Development of indole-based hydration-sensitive fluorescent nucleoside analogues: experimental and computational...

Area of Science:

• Biochemistry
• Molecular Biology
• Organic Chemistry

Background:

• Natural nucleobases lack intrinsic fluorescence, limiting direct observation of DNA/RNA dynamics.
• Fluorescent nucleoside analogues (FNAs) are crucial for studying nucleic acid structures but often have limitations.
• Development of novel FNAs with tailored photophysical properties is essential for advanced biological studies.

Purpose of the Study:

• To synthesize and characterize novel indole-based, hydration-sensitive fluorescent nucleoside analogues (FNAs).
• To evaluate the utility of these new FNAs as probes for DNA/RNA conformations and conformational changes.
• To understand the photophysical mechanisms underlying the fluorescence behavior of these FNAs.

Main Methods:

• Synthesis of indole-based nucleoside analogues: indole-4-carboxaldehyde-2'-deoxyribonucleoside (I4A-NS) and 4-acetylindole-2'-deoxyribonucleoside (4AcI-NS).
• Characterization of photophysical properties, including fluorescence quantum yield, lifetime, and emission wavelength in various solvents.
• Incorporation of FNAs into single- and double-stranded DNA to study fluorescence changes.
• Density functional theory (DFT) calculations to elucidate fluorescence mechanisms.

Main Results:

• The synthesized FNAs (I4A-NS and 4AcI-NS) pair with native bases without disrupting DNA structure.
• These FNAs exhibit strong fluorescence in protic solvents (e.g., water) with large Stokes shifts.
• Significant changes in fluorescence intensity and wavelength were observed upon DNA incorporation, correlating with hydration state and quenching.
• DFT calculations revealed that hydrogen bonding enhances fluorescence quantum yield by suppressing non-radiative decay.

Conclusions:

• The novel indole-based FNAs provide an expanded toolkit for fluorescence-based nucleic acid research.
• Their hydration sensitivity and tunable fluorescence properties enable detailed studies of DNA/RNA environments.
• These FNAs offer a promising platform for developing advanced biosensors and imaging agents for nucleic acids.