We discuss a nanoengineering approach for supramolecular chemistry and self assembly. The collective properties and biofunctionalities of molecular ensembles depend not only on individual molecular building blocks but also on organization at the molecular or nanoscopic level. Complementary to ''bottom-up'' approaches, which construct supramolecular ensembles by the design and synthesis of functionalized small molecular units or large molecular motifs, nanofabrication explores whether individual units, such as small molecular ligands, or large molecules, such as proteins, can be positioned with nanometer precision. The separation and local environment can be engineered to control subsequent intermolecular interactions. Feature sizes as small as 2 ؋ 4 nm 2 (32 alkanethiol molecules) are produced. Proteins may be aligned along a 10-nm-wide line or within two-dimensional islands of desired geometry. These high-resolution engineering and imaging studies provide new and molecular-level insight into supramolecular chemistry and self-assembly processes in bioscience that are otherwise unobtainable, e.g., the influence of size, separation, orientation, and local environment of reaction sites. This nanofabrication methodology also offers a new strategy in construction of two-and three-dimensional supramolecular structures for cell, virus, and bacterial adhesion, as well as biomaterial and biodevice engineering. S upramolecular chemistry has become an area of intense research (1-4), partly inspired by biological ensembles in nature, such as collagen and enzymes or protein assemblies in general. In nature, the collective properties and biofunctionalities of these ensembles depend not only on the individual molecular units but also (perhaps even more importantly) on the organization at the molecular or nanoscopic level (1, 2, 4, 5). Such organization dependence can be attributed to polyvalent interactions in biological systems (6). ''Bottom-up'' approaches have been taken to mimic nature and have resulted in creative synthesis of small molecular units (7,8) and large molecular motifs (9). These molecular building blocks contain the desired charge, polarization, or chemical functionalities that will affect intermolecular interactions such as van der Waals forces, hydrogen bonding, polar attractions, and͞or hydrophobic interactions (7-9). These interactions dictate the subsequent assembly into supramolecular structures (4, 9-11). Complementary to these synthetic approaches, we explore whether individual units such as small molecular ligands or large molecules such as proteins can be positioned with nanometer precision by using nanoengineering methodologies. The separation and local environment can be engineered to influence subsequent intermolecular interactions.Micrometer-sized patterns of biomolecules can be produced by using relatively well known microfabrication technologies. Without using templates, DNA micropatterns may be directly produced by using photolithography (12)(13)(14). Micropatterns of proteins have also been ...