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Updated: Sep 13, 2025

Studying DNA Looping by Single-Molecule FRET
Published on: June 28, 2014
The Excess Polarizability of Single-Stranded DNA Molecules in Solution: A Linear Response Theory in the Polarizable
1Dipartimento di Scienze Chimiche, della Vita e della Sostenibilitá Ambientale, Universitá degli Studi di Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy.
Abstract:
The excess polarizability of a molecular solute describes the interaction energy between a molecular solute and a macroscopic optical field that polarizes the solute itself, as compared to the same interaction process involving solvent molecules. The excess polarizability is involved in the physical mechanism that triggers the signals in the whispering gallery mode (WGM), a biosensing technique (denoted as WGM) for detecting biomolecules. The interpretation of the WGM signals requires information on the excess polarizability of the biomolecule of interest, which, until now, could be obtained from experimental measurements of the refractive index of solutions. Here, we present a quantum chemical theory for determining the excess polarizability using the effective linear response theory in the polarizable continuum model (PCM-eLRT) for solvation. As a proof-of-concept, the PCM-eLRT is applied at the TD-DFT level of electronic structure methodology to the calculation of the excess polarizability of single-stranded DNA molecules constituted up to 14-mer oligonucleotides, showing remarkable agreement with available experimental data.
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