Solution structure of a DNA duplex containing a guanine-difluorotoluene pair: a wobble pair without hydrogen bonding?

The incorporation of synthetic nucleoside analogues into DNA duplexes provides a unique opportunity to probe both structure and function of nucleic acids. We used 1H and 19F NMR and molecular dynamics calculations to determine the solution structures of two similar DNA decamer duplexes, one containing a central G-T mismatched or "wobble" base pair, and one in which the thymine in this base pair is replaced by difluorotoluene (a thymine isostere) creating a G-F pair. Here, we show that the non-hydrogen-bonding G-F pair stacks relatively well into the helix and that the distortions caused by each non-Watson-Crick G-T or G-F base pair are quite localized to a three base pair site around the mismatch. A detailed structural analysis reveals that the absence of hydrogen bonding introduces more dynamic motion into the G-F pair relative to G-T and permits the G-F pair to exhibit stacking and conformational features characteristic of both a Watson-Crick base pair (on the guanine containing strand) and a wobble base pair (on the strand containing the difluorotoluene). We used these results to posit a rationale for recognition and repair of mismatch sites in DNA.     

Exotic cohomology for

We show that for the mod group cohomology of is not detected on diagonal matrices.

     

The generalized Burnside ring and theK-theory of a ring with roots of unity

We prove that ifR is a suitable ring and a finite Abelian subgroup of the multiplicative group ofR, then the Hurewicz map from the stable homotopy ofB toK _* R factors geometrically through a mapK _* E K _* R, whereE is an appropriate finite field.     

Comparative Electrochemical Charge Storage Properties of Bulk and Nanoscale Vanadium Oxide Electrodes

Journal of Solid State Electrochemistry - Vanadium oxide nanostructures have been widely researched as a cathode material for Li-ion batteries due to their layered structure and shorter Li+...     

Twisted equivariant K-theory for proper actions of discrete groups

We will make a construction of twisted equivariant K-theory for proper actions of discrete groups by using ideas of Lück and Oliver (Topology 40:585–616, 2001) to expand a construction of Adem and Ruan (Comm. Math. Phys. 237:533–556, 2003).     

Constrained graph layout by stress majorization and gradient projection

The adoption of the stress-majorization method from multi-dimensional scaling into graph layout has provided an improved mathematical basis and better convergence properties for so-called “force-directed placement” techniques. In this paper we explore algorithms for augmenting such stress-majorization techniques with simple linear constraints using gradient-projection optimization techniques. Our main focus is a particularly simple class of constraints called “orthogonal-ordering constraints” but we also discuss how gradient-projection methods may be extended to solve more general linear “separation constraints”. In addition, we demonstrate several graph-drawing applications where these types of constraints can be very useful.     

An adeno-associated viral vector transduces the rat hypothalamus and amygdala more efficient than a lentiviral vector

Background  

This study compared the transduction efficiencies of an adeno-associated viral (AAV) vector, which was pseudotyped with an AAV1 capsid and encoded the green fluorescent protein (GFP), with a lentiviral (LV) vector, which was pseudotyped with a VSV-G envelop and encoded the discosoma red fluorescent protein (dsRed), to investigate which viral vector transduced the lateral hypothalamus or the amygdala more efficiently. The LV-dsRed and AAV1-GFP vector were mixed and injected into the lateral hypothalamus or into the amygdala of adult rats. The titers that were injected were 1 × 10⁸ or 1 × 10⁹ genomic copies of AAV1-GFP and 1 × 10⁵ transducing units of LV-dsRed.     

Dispersion, static correlation, and delocalisation errors in density functional theory: an electrostatic theorem perspective

Dispersion, static correlation, and delocalisation errors in density functional theory are considered from the unconventional perspective of the force on a nucleus in a stretched diatomic molecule. The electrostatic theorem of Feynman is used to relate errors in the forces to errors in the electron density distortions, which in turn are related to erroneous terms in the Kohn-Sham equations. For H(2), the exact dispersion force arises from a subtle density distortion; the static correlation error leads to an overestimated force due to an exaggerated distortion. For H(2)(+), the exact force arises from a delicate balance between attractive and repulsive components; the delocalisation error leads to an underestimated force due to an underestimated distortion. The net force in H(2)(+) can become repulsive, giving the characteristic barrier in the potential energy curve. Increasing the fraction of long-range exact orbital exchange increases the distortion, reducing delocalisation error but increasing static correlation error.