Effect of Base Sequence on G-Wire Formation in Solution

The formation and dimensions of G-wires by different short G-rich DNA sequences in solution were investigated by dynamic light scattering (DLS) and polyacrilamide gel electrophoresis (PAGE). To explore the basic principles of wire formation, we studied the effects of base sequence, method of preparation, temperature, and oligonucleotide concentration. Both DLS and PAGE show that thermal annealing induces much less macromolecular self-assembly than dialysis. The degree of assembly and consequently length of G-wires (5-6 nm) are well resolved by both methods for DNA sequences with intermediate length, while some discrepancies appear for the shortest and longest sequences. As expected, the longest DNA sequence gives the longest macromolecular aggregates with a length of about 11 nm as estimated by DLS. The quadruplex topologies show no concentration dependence in the investigated DNA concentration range (0.1 mM–0.4 mM) and no structural change upon heating

Paleo-sea surface temperature calculations in the equatorial east Atlantic from Mg/Ca ratios in planktic foraminifera: A comparison to sea surface temperature estimates from UK'37, oxygen isotopes, and foraminiferal transfer function

We present two ∼270 kyr paleo-sea surface temperature (SST) records from the Equatorial Divergence and the South Equatorial Current derived from Mg/Ca ratios in the planktic foraminifer Globigerinoides sacculifer. The present study suggests that the magnesium signature of G. sacculifer provides a seasonal SST estimate from the upper ∼50 m of the water column generated during upwelling in austral low-latitude fall/winter. Common to both down-core records is a glacial-interglacial amplitude of ∼3°–3.5°C for the last climatic changes and lower Holocene and glacial oxygen isotope stage 2 temperatures compared with interglacial stage 5.5 and glacial stage 6 temperatures, respectively. The comparison to published SST estimates from alkenones, oxygen isotopes, and foraminiferal transfer function from the same core material pinpoints discrepancies and conformities between methods

G-quadruplex nucleic acids

2 pages.-- PMID: 20814544 [PubMed].-- PMCID: PMC2931383].Peer reviewe

Disodium guanosine 5\u27-monophosphate self-associates into nanoscale cylinders at pH 8: a combined diffusion NMR spectroscopy and dynamic light scattering study

We report a combined NMR and dynamic light scattering (DLS) study on the size of supramolecular structures formed by disodium guanosine 5\u27-monophosphate, Na2(5\u27-GMP), at pH 8. In general, two distinct types of aggregate species are present in an aqueous solution of Na2(5\u27-GMP). One type consists of stacking 5\u27-GMP monomers, and the other contains stacking G-quartets. Both types of aggregates can be modeled as rodlike cylinders. The cylinder diameter is 10 and 26 A for monomer aggregates and quartet aggregates, respectively. For Na2(5\u27-GMP) concentrations between 18 and 34 wt %, the cylinders formed by stacking G-quartets have an average length between 8 and 30 nm, corresponding to a stack of ~24-87 G-quartets. These nanoscale aggregates are significantly larger than what had previously been believed for Na2(5\u27-GMP) self-associationat pH 8. The length of both types of 5\u27-GMP aggregates was found to increase with Na2(5ć-GMP) concentration but was insensitive to the added NaCl in solution. While the aggregate size for monomer aggregates increases with a decrease in temperature, the size of G-quartet aggregates is essentially independent of temperature. We found that the size of G-quartet aggregates is slightly larger in D2O than in H2O, whereas the size of monomer aggregates remains the same in D2O and in H2O. We observed a linear relationship between the axial ratio of the 5ć-GMP cylinders and the Na2(5\u27-GMP) concentration for both types of 5ć-GMP aggregates, which suggests a common stacking mechanism for monomers and G-quartets

Molecular recognition of a lipophilic guanosine derivative in Langmuir films at the air-water interface

Molecular recognition of a lipophilic deoxyguanosine derivative at the air-water interface was investigated by film balance experiments and Brewster Angle Microscopy. Results showed that guanosine, despite strong tendency towards self-assembly, interacts with both complementary and noncomplementary liponucleosides (lipophilic derivatives of deoxycytidine and deoxythymidine). At surface pressures below 17\uc2 mN/m, attractive and repulsive interactions were present in case of both mixed monolayers and were the strongest at guanosine molar fractions of 0.5 and 0.75. At higher values of surface pressure, deoxyguanosine-deoxycytidine interactions were strictly attractive and were present only for monolayers with guanosine molar fraction of 0.75. On the contrary, attractive and repulsive interactions remained present in case of deoxyguanosine-deoxythymidine mixed monolayers. This indicates that interactions between guanosine and cytidine are much stronger than guanosine-thymidine interactions. Interactions for none of the nucleoside pairs, however, are specific and \ucf\u80\ue2\u80\u93stacking interactions between the aromatic planes of liponucleoside derivatives probably dominate over hydrogen bonding interactions. This article is part of a Special Issue entitled \ue2\u80\u9cG-quadruplex\ue2\u80\u9d Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio