Research in the Núñez Lab

The DNA double helix described by Watson and Crick in 1952 is beautiful, regular, symmetrical, canonical, even iconic, and yet that structure is also misleading because it seems so perfect, inviolate, and static. In reality, the DNA inside of our cells is scrunched and packaged; it binds a variety of ions, small molecules, and proteins; it's folded and looped; it wiggles, bends, and twists; it's being ripped open and copied; it's being damaged and repaired.  In short, it's dynamic and complex, and there is still a lot about it that we are still figuring out (which is exciting!).

In this lab, we explore how some of these complications intersect to affect the function of DNA. For example, how does DNA that has been damaged interact with the proteins that make up chromatin, and does that chromatin packaging make DNA repair more difficult?  Does damaged DNA move more dynamically than undamaged DNA?  Do other DNA shapes like quadruplexes actually form inside of cells and affect gene expression?  How do viral nucleic acids (DNA and RNA) interact with proteins?

To answer these questions we bring together tools of molecular biology, classical biochemistry, chemistry, and physics including  enzymatic and chemical modification of DNA, gel electrophoresis, mass spectrometry, nuclear magnetic resonance spectroscopy, and DNA pulling with optical tweezers.  

Biofilms are complex microbial communities that grow at interfaces.  Bacteria in biofilms are phenotypically different than their planktonic (free swimming) relatives; they adapt to the communal, sessile lifestyle by expressing a specific complement of genes that allows them to optimize their motility, adhesion, and metabolism for this specialized environment.  Within these communities bacteria organize themselves to form complex architectures, differentiate to carry out distinct roles, and communicate with other cells using small molecules in ways that were once thought to be characteristic only of eukaryotes.  

Biofilms are robust, dynamic, and difficult to control or destroy, which makes potential removal agents of great interest in medical, industrial, and agricultural settings. Our interest has focused on understanding how bacterial cells in these complex communities adhere to surfaces and to one another, and on understanding how biofilms might be broken down using biological agents including the bacterial predator Bdellovibrio bacteriovorus. 

Our favorite tool for examining bacterial biofilms is atomic force microscopy (AFM), a type of scanning probe microscopy. With AFM a very small, sharp probe is scanned across a surface, and small deflections of the probe are measured to detect changes in the topography of the surface.  With soft biological samples such as macromolecules and cells, AFM can routinely resolve structures that are tens or hundreds of nanometers in size. As optical microscopy is to vision, AFM is to Braille: because the tip touches the surface, the technique can potentially reveal not only information about shape and size, but also about tip-sample interactions involving texture, adhesion, and elasticity of the sample.  By adhering cells to the tip we can directly measure the forces associated with cell-cell interactions.