UV-Vis Action Spectroscopy Reveals Structures of DNA Codon Trinucleotide Cation Radicals

Area of Science:

• Physical Chemistry
• Molecular Spectroscopy
• Computational Chemistry
• Biophysical Chemistry

Background:

• DNA trinucleotide codons (AAA, AAC, AAT, ATA, TAA) are fundamental units of genetic information.
• Understanding the gas-phase properties of DNA fragments is essential for developing advanced analytical techniques and comprehending their behavior under various conditions.

Purpose of the Study:

• To perform a comprehensive spectroscopic study of gas-phase cation and dication radicals of DNA trinucleotide codons.
• To elucidate the structures, energies, excited states, and vibronic spectra of these radical ions using computational analysis.
• To investigate the influence of charge state and hydrogen atom migration on the stability and reactivity of codon radical ions.

Main Methods:

• Generation of multiply charged noncovalent complex ions of codons with dibenzo-18-crown-6 ether (DBCE) via electrospray protonation.
• Electron transfer dissociation (ETD) to generate codon cation radicals, dication radicals, and doubly reduced ions.
• UV-Vis photodissociation spectroscopy (210-700 nm) to obtain action spectra.
• Time-dependent density functional theory (TD-DFT) calculations to determine vibronic absorption spectra and ion structures.

Main Results:

• Stable hydrogen-rich cation radicals ((AAA + 2H)^+•, (AAC + 2H)^+•, (AAT + 2H)^+•, (ATA + 2H)^+•, (TAA + 2H)^+•) and dication radicals ((AAA + 3H)^2+•, (AAC + 3H)^2+•) were successfully generated.
• The (AAA + 2H)^+• cation radical adopted a zwitterionic structure, while the (AAA + 3H)^2+• dication radical underwent hydrogen migration to the 5'-adenine.
• Action spectra indicated hydrogen atom migrations in (AAT + 2H)^+•, (AAC + 2H)^+•, and (AAC + 3H)^2+•, leading to the formation of dihydrothymine and dihydroadenine derivatives.

Conclusions:

• The study reveals distinct structural preferences and isomerization pathways for DNA codon radical ions based on their charge state and nucleobase sequence.
• Hydrogen atom migration plays a significant role in the stabilization and transformation of these radical ions in the gas phase.
• Computational modeling combined with experimental spectroscopy provides detailed insights into the complex behavior of DNA fragments.