The base-pairing ability of the base pair-mimic nucleosides

Area of Science:

• Molecular Biology
• Biochemistry
• Organic Chemistry

Background:

• A deoxyadenosine derivative (A(phe)) exhibits strong base stacking in DNA duplexes.
• DNA polymerases selectively incorporate dTTP opposite A(phe) in template DNA.
• The conformation of A(phe) likely differs between solution and polymerase reactions.

Purpose of the Study:

• To investigate the structural behavior of thymine bases opposite A(phe) in DNA duplexes.
• To understand the conformational changes of A(phe) during DNA polymerase reactions.

Main Methods:

• Chemical modification of thymine bases using KMnO(4) and CMCT (1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate).
• Analysis of thymine base accessibility and conformation within the DNA duplex.

Main Results:

• Thymine bases opposite A(phe) were efficiently flipped out of the DNA helix.
• This flipping out was comparable to the behavior observed in single-stranded DNA.
• The chemical modification patterns indicated significant structural alterations around the A(phe) base.

Conclusions:

• The A(phe) modification induces a conformational change, leading to thymine base extrusion.
• This base flipping mechanism explains the selective incorporation of dTTP by DNA polymerases.
• The study provides insights into the structural basis of DNA-templated nucleotide incorporation.