No abstract

In the current study, we used a combination of gel electrophoresis, circular dichroism, and UV melting analysis to investigate the structure and stability of G-quadruplexes formed by long telomeric DNAs from Oxytricha and human, where the length of the repeat (n)=4 to 12. We found that the Oxytricha telomeric DNAs, which have the sequence (TTTTGGGG)n, folded into intramolecular and intermolecular G-quadruplexes depending on the ionic conditions, whereas human telomeric DNAs, which have the sequence (TTAGGG)n, formed only intramolecular G-quadruplexes in all the tested conditions. We further estimated the thermodynamic parameters of the intramolecular G-quadruplex. We found that thermodynamic stabilities of G-quadruplex structures of long telomeric DNAs (n=5 to 12) are mostly independent of sequence length, although telomeric DNAs are more stable when n=4 than when n>or=5. Most importantly, when n is a multiple of four, the change in enthalpy and entropy for G-quadruplex formation increased gradually, demonstrating that the individual G-quadruplex units are composed of four repeats and that the individual units do not interact. Therefore, we propose that the G-quadruplexes formed by long telomeric DNAs (n>or=8) are bead-on-a-string structures in which the G-quadruplex units are connected by one TTTT (Oxytricha) or TTA (human) linker. These results should be useful for understanding the structure and function of telomeres and for developing improved therapeutic agents targeting telomeric DNAs.

We systematically and quantitatively investigated the structure and thermodynamics of G-quadruplexes of RNAs and corresponding DNAs of the same sequences under molecular crowding conditions that mimic the high osmotic stress induced by the numerous molecules inside of living cells. Structural analyses demonstrated that various telomere RNA sequences folded into parallel-stranded G-quadruplexes in a manner independent of the surrounding conditions with different cations under both dilute and molecular crowding conditions. In contrast, DNA G-quadruplexes showed structural polymorphism. Moreover, we demonstrated that the G-quadruplexes of the RNA sequences were more stable than those of the same DNA sequences. These results show that a single and robust RNA G-quadruplex structure can exist in a manner independent of the sequence and surrounding conditions. To confirm this, we studied a guanine-rich sequence located in the 5'-untranslated region of human bcl-2 mRNA that is thought to play a role in translation. The results revealed a stable parallel G-quadruplex that formed under all conditions tested. For example, a bcl-RNA G-quadruplex in the presence of 5 mM KCl [free energy change at 25 degrees C (DeltaG degrees (25)) of -5.42 kcal/mol] was more stable than its corresponding DNA G-quadruplex (DeltaG degrees (25) = -2.31 kcal/mol). Our results further indicated that water molecules binding to the 2'-OH group of RNA G-quadruplexes play a critical role in their formation and stability.

The structure and stability of long telomeric DNAs, (T(2)AG(3))(n) (n = 4-20), were studied under dilute and molecular crowding conditions in the presence of Na(+) and K(+). Structural analysis showed that the long telomeric DNAs formed intramolecular G-quadruplexes under all conditions. In the presence of Na(+), the telomeric DNAs formed an antiparallel G-quadruplex under both dilute and molecular crowding conditions. However, in the presence of K(+), molecular crowding induced a conformational change from mixed to parallel. These results are consistent with numerous structural studies for G-quadruplex units under molecular crowding conditions. Thermodynamic analysis showed that G-quadruplexes under the molecular crowding conditions were obviously more stable than under dilute condition. Interestingly, this stabilization effect of molecular crowding was reduced for the longer telomeric DNAs, indicating that the G-quadruplex structure of long telomeric DNAs is not as stable under molecular crowding conditions, as implied from the large stabilization of isolated G-quadruplex units as previously reported. Moreover, a hydration study revealed that upon structure folding, the interior of a G-quadruplex unit was dehydrated, whereas the linker between two units was more hydrated. It is thus possible to propose that the linkers between G-quadruplex units are ordered structures but not random coils, which could have an important influence on the stability of the entire structure of long telomeric DNAs. These results are significant to elucidate the biological characteristics of telomeres, and can aid in the rational design of ligands and drugs targeting the telomere and related proteins.

No abstract

Molecular dynamics (MD) simulations were performed to study interaction between the graphene nanoribbon (GNR) and single-wall carbon nanotube (SWCNT). The GNR enters the SWCNT spontaneously to display a helical configuration which is quite similar to the chloroplast in the spirogyra cell. This unique phenomenon results from the combined action of the van der Waals potential well and the π-π stacking interaction. The size of SWCNT and GNR should satisfy some certain conditions in the helical encapsulation process. A DNA-like double helix would be formed inside the SWCNT with the encapsulation of two GNRs. A water cluster enclosed in the SWCNT has great effect on the formation of the GNR helix in the tube. Furthermore, we also studied the possibility that the spontaneous encapsulation of GNR is used for substance delivery. The expected outcome of these properties is to provide novel strategies to design nanoscale carriers and reaction devices.

No abstract

Climate-induced nonlinearity in biological variability and non-stationary relationships with physical drivers are crucial to understand responses of marine organisms to climate variability. These phenomena have raised concerns in the northeastern North Pacific, but are out of the spotlight in the northwestern North Pacific in spite of potential implications for this productive system under increased climate variability. Pelagic communities in the Kuroshio ecosystem have both ecological and economic importance. However, patterns of climate-induced nonlinearity in pelagic communities are not well understood, and existence of non-stationarity in their relationships with physical drivers remains obscure. Here, we compile large numbers of climatic, oceanic and biological long-term time-series data and employ diverse statistical techniques to reveal such climate-induced nonlinearity and non-stationarity. Results show that pelagic communities in the Tsushima and Pacific areas (major areas in the Kuroshio ecosystem) had regime shifts in the late 1990s and late 1980s, respectively. Winter sea surface temperatures in the Kuroshio Current path and in the eastern part of East China Sea, which are respectively affected by the Kuroshio Current and Siberian High, correlate with dominant variability patterns in their pelagic communities. Furthermore, non-stationarity was identified with threshold years in the 1990s in the Tsushima area and in the 1980s in the Pacific area as a possible result of the declined variances in the Siberian High and Aleutian Low, respectively. Our findings provide insights on spatial differentiation of climate-induced nonlinearity and nonstationarity, which are valuable for the management of pelagic communities in the northwestern North Pacific under changing climatic conditions. K E Y W O R D S climate variability, ecological threshold, Kuroshio Current, non-stationary relationship, pelagic species, regime shift 7 3.4 Non-stationarity in community-environment relationships 7 4 DISCUSSION 9 4.1 Similarity and difference between the variability patterns 9 4.2 SST effects on pelagic communities 11 4.3 Climate effects on the SST fields 11 4.4 Climate-induced non-stationarity and its implications for fisheries management 12 ACKNOWLEDGEMENTS 13