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A fundamental feature of life is the interaction between its component parts, without which life would not exist. Interaction occurs at all levels. At the molecular level, proteins and nucleic acids form complexes that create the structural and functional entity, which is the cell. Cells interact to form multicellular organisms (eukaryotes) or communities (prokaryotes). At both the molecular and cellular levels, interaction involves communication in addition to association. It is by way of these communications that most of the miracles of nature are achieved. We are interested in understanding how molecules and cells coordinate their activities to achieve functions that they cannot do individually.  Read more about


Plant health and growth is tied to the communications that occur under the soil with the microbial community that makes up the rhizosphere, a thin film around the roots of each plant. The plant provides nutrients to attract microbes and sends out enzymes and chemicals to fight off pathogens. To now, understanding the communications between plants and microbes in the soil has required removing the rhizosphere and analyzing it in the laboratory.

Growth factors regulate proliferation and cellular activities that result in coordinated growth and differentiation of animal tissues. To achieve their effects, growth factors regulate gene expression and thus the production of new proteins. Proteins that are secreted are often involved in coordinating cell growth in multicellular tissues. Dr. Nilsen-Hamilton has discovered several secreted proteins that are regulated by growth factors.

Many biological agents, such as viruses and bacterial toxins, could be used to threaten a Nation if they were in the wrong hands. To protect ourselves against such threats, we are developing sensors based on aptamers that can detect these threats in the air and give early warning of their presence.

To understand how cells communicate, the most desirable condition is to monitor them while in their natural state surrounded by other cells as in the tissue. To accomplish this, reporters are needed with signals that can be read from living cells. Although protein reporters have been used for many years, they have the major disadvantage that they provide a signal that is delayed many hours after the gene is activated. RNA aptamers can fold to their active forms inside cells and are a good option as components of reporters that give an immediate signal of transcription.

The presence of mobile aptamers ​in the cell presents the possibility that they would bind their small molecule targets and move them away from the membrane, thereby increasing the intracellular concentration of the aptamer target by preventing its export. This would provide a means of increasing the effectiveness of drugs.

Aptamers can be selected to be highly specific and to have high affinities for their targets. They are also very stable to heat and long-term storage. The added advantage that aptamers generally change in structure upon binding their specific ligand makes it possible to incorporate them into a variety of analytical devises. The Nilsen-Hamilton lab has collaborated with several groups to select new aptamers, to understand how their structures are influenced by ligand binding, and to develop analytical instruments that use aptamers to detect biological compounds and chemicals.

Materials based on organized nanostructures can have unique properties. For example, small gold rings (split ring resonators) in nanometer scales can "bend" light in ways as to make what is behind them invisible. These are called metamaterials. We are using DNA to make templates for metamaterials that can be linked in 3D and coated with metals (either silver or gold) that convert the arrays of resonators. DNA structures are being created using several different procedures that include DNA origami, DNA tiling and ligation of restriction fragments.

The magnetotactic bacteria have in common the ability to create nanomagnets that they use for detecting the earth’s magnetic poles. It is believed that their benefit for making the magnetic nanoparticles is the directional information they receive from the nanomagnets aligned as a compass. Using this directional information the cells can quickly identify points of the compass so that they can then identify the vertical axis that allows them to move up and down in their water environment.