etching hole plus nanotube method [52].…”

“…These studies were mostly focused on the synthesis, organization/immobilization, modification, and simple characterization of the biomaterials [148]. Although, it was realized to controllably deposit molecules of interest to desired locations on substrate using AFM based dippen nanolithography [90] and/or stamp printing methods [91]. Electrical properties of single biomaterial were measured using CAFM or STM in combination with nanoparticles [151].…”

Self‐Assembly Meets Nanofabrication: Recent Developments in Microcontact Printing and Dip‐Pen Nanolithography

“…Whether this is sufficient to explain the formation of highly ordered SAMs is not clear, as there are no detailed studies of SAM formation in neat alkanethiols. Intriguingly though, chemical reactions leading to new covalent bonds between SAM end groups and molecules printed on top using μCP also seem to proceed much faster and without requiring activated functional groups or catalysts 20. 21 The formation of amide bonds between amine‐terminated SAMs and carboxylic acid “inks” seems to proceed without the need for activated esters or catalysts, and the effect is only observed when the “inks” are pressed onto the surface using PDMS stamps 20.…”