Figuring out DNA looping with unbelievably advanced technology

An article just out in PLOS Biology explores one of the most important, but also difficult to observe, phenomena related to DNA regulation.

Figure 1 from the paper: "Atomic Force Microscopy of Lac Repressor-DNA Complexes (A) Schematic structures of biotin (bio)- and digoxigenin (dig)-labeled DNA constructs with one (O-539 and O-349) or two (O-153-O and O-158-O) ideal lac operator sequences (white bars)... (B) AFM image of molecules adsorbed to a mica surface ... (C) Scatter plot of the DNA arm contour lengths in repressor-DNA complexes....(D and E) Left: projection images of two alternative three-dimensional structural models of looped complexes between Lac repressor (gray) and DNA (black) with two operators spaced approximately 50 nm apart. Right: the corresponding AFM images produced by numerical simulation of the AFM imaging process (see Materials and Methods). (F) Representative images (120 3 120 nm) of looped complexes with O-158-O or O-153-O DNA." (See original text for the full caption.)

Gene expression is regulated in part by the formation of DNA loops, in which a protein attaches to two parts of a DNA strand, pulling them together. Researchers at Brandeis have characterized and visualized the well known Lac repressor, a gene regulating protein in E.coli.

Two very cool techniques were used to study this system: Atomic force microscopy and tethered particle motion (TPM). TPM, developed at Brandeis, involves attaching a bead to a bit of DNA. You can't see the DNA as it moves around, but you can see the bead, even though it is very very tiny. This research has allowed the rejection of a number of previously hypothesized models for DNA folding.

Atomic force microscopy allows scientists to view the shape of the DNA molecules statically and TPM demonstrates the details of the movement of the DNA molecules.


Figure 5 from the paper: "Physical models corresponding to possible in-phase loop geometries."
Using these data, the apparently cash-strapped but ingenious researchers at Brandeis used binder clips and tape to create three dimensional models of the DNA loops. Or at least, that is what they claimed when the departmental dean walked in on them and they were playing wit the paper clips.

But no, seriously, they actually used basic office supplies to make these models, which worked as well as any other material to determine the viability of some of the shape changes that were hypothesizes.

Jeff Gelles, one of the scientists involved in this research, explains: "What we demonstrated in this paper is that, contrary to what many scientists thought, the structure of the protein is flexible and can take on different shapes, helping to minimize DNA bending or twisting in loops, and thus, maximize stable gene regulation. We believe the protein has the ability to change its shape to accommodate different sized loops and different amounts of DNA, helping cells maintain genes in a switched on or switched off state. We think it is possible that the characteristics of this genetic switch are examples of a general phenomenon that helps explain gene regulation."

This could have applications in developing antibiotics.


Citation: Wong OK, Guthold M, Erie DA, Gelles J (2008) Interconvertible Lac repressor-DNA loops revealed by single-molecule experiments. PLoS Biol 6(9): e232. doi:10.1371/journal.pbio.0060232

The paper is here.


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