Determination by MAD-DM of the structure of the DNA duplex d[ACGTACG(5-BrU)]2 at 1.46 Å and 100 K

A four-wavelength MAD experiment on a new brominated octanucleotide is reported here. d[ACGTACG(5-BrU)], C77H81BrN30O32P7, (DNA) = 2235, tetragonal, P43212 (No. 96), a = 43.597, c = 26.268 Å, V = 49927.5 Å3, Z = 8, T = 100 K, R = 10.91% for 4312 reflections between 15.0 and 1.46 Å resolution. The self-complementary brominated octanucleotide d[ACGTACG(5-BrU)]2 has been crystallized and data measured to 1.45 Å at both 293 K and a second crystal flash frozen at 100 K. The latter data collection was carried out to the same resolution at the four wavelengths 0.9344, 0.9216, 0.9208 and 0.9003 Å, around the Br K edge at 0.92 Å and the structure determined from a map derived from a MAD data analysis using pseudo-MIR methodology, as implemented in the program MLPHARE. This is one of the first successful MAD phasing experiments carried out at Sincrotrone Elettra in Trieste, Italy. The structure was refined using the data measured at 0.9003 Å, anisotropic temperature factors and the restrained least-squares refinement implemented in the program SHELX96, and the helical parameters are compared with those previously determined for the isomorphous d(ACGTACGT)2 analogue. The asymmetric unit consists of a single strand of octamer with 96 water molecules. No countercations were located. The A-DNA helix geometry obtained has been analysed using the CURVES program.

Structure of the DNA octanucleotide d(ACGTACGT)2

d(ACGTACGT), C78H84N30O32P7.20H2O, Mr (DNA) = 2170, tetragonal, P43212 (No 96), a = 42.845 (1), b = 42.845(1), c = 24.804 (1) Å, V = 45532.5 (2) Å3, z = 8,(MoK) = 0.71069 Å,µ(MoK) = 0.10 mm-1, T = 295 K, R = 0.18 for 1994 unique reflections between 5.0 and 1.9 Å resolution. The self-complementary octanucleotide d(ACGTACGT)2 has been crystallized and its structure determined to a resolution of 1.9 Å. The asymmetric unit consists of a single strand of octamer with 20 water molecules. It is only the second example of an octanucleotide having terminal A·T base pairs whose structure has been determined by X-ray crystallography. The sequence adopts the modified A-type conformation found for all octanucleotide duplexes studied to date with the helix bent by approximately 15° and an average tilt angle of 0°. Unusually the data collection was carried out using a 3 kW molybdenum sealed-tube source. The conformational details are discussed in comparison with other closely related sequences.

Electrochemical sensing of 2D condensation in amyloid peptides

The interfacial behavior of the model amyloid peptide octamer YYKLVFFC (peptide 1) and two other amyloid peptides YEVHHQKLVFF (peptide 2) and KKLVFFA (peptide 3) at the metal|aqueous solution interface was studied by voltammetric and constant current chronopotentiometric stripping (CPS). All three peptides are adsorbed in a wide potential range and exhibit different interfacial organizations depending on the electrode potential. At the least negative potentials, chemisorption of peptide 1 occurs through the formation of a metal sulfur bond. This bond is broken close to −0.6 V. The peptide undergoes self-association at more negative potentials, leading to the formation of a “pit” characteristic of a 2D condensed film. Under the same conditions the other peptides do not produce such a pit. Formation of the 2D condensed layer in peptide 1 is supported by the time, potential and temperature dependences of the interfacial capacity and it is shown that presence of the 2D layer is reflected by the peptide CPS signals due to the catalytic hydrogen evolution. The ability of peptide 1 to form the potential-dependent 2D condensed layer has been reported neither for any other peptide nor for any protein molecule. This ability might be related to the well-known oligomerization and aggregation of Alzheimer amyloid peptides.