Biophysical and electrochemical studies of protein-nucleic acid interactions

This review is devoted to biophysical and electrochemical methods used for studying protein-nucleic acid (NA) interactions. The importance of NA structure and protein-NA recognition for essential cellular processes, such as replication or transcription, is discussed to provide background for description of a range of biophysical chemistry methods that are applied to study a wide scope of protein-DNA and protein-RNA complexes. These techniques employ different detection principles with specific advantages and limitations and are often combined as mutually complementary approaches to provide a complete description of the interactions. Electrochemical methods have proven to be of great utility in such studies because they provide sensitive measurements and can be combined with other approaches that facilitate the protein-NA interactions. Recent applications of electrochemical methods in studies of protein-NA interactions are discussed in detail

Synthetic biology to access and expand nature's chemical diversity

Bacterial genomes encode the biosynthetic potential to produce hundreds of thousands of complex molecules with diverse applications, from medicine to agriculture and materials. Accessing these natural products promises to reinvigorate drug discovery pipelines and provide novel routes to synthesize complex chemicals. The pathways leading to the production of these molecules often comprise dozens of genes spanning large areas of the genome and are controlled by complex regulatory networks with some of the most interesting molecules being produced by non-model organisms. In this Review, we discuss how advances in synthetic biology — including novel DNA construction technologies, the use of genetic parts for the precise control of expression and for synthetic regulatory circuits — and multiplexed genome engineering can be used to optimize the design and synthesis of pathways that produce natural products

Effect of the DNA End of Tethering to Electrodes on Electron Transfer in Methylene Blue-Labeled DNA Duplexes

Electron transfer (ET) in redox-labeled double-stranded (ds) DNA tethered to electrodes through the alkanethiol linker at either the 3′ or 5′ DNA end and bearing methylene blue (MB) conjugated to the opposite end of DNA is shown to depend on the DNA end of tethering to electrodes. For 3′ tethering, a nanoscale diffusion of the positively charged MB redox probe (and thus of the individual DNA molecules) to the negatively charged electrode surface provided the highest apparent diffusion and ET rates as a result of the tilting of 3′-tethered DNA (as compared to 5′-tethered DNA) versus the normal to the surface. Dynamic values of the tilting angle varied between 57 and 45° for 16-mer and 22-mer 3′-tethered DNA, and 5′-tethering was correlated with an upright orientation of DNA at the electrode surface. The values of the diffusion coefficient <i>D</i>_MB corrected for tilting angles were similar for 5′- and 3′-tethered DNA and ranged between 5.4 × 10^–12 and 2.5 × 10^–12 cm² s^–1, whereas the ET rate constant <i>k</i>_ET^dif fit the 4.7 × 10^–6–10.3 × 10^–6 cm s^–1 range for 22-mer and 16-mer dsDNA, respectively. Those values, when related to the nanometer (10^–7 cm) diffusion distances (the length of the studied DNA), allow relatively fast diffusion-limited ET at an apparent rate that may exceed the rate of the corresponding surface-confined ET process. This phenomenon is of particular importance for molecular electronics and electrochemical genosensor development