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New Size-Expanded Fluorescent Thymine Analogue: Synthesis, Characterization, and Application.

Shingo Hirashima1, Ji Hoon Han1, Hitomi Tsuno1

  • 1Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.

Chemistry (Weinheim an Der Bergstrasse, Germany)
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A new thymine nucleoside, diox T, offers high fluorescence and environmental sensitivity for DNA applications. This molecule enables sensitive detection of DNA base pairs, advancing chemical biology research.

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DNAfluorescent nucleosidessingle nucleoside polymorphism (SNP) typingthymine

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Area of Science:

  • Chemical Biology
  • Biophysical Chemistry
  • Nucleoside Chemistry

Background:

  • Development of novel nucleoside analogs is crucial for advancing DNA-based technologies.
  • Thymine surrogates with enhanced photophysical properties are needed for sensitive molecular probes.

Purpose of the Study:

  • To synthesize and characterize a size-expanded thymine nucleoside, diox T.
  • To evaluate the photophysical properties and DNA incorporation of diox T.
  • To explore the application of diox T in DNA base-pair discrimination and polymorphism typing.

Main Methods:

  • Synthesis of the diox T nucleoside.
  • Photophysical characterization including quantum yield determination.
  • Incorporation of diox T into single- and double-stranded DNA.
  • Fluorescence spectroscopy to analyze base-pairing interactions and environmental sensitivity.
  • Demonstration of single nucleoside polymorphism typing.

Main Results:

  • Diox T exhibits a high quantum yield (0.36) and environmental sensitivity.
  • Incorporated diox T shows excellent photophysical properties in DNA (average quantum yield 0.20).
  • Diox T's fluorescence depends on neighboring bases without destabilizing DNA duplexes.
  • The adenine-diox T base pair shows higher fluorescence than mismatched pairs, with self-quenching effects.
  • Polymorphism typing successfully discriminated adenine using diox T.

Conclusions:

  • Diox T is a promising thymine surrogate with desirable photophysical characteristics for DNA applications.
  • Its unique fluorescence properties enable sensitive detection of specific base pairs.
  • Diox T holds potential for diverse applications in chemical biology, including genetic analysis.