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Area of Science:

  • Medicinal Chemistry
  • Oligonucleotide Therapeutics
  • Structural Biology

Background:

  • Carbocyclic ribonucleosides offer potential advantages in oligonucleotide therapeutics.
  • Efficient synthesis of modified nucleoside building blocks is crucial for developing novel therapeutics.

Purpose of the Study:

  • To develop scalable syntheses for carbocyclic ribonucleotide phosphoramidites and solid-support building blocks.
  • To evaluate the impact of carbocyclic RNA (car-RNA) modifications on duplex stability and conformation.

Main Methods:

  • Convenient and scalable synthetic routes were established for all four carbocyclic ribonucleotide phosphoramidites.
  • Solid-phase synthesis was employed to incorporate the uridine solid-support building block.
  • Crystallographic analysis was used to confirm the stereochemistry of the synthesized building blocks.
  • Thermodynamic stability of modified and unmodified RNA duplexes was assessed.
  • Circular dichroism spectroscopy was utilized to analyze the global conformations of the duplexes.

Main Results:

  • Scalable syntheses for all four carbocyclic ribonucleotide phosphoramidites and the uridine solid-support building block were successfully developed.
  • Crystallographic data confirmed the precise configuration and stereochemistry of these novel building blocks.
  • Oligonucleotide duplexes incorporating carbocyclic RNA modifications exhibited decreased thermodynamic stability compared to unmodified RNA duplexes.
  • Circular dichroism spectroscopy revealed that the global conformations of carbocyclic RNA-containing duplexes were comparable to those of standard RNA duplexes.

Conclusions:

  • The developed synthetic methods provide essential building blocks for carbocyclic RNA therapeutics.
  • Carbocyclic RNA modifications impact duplex stability but not global conformation, suggesting potential for therapeutic applications.
  • Further studies are warranted to explore the therapeutic potential and optimize the design of carbocyclic RNA-containing oligonucleotides.