Microarrays

Identifying transcription-factor binding sites

Unraveling the complex circuitry that underlies cellular transcription is a major challenge facing biologists; now a new tool will offer much-needed assistance in tackling this problem. Berger et al. have developed a specialized protein binding microarray, comprised of short, carefully selected DNA sequences, that can be used to identity the unique DNA sequences to which a particular transcription factor binds.

Berger, M.F. et al. Nat. Biotechnol.; published online (24 September 2006).

Protein Biochemistry

Predicting protein orientation on surfaces

Protein immobilization on surfaces is necessary for the use of research tools like protein microarrays. The orientation of a protein on the surface is crucial for its proper functioning, but it is extremely difficult to determine with available experimental approaches. Talasaz et al. now describe a computational structural simulation method that can be used to predict protein orientation on surfaces using electrostatic interaction information.

Talasaz, A.H. et al. Proc. Natl. Acad. Sci. USA 103, 14773–14778 (2006).

Spectroscopy

Extending the limits of top-down proteomics

In the 'top-down' approach to mass spectrometry–based protein analysis, intact protein ions are introduced via electrospray ionization into a mass spectrometer, where they undergo fragmentation and subsequent detection. Larger proteins, however, could not be readily analyzed using this method. By applying more energetic conditions during fragmentation, Han et al. now show that the top-down approach can be used to fragment proteins as large as 229 kDa. This should help extend the application of top-down approaches to broader proteomic studies.

Han, X. et al. Science 314, 109–112 (2006).

RNA Interference

Faster cloning of inverted repeats for RNAi

Cloning of inverted repeats is often the bottleneck in RNA interference experiments. Bao and Cagan constructed pGEM-WIZ, a 3.1-kb vector for assembling inverted repeats for any Drosophila sp. gene. The smaller plasmid size allows a clone with an insert to be distinguished from the vector by size, and plasmids containing an inverted repeat, which replicate more slowly in Escherichia coli, can be quickly identified by their lower copy number.

Bao, S. & Cagan, R. et al. RNA 12, 2020–2024 (2006).

Chemical Tools

Replacement surgery with unnatural amino acids

To substitute a 'key' aromatic residue in the lock-and-key joint of the glutathione transferase enzyme, Hegazy et al. turned to combinatorial chemistry. They replaced the key tyrosine with a cysteine and then chemically derivatized this residue to obtain enzyme variants with a wide range of catalytic activities and affinities for the substrate—providing an alternative method for the introduction of unnatural amino acids.

Hegazy, U.M. et al. Chem. Biol. 13, 929–936 (2006).