Satoru Nagatoishi

DNA tetraplex structure formation from human telomeric repeat motif (TTAGGG):(CCCTAA) in nanocavity water pools of reverse micelles

In an equimolar ratio the human telomeric oligonucleotides d[AGGG(TTAGGG)(3)] and d[(CCCTAA)(3)CCCT] formed mixed structures of duplex and tetraplex in bis(2-ethylhexyl)sulfosuccinate reverse micelles; only the duplex was observed in aqueous buffer. This finding suggests that heterogeneous confined media in the cell nucleus might induce a significant fraction of the telomeric region of genomic DNA to adopt non-canonical tetraplex structure.

Hydration is Required in DNA G-Quadruplex-Protein Binding

Various nucleic acid structures other than just the duplex structure play important roles in binding to proteins in cellular systems and in functional nanodevices. The G-quadruplex structure, which consists of four strands of guanine-rich base sequences, is one of the attractive high-order structures of nucleic acids. G-quadruplex formation can be used as a genetic control element because G-quadruplex is thought to occur in living cells. Furthermore, the structure is already used as a powerful tool in molecular probes and nanomachines. 4] The G-quadruplex structure is generally stabilized by binding to cations. We reported previously the effect of cations on the thermodynamics of G-quadruplex structures for both short oligonucleotides and long telomeric DNA. In addition, we proposed the application of G-quadruplex structures in functional biomaterials, such as G-wires and logic gates. Therefore, a quantitative study of G-quadruplex stabilization would provide significant information for biological functions and biotechnological applications of the G-quadruplex. The G-quadruplex structure is also stabilized by binding to proteins. G-quadruplex structures that bind to proteins are reported to play important roles in transcription and cell cycle control, and can be used in nanodevice protein sensors. We also reported recently that the G-quadruplex structure is stabilized in the presence of histone-mimicking peptides. Despite these findings, the mechanical and quantitative details by which proteins bind to and stabilize the G-quadruplex structure remain unclear. Such information should be useful for further development of functional nucleic-acid–protein systems. We report here the thermodynamics of binding in a model G-quadruplex–protein system. In our model system a DNA aptamer, 5’-GGTTGGTGTGGTTGG-3’ (TBA), and thrombin were used to study the G-quadruplex (the aptamer forms an antiparallel G-quadruplex structure, Figure 1A), and its binding to thrombin, a protein that is known to bind specifically to TBA (Figure 1B). The thermodynamic study was investigated

Interaction of water with the G-quadruplex loop contributes to the binding energy of G-quadruplex to protein

Unlike DNA duplexes that release water upon interaction with protein, the binding of DNA G-quadruplex of the thrombin-binding aptamer (TBA) to thrombin takes up water. Here, to reveal the mechanism of water uptake, we designed four mutants of TBA (ΔT3, ΔT7, ΔT9, ΔT12), in which thymine residues (T3, T7, T9 and T12) were deleted from the loop regions of TBA G-quadruplex. For the mutants the thermodynamics and the osmolyte effects on the interactions with thrombin were investigated. The mutants ΔT3, ΔT9 and ΔT12 decreased the binding constants of the G-quadruplex to thrombin. Furthermore, an osmotic stress analysis indicated that the number of water molecules binding to the complex decreased in the mutants ΔT3 and ΔT9. The decrease in the binding affinity was related to loss of binding of the loop nucleotides to water molecules. Therefore, the interaction between loops of the G-quadruplex and water molecules contributed to the binding energy of G-quadruplex to protein. Our study suggests that water binding is essential for the binding of G-quadruplex to protein.