Theoretical design of antisense RNA structures substantially improves annealing kinetics and efficacy in human cells
- 1 January 1998
- journal article
- research article
- Published by Springer Nature in Nature Biotechnology
- Vol. 16 (1) , 64-68
- https://doi.org/10.1038/nbt0198-64
Abstract
The success of antisense therapeutics is not predictable despite their widespread use in biotechnology and molecular medicine. The relationship between RNA structure and biological effectiveness is largely not understood; however, antisense RNA-mediated effects in vivo seem to be related to annealing kinetics in vitro. This study suggests that terminal unpaired nucleotides and overall flexibility of antisense RNA directed against the human immunodeficiency virus type 1 (HIV-1) are related to fast RNA-RNA annealing in vitro as well as to strong inhibition of virus replication in human cells. Annealing rate constants of computer-selected antisense RNA species approach the values for natural antisense RNA in the order of 10(6) M-1s-1. When considering the unfavorable stability in cellular extracts of antisense RNA species that were found to anneal fast in vitro, an antisense effect against HIV-1 in human cells was observed that was 10- to 10,000-fold stronger than that measured for species predicted to anneal slowly. A computer-supported structural design of antisense RNA can serve as a platform to determine RNA-RNA association in vitro and biological effectiveness in living cells.Keywords
This publication has 37 references indexed in Scilit:
- Implications of RNA Structure on the Annealing of a Potent Antisense RNA Directed against the Human Immunodeficiency Virus Type 1Biochemistry, 1997
- Antisense RNA Control in Bacteria, Phages, and PlasmidsAnnual Review of Microbiology, 1994
- Dynamic RNA-RNA Interactions in the SpliceosomeAnnual Review of Genetics, 1994
- Complementary Large Loops Determine the Rate of RNA Duplex Formation in Vitro in the Case of an Effective Antisense RNA Directed Against the Human Immunodeficiency Virus Type 1Journal of Molecular Biology, 1993
- Regulation of plant gene expression by antisense RNAFEBS Letters, 1990
- Control of colE1 plasmid replicationJournal of Molecular Biology, 1990
- Insertion sequence IS10 anti-sense pairing initiates by an interaction between the 5′ end of the target RNA and a loop in the anti-sense RNAJournal of Molecular Biology, 1989
- Control of cole 1 plasmid replication: Enhancement of binding of RNA I to the primer transcript by the rom proteinCell, 1984
- Thermodynamics and kinetics of the helix‐coil transition of oligomers containing GC base pairsBiopolymers, 1973
- Excluded volume effects on the rate of renaturation of DNABiopolymers, 1971