RNA-Binding affinities and crystal structure of oligonucleotides containing five-atom amide-based backbone structures

Area of Science:

• Biochemistry
• Molecular Biology
• Medicinal Chemistry

Background:

• Nucleic acid analogues are crucial for understanding DNA and RNA structure-function relationships.
• Most analogues maintain the native four-atom linker, but variations are explored for novel properties.
• Previous studies showed slight destabilization of RNA-DNA hybrids with amide-linked dimers.

Purpose of the Study:

• To investigate how different five-atom amide linker chemistries affect the RNA-binding affinity of modified DNA strands.
• To analyze the thermodynamic stability of RNA-DNA duplexes containing varying numbers of modified dimers.
• To explore the impact of stereochemistry within the amide linker on duplex stability.

Main Methods:

• Synthesis of five distinct amide-linked nucleoside dimers, including variations with and without 2'-methoxy groups.
• Incorporation of one to seven consecutive modified dimers into DNA strands.
• Thermodynamic analysis of DNA-RNA duplex formation using techniques like isothermal titration calorimetry.
• Circular Dichroism (CD) spectroscopy and X-ray crystallography to assess structural integrity.

Main Results:

• Several five-atom amide-linked dimers significantly enhanced RNA-binding affinity compared to native DNA.
• Linker stereochemistry at the chiral center differentially affected duplex stability.
• The presence of one to seven modified dimers did not disrupt the overall duplex geometry, as confirmed by structural studies.
• Methoxy modifications influenced binding affinity and duplex stability.

Conclusions:

• Novel five-atom amide linkers can be designed to improve DNA-RNA hybrid stability.
• Stereochemistry plays a critical role in modulating the binding affinity of modified nucleic acids.
• Stable cross-pairing between DNA and RNA does not necessitate identical linker lengths, challenging previous assumptions.