Nature Biotechnology pp 631 - 635 and pp 621 - 622

Existing ways of labeling and visualizing DNA and protein molecules rely on a limited palette of radioactive elements, chemical dyes, or natural fluorescent protein molecules, such as green fluorescent protein. Biological research urgently needs a wider array of reliable, robust, and safe labeling molecules to facilitate studies for determining the types of molecules present in a cell, their cellular location, activity, and concentration. Now, a team of scientists led by Shuming Nie of Indiana University has invented a way to bar code DNA using tiny light-emitting crystals known as quantum dots. By embedding these quantum dots in microbeads bearing short strands of DNA, the researchers have created labels that can recognize particular DNA molecules of interest and tag them with a unique identification code.

Alternative labeling techniques, which often rely on radioactivity or organic dyes, have several drawbacks: Radioactive markers can have short half-lives and are toxic, while organic dyes come in a limited number of colors and may lose their glow too quickly. Quantum-dot microbeads are superior to these approaches in several ways. For instance, compared with organic dyes, quantum dots are brighter, more stable, and give sharper signals. Moreover, the color of a quantum dot can easily be changed by changing its size, yet differently colored dots can all be excited by a single wavelength of light—an approach not possible with other labeling systems.

The researchers predict that several tens of thousands of uniquely coded beads could be built using different combinations of colors and intensity levels. These molecular ID codes could then be used to simultaneously analyze a large number of molecules. Ultimately, the codes should be easily be tagged onto both nucleic acids and proteins—facilitating research in many areas of biomedical research, including drug screening, gene expression studies, and clinical diagnostics.

Nature Biotechnology pp 636 - 639 and pp 622 - 623

Sequencing DNA without gels seems pretty far-fetched. But Stefan Howorka and colleagues have shown that this may be possible. They have exploited the electrical conductivity properties of a nanopore—membrane-embedded proteins that form a channel—to detect single nucleotide changes in a sequence of DNA.

As a molecule moves through a nanopore, there are characteristic electrical conductivity changes that can be measured. Such conductivity profiles correspond with the size (and other characteristics) of the molecule moving through the pore.

The authors engineered a nanopore, tethering a short sequence of DNA at the entrance of the pore. Then they distinguished the DNA molecules drawn into the pore by examining the changes in current flow through the pore: Those DNA sequences that complemented the tethered DNA likely formed a duplex with the tethered molecule before passing through the membrane, producing a current reduction that was of longer duration than that generated by sequences containing mismatches. The researchers also determined the partial sequence of a DNA strand tethered to a nanopore by applying a series of DNA molecules of known sequence to the pore.

However, before nanopores can be used for routine DNA analysis and sequencing, further work needs to be done to engineer more robust and reproducible nanopores and, for sequencing, their fabrication into arrays.

Nature Biotechnology pp 668 - 672 and pp 624 - 625

Corn rootworms (Diabrotica spp) are a persistent pest causing around $1 billion in damage to corn crops each year in the United States alone. To combat this problem, researchers have developed a genetically modified corn plant that gives the munching marauders a dose of deadly proteins.

Currently, corn rootworm infestations are treated either with insecticides or through crop rotation (when a crop other than corn is planted while the soil is still infected with rootworm eggs). Neither solution is ideal: rootworms have become resistant to insecticides; and delayed egg "hatching" enables the larvae to emerge just in time for the next planting of corn. So, building on work done on other transgenic crops, Dan Moellenbeck and colleagues expressed two novel native proteins—so-called endotoxins—from a common soil bacterium Bacillus thuringiensis (Bt), whose toxins have been used previously in GM corn. Field trials of the new Bt endotoxin-expressing corn suggest that the plants suffer much less damage from the rootworm larvae than wild-type corn. The modified plants provided equivalent protection to wildtype plants treated with insecticide.

Although Bt technology has been applied before—for example, to protect plants against corn borer and Colorado potato beetle—this novel application could provide a new weapon against a serious corn pest and help reduce the use of insecticides. As with other types of Bt (or GM) corn, however, research is urgently needed to understand how to avoid the emergence of resistance to the toxin in the target pest, how to prevent cross contamination of conventional crops and wild relatives with the transgene, the safety of the Bt corn for use as a foodstuff, and its resistance to all members of the rootworm family that cause crop infestations.