In many organisms, including plants, nucleic acid bases and derivatives such as caffeine are transported across the plasma membrane. Cytokinins, important hormones structurally related to adenine, are produced mainly in root apices, from where they are translocated to shoots to control a multitude of physiological processes. Complementation of a yeast mutant deficient in adenine uptake (fcy2) w...

Submitted for the MAR06 Meeting of The American Physical Society A Density Functional Theory Study of the Non-local Correlations between Nucleic Acid Base Pairs VALENTINO R. COOPER, TIMO THONHAUSER, DAVID C. LANGRETH, Rutgers University — The interactions of nucleic acid bases are fundamentally important in determining the behavior and structure of biologically important molecules such as DNA a...

Hydrogen bonds (H-bonds) formed between nucleobases play an important role in the construction of various nucleic acid structures. The H-donor and H-acceptor pattern of a nucleobase is responsible for selective and correct base pair formation. Herein, we describe an 8-thioadenine nucleobase analogue and an 8-thiohypoxanthine nucleobase analogue with a photolabile 6-nitroveratryl (NV) group on t...

We present a new versatile program, SCHNAaP, for the analysis of double-helical nucleic acid structures. The program uses mathematically rigorous and fully reversible procedures for calculating the structural parameters: the Cambridge University Engineering Department Helix computation Scheme (CEHS) is used to determine the local helical parameters and an analogous procedure is used to determin...

We propose a rapid chemical strategy for identifying base pairs in structured nucleic acid systems. The approach goes beyond traditional chemical mapping approaches by monitoring perturbations of each residue's chemical accessibility in response to systematic mutagenesis of residues that are distant in sequence but nearby in three dimensions. As a proof of concept, we present high-throughput di...

We present a comprehensive software package, 3DNA, for the analysis, reconstruction and visualization of three-dimensional nucleic acid structures. Starting from a coordinate file in Protein Data Bank (PDB) format, 3DNA can handle antiparallel and parallel double helices, single-stranded structures, triplexes, quadruplexes and other complex tertiary folding motifs found in both DNA and RNA stru...

background: we examined a molecular method with a single-pcr for amplification of a part of cp5 gene enabling us to differen­tiate the pathogenic species, entamoeba histolytica , from the non-pathogenic species, e. dispar . methods: we developed a single pcr method for this purpose.  after investigation of genbank, primer pairs were de­signed from highly conserved regions of cysteine proteinase...

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Base extrusion is a major structural feature at the junction between B- and Z-DNA (the B-Z junction) where a base pair is broken, and the two bases are extruded from the double helix. Despite the demonstration of base extrusion at the B-Z junction, it is not clear whether a similar base extrusion occurs at other types of junctions involving the left-handed Z conformation. Here, we investigate s...