Overview of the structure of all-AT oligonucleotides: organization in helices and packing interactions.
We present the crystalline organization of 33 all-AT deoxyoligonucleotide duplexes, studied by x-ray diffraction. Most of them have very similar structures, with Watson-Crick basepairs and a standard average twist close to 36 degrees. The molecules are organized as parallel columns of stacked duplexes in a helical arrangement. Such organization of duplexes is very regular and repetitive: all sequences show the same pattern. It is mainly determined by the stacking of the terminal basepairs, so that the twist in the virtual TA base step between neighbor duplexes is always negative, approximately -22 degrees. The distance between the axes of parallel columns is practically identical in all cases, approximately 26 A. Interestingly, it coincides with that found in DNA viruses and fibers in their hexagonal phase. It appears to be a characteristic distance for ordered parallel DNA molecules. This feature is due to the absence of short range intermolecular forces, which are usually due to the presence of CG basepairs at the end of the oligonucleotide sequence. The duplexes apparently interact only through their diffuse ionic atmospheres. The results obtained can thus be considered as intermediate between liquid crystals, fibers, and standard crystal structures. They provide new information on medium range DNA-DNA interactions.
Campos
Lourdes
L
Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, E-08028 Barcelona, Spain.
Valls
Núria
N
Urpí
Lourdes
L
Gouyette
Catherine
C
Sanmartín
Trinidad
T
Richter
Michael
M
Alechaga
Elida
E
Santaolalla
Alicia
A
Baldini
Roberto
R
Creixell
Marc
M
Ciurans
Ruth
R
Skokan
Petr
P
Pous
Joan
J
Subirana
Juan A
JA
D001482:Base Composition; D020029:Base Pairing; D003460:Crystallization; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D009991:Oscillometry; D013696:Temperature; D014961:X-Ray Diffraction
D009841:Oligonucleotides