Intraduplex interactions involving the 20th residues in the DD1a (), DD1b () and DD2 () DNA:DNA duplexes, and the 5th residues in the DR2a (), DR2b () and DR2c () DNA:RNA duplexes

<p><b>Copyright information:</b></p><p>Taken from "Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules"</p><p></p><p>Nucleic Acids Research 2007;35(6):1969-1977.</p><p>Published online 6 Mar 2007</p><p>PMCID:PMC1874594.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> The carbon atoms in the aminohexyl, carbamoyl and methoxyl modifications are colored green, and the water molecules are colored pale blue. Broken and dotted lines indicate possible hydrogen bonds and van der Waals interactions, respectively. The values indicated are in angstroms (Å)

Hydration structures in the minor grooves of the unmodified (), DD1a (), DD1b () and DD2 () DNA:DNA duplexes

<p><b>Copyright information:</b></p><p>Taken from "Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules"</p><p></p><p>Nucleic Acids Research 2007;35(6):1969-1977.</p><p>Published online 6 Mar 2007</p><p>PMCID:PMC1874594.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> The unmodified duplex is shown in blue lines while the present duplexes are shown in red lines. The aminohexyl, carbamoyl and methoxyl groups are colored green. In the unmodified duplex, the cyan spheres are water molecules and the gray spheres are solvent molecules partially occupied by sodium ions and water molecules. In DD1a and DD1b, the water molecules are in cyan, and the potassium ions are in gray

The minor groove widths in the DD1a (open square), DD1b (○), DD2 (open triangle) and unmodified (multi) DNA:DNA duplexes, and in the DR2a(filled square), DR2b (filled circle), DR2c (filled triangle) and unmodified (asterisk) DNA:RNA hybrid duplexes

<p><b>Copyright information:</b></p><p>Taken from "Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules"</p><p></p><p>Nucleic Acids Research 2007;35(6):1969-1977.</p><p>Published online 6 Mar 2007</p><p>PMCID:PMC1874594.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> The minor groove width is defined as the distance between the closest interstrand phosphates, diminished by 5.8 Å to account for the van der Waals radii of the phosphate groups (). X is thymine in the unmodified duplexes and U or U in the modified duplexes

Structures of the modified nucleoside analogs (), sequences and numbering schemes (), and thermal denaturation of the DNA:DNA and DNA:RNA duplexes ()

<p><b>Copyright information:</b></p><p>Taken from "Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules"</p><p></p><p>Nucleic Acids Research 2007;35(6):1969-1977.</p><p>Published online 6 Mar 2007</p><p>PMCID:PMC1874594.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> The thermal denaturation of the duplexes was performed as described in ()

Final 2 − maps contoured at 1σ level for the base pairs: U8:A17 in DD1b () and U5:A14 in DR2a ()

<p><b>Copyright information:</b></p><p>Taken from "Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules"</p><p></p><p>Nucleic Acids Research 2007;35(6):1969-1977.</p><p>Published online 6 Mar 2007</p><p>PMCID:PMC1874594.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p

Structure of D-3-hydroxybutyrate dehydrogenase prepared in the presence of the substrate D-3-hydroxybutyrate and NAD+.

International audienceD-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis catalyzes the reversible conversion between D-3-hydroxybutyrate and acetoacetate. The enzyme was crystallized in the presence of the substrate D-3-hydroxybutyrate and the cofactor NAD(+) at the optimum pH for the catalytic reaction. The structure, which was solved by X-ray crystallography, is isomorphous to that of the complex with the substrate analogue acetate. The product as well as the substrate molecule are accommodated well in the catalytic site. Their binding geometries suggest that the reversible reactions occur by shuttle movements of a hydrogen negative ion from the C3 atom of the substrate to the C4 atom of NAD(+) and from the C4 atom of NADH to the C3 atom of the product. The reaction might be further coupled to the withdrawal of a proton from the hydroxyl group of the substrate by the ionized Tyr155 residue. These structural features strongly support the previously proposed reaction mechanism of D-3-hydroxybutyrate dehydrogenase, which was based on the acetate-bound complex structure