Structure and Dynamics of Electron Injection and Charge Recombination in i-Motif DNA Conjugates

Area of Science:

• Biophysical Chemistry
• Molecular Biophysics
• DNA Nanotechnology

Background:

• Intramolecular i-motifs are DNA secondary structures formed by hemiprotonated cytosine-cytosine base pairs.
• Stilbenediether (Sd) and perylenediimide (PDI) are chromophores used to study electron transfer dynamics.
• Understanding electron transfer in DNA is crucial for developing molecular electronics and sensors.

Purpose of the Study:

• To investigate the dynamics of electron injection and charge recombination in i-motif DNA conjugates.
• To compare electron transfer in i-motifs with cytosine-cytosine base pairs to those in hairpin DNA with cytosine-guanine or 5-fluorouracil-adenine base pairs.
• To elucidate the role of i-motif structure in modulating electron transport.

Main Methods:

• Circular dichroism (CD) spectroscopy to confirm i-motif formation.
• Steady-state and time-resolved fluorescence spectroscopy to assess chromophore quenching.
• Femtosecond transient absorption (fsTA) spectroscopy to determine electron injection and charge recombination dynamics.

Main Results:

• Circular dichroism confirmed i-motif formation with and without Sd and PDI chromophores.
• Sd fluorescence was quenched, indicating electron donation to C-C base pairs, while PDI fluorescence was partially quenched.
• Ultrafast electron injection (<0.8 ps) into the i-motif was observed, but charge transport to the PDI trap was absent.
• Absence of charge transport was attributed to the stacked structure of hemiprotonated C-C base pairs in the i-motif.

Conclusions:

• Electron injection into i-motif DNA is highly efficient and ultrafast.
• The stacked structure of hemiprotonated C-C base pairs in i-motifs impedes long-range charge transport.
• This finding has implications for the design of DNA-based molecular wires and electronic devices.