Probing the relative orientation of molecules bound to DNA through controlled interference using second-harmonic...

Area of Science:

• Molecular Biophysics
• Nonlinear Optics
• Biochemistry

Background:

• Double-stranded DNA (dsDNA) interactions with intercalated molecules are crucial for understanding biological processes and developing novel therapeutics.
• Second-harmonic generation (SHG) is a nonlinear optical phenomenon sensitive to molecular arrangement and electronic properties.
• Controlling and measuring SHG from specific molecular arrangements within DNA can provide unique structural information.

Purpose of the Study:

• To develop and demonstrate a method for controlling and measuring the interference of radiated second-harmonic electric fields from oriented molecules within dsDNA.
• To investigate the influence of relative molecular orientation on SHG intensity.
• To establish a simple model explaining the observed SHG interference patterns.

Main Methods:

• Intercalation of oriented molecules into double-stranded DNA.
• Measurement of radiated second-harmonic generation (SHG) intensity.
• Analysis of SHG intensity based on a model accounting for field interferences.

Main Results:

• Demonstrated control and measurement of SHG interference from intercalated molecules in dsDNA.
• Showcased significant dependence of SHG intensity on the relative molecular orientation of the two intercalated molecules.
• Validated a simple model accurately describing the interference effects of radiated fields.

Conclusions:

• The relative orientation of intercalated molecules in dsDNA critically affects SHG intensity.
• The developed technique provides a sensitive method for probing molecular arrangements within DNA.
• This approach holds potential for studying structural dynamics in DNA-biomolecule complexes.