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Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...

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Related Experiment Video

Updated: Jul 17, 2026

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution
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Light-Nucleotide versus Ion-Nucleotide Interactions for Single-Nucleotide Resolution.

Mohsen Farshad1, Jayendran C Rasaiah1

  • 1Department of Chemistry, University of Maine, Orono, Maine 04469, United States.

The Journal of Physical Chemistry. B
|March 10, 2021
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Summary

Light-nucleotide interactions offer superior resolution for DNA sequencing compared to ionic currents. Optical techniques like SERS and TERS can improve nucleotide characterization in nanopore sequencing.

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Area of Science:

  • Nanopore sequencing
  • Biophysics
  • Spectroscopy

Background:

  • Current nanopore DNA sequencing relies on ion-nucleotide interactions, which have limited resolution.
  • Existing methods using ionic currents for single-stranded DNA (ss-DNA) sequencing show overlapping signals for different nucleotides.
  • Base-calling algorithms struggle with insufficient information from ion-nucleotide interactions.

Purpose of the Study:

  • To investigate light-nucleotide interactions as a more discriminative method for nanopore DNA sequencing.
  • To compare the information content of light-nucleotide interactions with traditional ion-nucleotide interactions.
  • To explore optical techniques for enhanced nucleotide characterization in nanopore sequencing.

Main Methods:

  • Density Functional Theory (DFT) calculations for light-nucleotide interactions.
  • Molecular Dynamics (MD) simulations of nucleotide translocation through nanopores.
  • Analysis of UV-vis and Raman spectra of nucleotides, nucleosides, and nucleobases.
  • Comparison of ionic current data with spectral data.

Main Results:

  • Ionic currents from transverse and longitudinal simulations showed significant overlap for different nucleotide translocations (A16, G16, T16, C16).
  • UV-vis and Raman spectra exhibited higher resolution for distinguishing single nucleotides, nucleosides, and nucleobases.
  • Light-nucleotide interactions provided more discriminative information than ion-nucleotide interactions for sequencing.

Conclusions:

  • Light-nucleotide interactions offer a more effective approach for nucleotide characterization in nanopore DNA sequencing.
  • Optical techniques such as surface-enhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS) are promising for implementation.
  • Plasmon excitation can be utilized to control light localization and nucleotide translocation rates.