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. 2024 Dec 10;25(24):13240.
doi: 10.3390/ijms252413240.

Sequence-Specific Free Energy Changes in DNA/RNA Induced by a Single LNA-T Modification in Antisense Oligonucleotides

Elisa Tomita-Sudo  1 , Tomoka Akita  2 , Nae Sakimoto  1 , Saori Tahara-Takamine  2 , Junji Kawakami  1   2
Affiliations

Sequence-Specific Free Energy Changes in DNA/RNA Induced by a Single LNA-T Modification in Antisense Oligonucleotides

Elisa Tomita-Sudo et al. Int J Mol Sci. .

Abstract

2',4'-methylene bridged nucleic acid/locked nucleic acid (2',4'-BNA/LNA; LNA) is a modified nucleic acid that improves the function of antisense oligonucleotide therapeutics. In particular, LNA in the DNA strand increases its binding affinity for the target RNA. Predicting the binding affinities of LNA-containing antisense oligonucleotides and RNA duplexes is useful for designing antisense oligonucleotides. The nearest neighbor parameters may be useful for binding affinity prediction, similar to those for natural nucleic acids. However, the sequence dependence of the thermodynamic stability of DNA/RNA duplexes containing LNA remains unexplored. Therefore, in this study, we evaluated the thermodynamic stabilities of DNA/RNA duplexes containing a single LNA modification in the DNA strand. We found that LNA-stabilized DNA/RNA duplexes averaged -1.5 kcal mol-1. Our findings suggest that the thermodynamic stabilization effect of LNA is sequence-specific.

Keywords: LNA-containing antisense oligonucleotides; locked nucleic acid; thermodynamic stability.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
CD spectra of (A) i, (B) ii, (C) iii, and (D) iv DNA/RNA duplexes. The total concentration of the oligonucleotides (Ct) was 30 μM. The direction of the arrow indicates the temperature change from 20 °C to 60 °C.
Figure 2
Figure 2
ΔΔG°37 values of i–iv series duplexes. The dotted line indicates the average ΔΔG°37 for duplexes containing the same N1N2(L)N3 triplet.
Figure 3
Figure 3
ΔΔH° (upper panel) and −TΔΔS° (lower panel) values of i–iv series duplexes. The dotted line indicates the average ΔΔH° or −TΔΔS° for duplexes containing the same N1N2(L)N3 triplet.
Figure 4
Figure 4
Predicted ΔG°37 of the triplets including LNA substitution. ΔG°37 of the triplets obtained in this study are listed in decreasing order. The black bar indicates the predicted ΔG°37 of the natural-type DNA/RNA duplex in the presence of 100 mM NaCl, obtained by multiplying the ΔG°37 of the triplet predicted from the NN parameters in the presence of 1 M NaCl by 0.63 (according to Nakano S. et al. [37]). The white bars are the ΔΔG°37 obtained in this study.
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