5ANA

THE CRYSTAL STRUCTURE OF D(GTACGTAC) AT 2.25 ANGSTROMS RESOLUTION. ARE THE A-DNA'S ALWAYS UNWOUND APPROXIMATELY 10 DEGREES AT THE C-G STEPS

Summary for 5ANA

• Entry DOI: 10.2210/pdb5ana/pdb
• Descriptor: DNA (5'-D(*GP*TP*AP*CP*GP*TP*AP*C)-3'), MAGNESIUM ION (3 entities in total)
• Functional Keywords: a-dna, double helix, dna
• Total number of polymer chains: 1
• Total formula weight: 2450.92

Authors

Takusagawa, F. (deposition date: 1989-10-31, release date: 1990-04-15, Last modification date: 2024-03-06)

Primary citation

Takusagawa, F.
The crystal structure of d(GTACGTAC) at 2.25 A resolution: are the A-DNA's always unwound approximately 10 degrees at the C-G steps
J.Biomol.Struct.Dyn., 7:795-809, 1990

PubMed Abstract: The structure of the self-complementary octamer d(GTACGTAC) has been analyzed by a single crystal X-ray diffraction method at 2.25 A resolution. The crystallographic R factor was 0.184 for all 1233 reflections at this resolution. In spite of the alternating purine-pyrimidine sequence, d(GTACGTAC) adopts the A-form conformation rather than the left-handed Z-form. The average helix twist and the mean rise per base pair are 32.1 degrees and 3.18 A, respectively. The d(GTACGTAC) helix is characterized by a wide open major groove and small base-pair tilt (9.7 degrees). The partial unwinding of the helix is observed only at the central pyrimidine-purine C-G step, but not at the other pyrimidine-purine T-A steps. Based on this study and six other X-ray studies, we propose a hypothesis that the A-DNA's are always unwound approximately 10 degrees at the C-G steps. Significant differences in base-pair stacking modes are seen between the purine-pyrimidine step and the pyrimidine-purine step. All deoxyribose rings adopt the C3'-endo conformation. All backbone torsion angles fall into the range expected for the A-DNA form, except for the nucleotide G5, whose alpha and gamma torsion angles adopt the trans, trans conformation instead of the common gauche-, gauche+ conformation.

PubMed: 2310515

Experimental method

X-RAY DIFFRACTION (2.25 Å)