Prediction of antisense oligonucleotide efficacy by in vitro methods

Матвеева, О. В.; Felden, Brice; Tsodikov, Alexander; Johnston, Joseph F.; Monia, Brett P.; Atkins, John F.; Gesteland, Raymond F.; Freier, Susan M.

doi:10.1038/4362

Cited by 38 publications

(12 citation statements)

References 11 publications

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“…In addition to filling this void, we are working toward addressing the question of whether high affinity binding in cell free assays corresponds to high affinity binding within a living cell. In the few cases where extensive comparison has been made, agreement between in vitro experiments and intracellular data suggests that binding affinity is a useful predictor of antisense activity (Matveeva et al, 1998). The computational strategy described here provides a convenient, inexpensive method for selecting candidate oligonucleotides to guide further exploration.…”

Section: Discussionmentioning

confidence: 85%

Prediction of antisense oligonucleotide binding affinity to a structured RNA target

Walton

Stephanopoulos

Yarmush

et al. 1999

Biotechnol. Bioeng.

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Section: Discussionmentioning

confidence: 85%

Prediction of antisense oligonucleotide binding affinity to a structured RNA target

Walton

Stephanopoulos

Yarmush

et al. 1999

Biotechnol. Bioeng.

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“…These results are consistent with the fact that not every ASO perfectly matched to an intended transcript reduces that transcript. This observation has been explained by differences in RNA accessibility due to secondary structure, protein binding, or processing kinetics [52][53][54]. Thus, a target site in an unintended transcript may be less accessible than that in the intended transcript or the unintended transcript itself may be less available for antisense targeting.…”

Section: Mismatches In the Gap Were More Likely To Be Selectivementioning

confidence: 99%

Likelihood of Nonspecific Activity of Gapmer Antisense Oligonucleotides Is Associated with Relative Hybridization Free Energy

Watt

Swayze

et al. 2020

Nucleic Acid Therapeutics

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Reduction of matched and nearly complementary unintended transcripts was evaluated for 96 antisense oligonucleotides (ASOs) and 832 nearly matched unintended transcripts. The ASOs were 16-20 nucleotide ''gapmers'' with a gap of 8-10 DNA residues and 2¢-O-methoxy-ethyl or constrained-ethyl substitutions in the wings. Most unintended transcripts were not reduced or were reduced with a potency more than 10-fold weaker than the intended transcript. For the unintended transcripts that were reduced, a strong correlation between relative potency of the intended versus the unintended transcript with predicted free energy of hybridization was observed. These results suggest ASO selectivity should be evaluated by testing for reduction of the unintended transcripts predicted to bind most stably to the ASO.

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“…Matveeva et al [86] reported an RNase H-based strategy for mapping RNAs which employs a pool of DNA fragments complementary to the target rather than a complete library of oligonucleotides. They determined accessible sites on c-raf mRNA for which cellular data on the antisense activity of several oligonucleotides were available [34].…”

Section: Digested Template Library Combined With Rnase Hmentioning

confidence: 99%

“…Matveeva et al [92] described a statistical evaluation of the degree of correlation between data of in vitro assays that measure human c-raf mRNA regional accessibility to ASOs and levels of intracellular mRNA reduction produced by these ASOs. Data generated with RNase H mapping [86] and gel-mobility shift assays [78,106] were used for the calculation of correlation coefficients.…”

Section: Correlation Between In Vitro Accessibility and Intracellularmentioning

confidence: 99%

Identifying Accessible Sites in RNA: The First Step in Designing Antisense Reagents

Pan

Clawson²

2006

CMC

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There is continued interest in development of antisense reagents (ASRs), including especially antisense oligonucleotides and small interfering RNAs, for experimental as well as therapeutic purposes. Optimization of ASRs begins with target site selection. Here we review protocols which have been developed to empirically determine effective target sites in RNAs. Such library selection technologies have demonstrated clear utility, and in vitro identification of sites has generally proven effective for cellular applications. A few groups are developing large combinatorial libraries and approaches to adapt use of such libraries to individual target RNAs, as well as learning algorithms to help with the optimization of target sites, particularly with respect to small interfering RNAs.

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Prediction of antisense oligonucleotide efficacy by in vitro methods

Cited by 38 publications

References 11 publications

Prediction of antisense oligonucleotide binding affinity to a structured RNA target

Prediction of antisense oligonucleotide binding affinity to a structured RNA target

Likelihood of Nonspecific Activity of Gapmer Antisense Oligonucleotides Is Associated with Relative Hybridization Free Energy

Identifying Accessible Sites in RNA: The First Step in Designing Antisense Reagents

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