Lea Spindler

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.

Guanosine Quadruplexes in Solution: A Small-Angle X-Ray Scattering Analysis of Temperature Effects on Self-Assembling of Deoxyguanosine Monophosphate

We investigated quadruplex formation in aqueous solutions of 2′-deoxyriboguanosine 5′-monophosphate, d(pG), which takes place in the absence of the covalent axial backbone. A series of in-solution small angle X-ray scattering experiments on d(pG) have been performed as a function of temperature in the absence of excess salt, at a concentration just above the critical one at which self-assembling occurs. A global fit approach has been used to derive composition and size distribution of the scattering particles as a function of temperature. The obtained results give thermodynamical justification for the observed phase-behavior, indicating that octamer formation is essential for quadruplex elongation. Our investigation shows that d(pG) quadruplexes are very suitable to assess the potential of G-quadruplex formation and to study the self-assembling thermodynamics.

G-Quadruplex Nucleic Acids

G-quadruplexes are a family of four-stranded structuresstabilized by guanine quartets, in which four planar guaninesestablish a cyclic array of hydrogen bonds. They are ofspecial interest due to the increasing evidence for theirformation in vivo and their possible implication in biology,especially at telomeres and as contributors to gene regulation.Moreover, G-quadruplexes are also formed as a result ofself-assembling processes of guanosine derivatives, yieldingseveral interesting motifs such as G-ribbons and G-wireswhich have peculiar electrical conductivity properties thatare being explored as molecular wires.This special issue is initiated with two articles discussingthe self-assembling properties of guanosine derivatives whichdescribe the basic principles of G-quadruplex formation. Thefirst article by Neviani et al. analyzes the presence of severallevels of organization of guanosine derivatives carryingone or two lipophilic units as observed by light scatteringtechniques and transmission electron microscopy (TEM)experiments. The second article by Mariani et al. describesa study on quadruplex formation of 2 -deoxyguanosinemonophosphate by small-angle X-ray scattering techniques.

The Effect of Temperature on the Self-Assembly of Deoxyguanosine 5'-Monophosphate in Pretransitional Region of the I-Ch Phase Transition

Temperature dependence of the self-assembly of deoxyguanosine 5′-monophosphate in pretransitional region of the I-Ch phase transition was investigated by dynamic light scattering. Measurements reveal the presence of two diffusive modes: the slower mode is attributed to the motion of large globular aggregates, while the faster mode is related to the translational motion of the self-assembled columnar stacks. By increasing temperature the number of assembled molecules decreases, as seen from a reduction in the fast mode amplitude, until this mode finally disappears. Dynamical behavior of the slow diffusive mode is more complex and coupled to the dynamics of the fast mode.

Dynamic Light Scattering in Pretransitional Region of the I Ch Phase Transition of Deoxyguanosine 5′-Monophosphate

Abstract Dynamic light scattering in the pretransitional region of the I→Ch phase transition of deoxyguanosine 5′-monophosphate reveals the presence of two diffusive modes. The slower mode is assigned to the translational motion of large spherical aggregates, similar to those observed in isotropic solutions of DNA and other polyelectrolytes. The faster mode is assigned to the translational motion of stacked arrays of guanosine tetramers and can be described by the polyion diffusion.