An ambiguous structure of a DNA 15-mer thrombin complex

Area of Science:

• Biochemistry
• Structural Biology
• Nucleic Acid Chemistry

Background:

• Thrombin plays a critical role in hemostasis.
• DNA G-quadruplexes are involved in various biological processes.
• Understanding thrombin-DNA interactions is crucial for therapeutic development.

Purpose of the Study:

• To crystallographically analyze the complex between thrombin and a specific DNA 15-mer (GGTTGGTGTGGTTGG).
• To compare the crystallographic structure with the solution NMR structure of the DNA 15-mer.
• To resolve structural ambiguities in the thrombin-DNA complex.

Main Methods:

• X-ray crystallography to determine the complex structure.
• Nuclear Magnetic Resonance (NMR) spectroscopy to determine the solution structure of the DNA 15-mer.
• Crystallographic data refinement to assess structural models.

Main Results:

• The crystallographic structure of the thrombin-DNA complex was redetermined with improved diffraction data.
• Two distinct structures of the DNA 15-mer were observed: one from X-ray crystallography and one from NMR.
• Both structures feature stacked G-quartets but differ in strand polarity and binding interaction (TGT loop vs. TT loop).
• Both models refined to a similar R value (0.16), creating ambiguity.

Conclusions:

• The study presents a disconcerting ambiguity regarding the thrombin-DNA complex structure.
• The crystallographic and NMR structures of the DNA 15-mer associate with thrombin differently.
• Independent physical or chemical evidence is required to definitively resolve the structural ambiguity.