Position-dependent effects on stability in tricyclo-DNA modified oligonucleotide duplexes
Damian Ittig1, Anna-Barbara Gerber, Christian J Leumann
1Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.
Nucleic Acids Research
|August 20, 2010
Summary
Tricyclo (tc)-nucleosides in RNA decrease binding affinity unless arranged continuously. In DNA, tc-nucleosides show varied effects, influencing RNAi and antisense therapy design.
Area of Science:
- Medicinal Chemistry
- Molecular Biology
- Biochemistry
Background:
- Oligonucleotides are crucial in therapeutic applications like antisense and RNA interference (RNAi).
- Modifying oligonucleotide backbones can alter their stability and binding properties.
- Tricyclo (tc) nucleosides represent a novel modification for oligonucleotide design.
Purpose of the Study:
- To synthesize and characterize oligonucleotides with tricyclo (tc) nucleosides.
- To evaluate the impact of tc-nucleoside arrangement on duplex stability and binding affinity.
- To investigate the conformational effects of tc-modifications in DNA and RNA.
Main Methods:
- Synthesis of oligodeoxyribonucleotides and oligoribonucleotides containing tc-nucleosides.
- Thermal denaturation studies (Tm) to assess duplex stability.
- Thermodynamic analysis (ΔH) of binding.
- Circular Dichroism (CD) spectroscopy.
- Molecular dynamics (MD) simulations.
Main Results:
- Non-continuous tc-residues in RNA significantly decrease duplex affinity due to reduced pairing enthalpy.
- Continuous arrangement of tc-residues in RNA restores Tm and enhances binding affinity.
- Oligodeoxyribonucleotides with tc-substitutions show minor changes in DNA duplex Tm but significant increases in RNA duplex Tm.
- RNA backbone tc-residues induce conformational changes in neighboring nucleotides, unlike DNA backbone tc-residues.
Conclusions:
- The arrangement of tc-nucleosides critically influences oligonucleotide duplex stability and binding affinity.
- Tc-nucleoside modifications in RNA have a more pronounced effect on conformation and binding than in DNA.
- These findings provide insights for designing tc-DNA oligonucleotides for therapeutic applications such as antisense and RNAi therapy.
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