Solution Structure of a Lanthanide-binding DNA Aptamer Determined Using High Quality pseudocontact shift restraints.

Area of Science:

• Structural Biology
• Biochemistry
• Nuclear Magnetic Resonance (NMR) Spectroscopy

Background:

• Lanthanide-binding aptamers (LnA) are recently identified nucleic acid molecules with unique metal-binding properties.
• Paramagnetic NMR restraints, such as pseudocontact shifts (PCS), offer valuable structural information but are challenging to obtain for nucleic acids.
• The rigidity of the LnA binding site is crucial for generating reliable anisotropic paramagnetic NMR restraints.

Purpose of the Study:

• To determine the high-resolution NMR structure of the lanthanide-binding aptamer (LnA).
• To demonstrate the utility of LnA for measuring anisotropic paramagnetic NMR restraints.
• To explore the application of PCS derived from LnA in nucleic acid structure determination.

Main Methods:

• High-resolution Nuclear Magnetic Resonance (NMR) spectroscopy was employed to elucidate the aptamer structure.
• Four different paramagnetic lanthanides were used to induce pseudocontact shifts (PCS).
• The determined structure was validated by its ability to reproduce the experimentally measured PCS.

Main Results:

• The high-resolution NMR structure of the lanthanide-binding aptamer (LnA) was successfully determined.
• The rigid lanthanide binding within LnA facilitated the measurement of anisotropic paramagnetic NMR restraints.
• The final aptamer structure exceptionally reproduced the experimentally measured PCS, validating the approach.

Conclusions:

• The determined LnA structure provides a robust platform for utilizing paramagnetic NMR effects in nucleic acid studies.
• This work demonstrates the potential for broader application of PCS in determining nucleic acid structures.
• Transplanting the LnA binding site into other DNA/RNA systems could enable new structural insights.