publictm: Published melting temperatures for LNA-modified...

In Santaris/affinity: Functions to do thermodynamics on oligonucleotides

Description

All published (until mid-2014) melting temperatures (tm) of LNA-modified phosphorothioate oligonucleotides binding to perfectly complementary RNA.

Usage

data(publictm)

Format

A dataframe with six columns. Each row represents either an oligonucleotide.

IDstudy

Unique oligonucleotide ID related to the study.

Sequence

The sequence and modification pattern of the oligonucleotide in camelcase(LNA:uppercase, DNA: lowercase).

Measure.Tm

The experimentally measured melting temperature.

IDref

The oligonucleotide ID used in the study.

Reference

The study reference.

Details

The contribution to the change in entropy (cal/(mol*K)).

Source

Collected from the studies referenced below.

References

Elmen, J. et al., 2008. LNA-mediated microRNA silencing in non-human primates. Nature, 452, pp.896-899.

Frieden, M. et al., 2003. Expanding the design horizon of antisense oligonucleotides with alpha-L-LNA. Nucleic Acids Research, 31, pp.6365-6372.

Hansen, J.B. et al., 2008. SPC3042: a proapoptotic survivin inhibitor. Molecular cancer therapeutics, 7, pp.2736-2745.

Lennox, K.A. et al., 2006. Characterization of modified antisense oligonucleotides in Xenopus laevis embryos. Oligonucleotides, 16, pp.26-42.

Obad, S. et al., 2011. Silencing of microRNA families by seed-targeting tiny LNAs. Nature Genetics, 43, pp.371-378.

Stanton, R.V. et al., 2012. Chemical Modification Study of Antisense Gapmers. Nucleic acid therapeutics, 22, pp.344-359.

Straarup, E.M. et al., 2010. Short locked nucleic acid antisense oligonucleotides potently reduce apolipoprotein B mRNA and serum cholesterol in mice and non-human primates. Nucleic Acids Research, 38, pp.7100-7111.

Yamamoto, T. et al, 2014. Evaluation of Multiple-Turnover Capability of Locked Nucleic Acid Antisense Oligonucleotides in Cell-Free RNase H-Mediated Antisense Reaction and in Mice. Nucleic Acids Therapeutics, in press.

Wahlestedt, C. et al., 2000. Potent and nontoxic antisense oligonucleotides containing locked nucleic acids. Proceedings of the National Academy of Sciences of the United States of America, 97, pp.5633-5638.

Examples

data(publictm)

## select oligos from Stanton et al., 2012
i <-  grep("Stanton",publictm$IDstudy)

## calculate tm adjusted for PS linkages
predtm <- calculate.affinity(publictm$Sequence[i])$tm

## plot the results
plot(publictm$Measured.Tm[i], predtm, pch=16, xlab="Measured Tm", ylab="Predicted Tm")

Santaris/affinity documentation built on May 9, 2019, 12:43 p.m.