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This study compared DNA (G3T) and RNA (g3u) quadruplexes, finding RNA analogues exhibit higher thermal stability. Substitutions revealed stacking interactions favor DNA, while loops enhance RNA quadruplex stability.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • G-quadruplexes are stable nucleic acid structures with potential applications.
  • The G3T DNA sequence forms a parallel quadruplex with high thermal stability.
  • The RNA analogue, g3u, shares the same folding topology and shows enhanced stability over G3T.

Purpose of the Study:

  • To investigate the thermal stability of G3T, g3u, and chimeric DNA-RNA quadruplexes.
  • To elucidate the contributions of specific nucleotide substitutions to quadruplex stability.
  • To understand the role of stacking interactions and loop regions in DNA vs. RNA quadruplexes.

Main Methods:

  • Melting experiments were conducted on G3T, g3u, and over 30 chimeric constructs.
  • Systematic substitution of DNA nucleotides (G) with RNA nucleotides (g) and loop thymines (T) with uracils (u) was performed.
  • Thermal stability was assessed by measuring melting temperatures (Tm) under varying conditions.

Main Results:

  • The all-RNA g3u quadruplex is approximately 13 °C more stable than the G3T DNA quadruplex.
  • Most G-to-g substitutions destabilized the G3T quadruplex, while only a few substitutions and loop T-to-u changes enhanced stability.
  • The combined stabilizing effects of specific substitutions in g3u outweighed the destabilizing effects of others, leading to its overall higher stability.
  • Stacking interactions are more favorable in parallel DNA quadruplexes, whereas chain-reversal loops are crucial for RNA quadruplex stability.

Conclusions:

  • RNA quadruplexes exhibit superior thermal stability compared to their DNA counterparts due to favorable loop structures.
  • Stacking interactions are more advantageous in DNA quadruplexes, particularly at the 5'-end.
  • These findings provide insights for the rational design of quadruplexes for biotechnological and therapeutic applications.