Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Replicative DNA polymerases typically exhibit strict geometric control over template and nucleotide recognition.
• A naturally occurring DNA polymerase I from Geobacillus stearothermophilus (Bst) unexpectedly synthesizes DNA from RNA and synthetic nucleic acid (XNA) templates.

Purpose of the Study:

• To investigate the mechanism by which Bst DNA polymerase recognizes and synthesizes DNA from diverse XNA templates.
• To elucidate the structural basis for the enzyme's ability to accommodate chemically distinct nucleic acid structures.

Main Methods:

• Crystallography was used to determine the structures of Bst DNA polymerase.
• Structures captured the enzyme post-DNA synthesis on 2'-deoxy-2'-fluoro-β-d-arabino nucleic acid (FANA) and α-l-threofuranosyl nucleic acid (TNA) templates.

Main Results:

• Crystal structures revealed the Bst DNA polymerase active site interacting with FANA and TNA templates.
• Analysis indicated that structural plasticity of the enzyme active site is key to accommodating diverse XNA templates.
• This plasticity is proposed as a mechanism for XNA-dependent DNA synthesis.

Conclusions:

• Bst DNA polymerase possesses an intrinsic ability to utilize diverse XNA templates for DNA synthesis.
• Enzyme structural plasticity is critical for this broad substrate recognition.
• Insights gained can guide the development of engineered polymerases with enhanced XNA synthesis activity.