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反义寡核苷酸序列穿透关系的研究。

Investigation of Sequence-Penetration Relationships of Antisense Oligonucleotides.

机构信息

Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, USA.

出版信息

Chembiochem. 2023 May 2;24(9):e202300009. doi: 10.1002/cbic.202300009. Epub 2023 Apr 4.


DOI:10.1002/cbic.202300009
PMID:36791388
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10305730/
Abstract

A major limitation for the development of more effective oligonucleotide therapeutics has been a lack of understanding of their penetration into the cytosol. While prior work has shown how backbone modifications affect cytosolic penetration, it is unclear how cytosolic penetration is affected by other features including base composition, base sequence, length, and degree of secondary structure. We have applied the chloroalkane penetration assay, which exclusively reports on material that reaches the cytosol, to investigate the effects of these characteristics on the cytosolic uptake of druglike oligonucleotides. We found that base composition and base sequence had moderate effects, while length did not correlate directly with the degree of cytosolic penetration. Investigating further, we found that the degree of secondary structure had the largest and most predictable correlations with cytosolic penetration. These methods and observations add a layer of design for maximizing the efficacy of new oligonucleotide therapeutics.

摘要

开发更有效的寡核苷酸治疗药物的主要限制因素是缺乏对其进入细胞质的理解。虽然之前的工作已经表明了骨架修饰如何影响细胞质渗透,但尚不清楚包括碱基组成、碱基序列、长度和二级结构程度在内的其他特征如何影响细胞质渗透。我们应用氯烷烃渗透测定法,该方法专门报告到达细胞质的物质,来研究这些特征对类似药物的寡核苷酸进入细胞质的影响。我们发现碱基组成和碱基序列有中等影响,而长度与细胞质渗透程度没有直接相关性。进一步研究发现,二级结构的程度与细胞质渗透的相关性最大且最可预测。这些方法和观察结果为最大限度地提高新寡核苷酸治疗药物的疗效增加了一层设计。

相似文献

[1]
Investigation of Sequence-Penetration Relationships of Antisense Oligonucleotides.

Chembiochem. 2023-5-2

[2]
Quantitative Measurement of Cytosolic and Nuclear Penetration of Oligonucleotide Therapeutics.

ACS Chem Biol. 2022-2-18

[3]
Quantitative measurement of cytosolic penetration using the chloroalkane penetration assay.

Methods Enzymol. 2020

[4]
Hairpin antisense oligonucleotides containing 2'-methoxynucleosides with base-pairing in the stem region at the 3'-end: penetration, localization, and Anti-HIV activity.

Biochem Biophys Res Commun. 1996-11-12

[5]
Parallel Screening Using the Chloroalkane Penetration Assay Reveals Structure-Penetration Relationships.

ACS Chem Biol. 2021-7-16

[6]
5-Dihydroxyboryluridine enhances cytosolic penetration of antisense oligonucleotides.

Chem Commun (Camb). 2023-7-11

[7]
Selecting optimal oligonucleotide composition for maximal antisense effect following streptolysin O-mediated delivery into human leukaemia cells.

Nucleic Acids Res. 1998-4-1

[8]
Importance of nucleotide sequence and chemical modifications of antisense oligonucleotides.

Biochim Biophys Acta. 1999-12-10

[9]
Antisense oligonucleotides with different backbones. Modification of splicing pathways and efficacy of uptake.

J Biol Chem. 1999-7-30

[10]
Bias in nucleotide composition of antisense oligonucleotides.

Antisense Nucleic Acid Drug Dev. 1996

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Recent advances in methods for quantifying the cell penetration of macromolecules.

Curr Opin Chem Biol. 2024-8

[2]
Comparing Cell Penetration of Biotherapeutics across Human Cell Lines.

ACS Chem Biol. 2024-6-21

[3]
Inclusive Pattern Generation Protocols to Decode Thiol-Mediated Uptake.

ACS Cent Sci. 2024-4-17

[4]
HOPS-Dependent Endosomal Escape Demands Protein Unfolding.

ACS Cent Sci. 2024-3-26

[5]
Novel STAT3 oligonucleotide compounds suppress tumor growth and overcome the acquired resistance to sorafenib in hepatocellular carcinoma.

Acta Pharmacol Sin. 2024-8

[6]
Investigating the Cytosolic Delivery of Proteins by Lipid Nanoparticles Using the Chloroalkane Penetration Assay.

Biochemistry. 2024-2-9

本文引用的文献

[1]
Evaluation of Gene Expression Knock-Down by Chemically and Structurally Modified Gapmer Antisense Oligonucleotides.

Chembiochem. 2022-8-3

[2]
Thoughts on how to think (and talk) about RNA structure.

Proc Natl Acad Sci U S A. 2022-4-26

[3]
Quantitative Measurement of Cytosolic and Nuclear Penetration of Oligonucleotide Therapeutics.

ACS Chem Biol. 2022-2-18

[4]
Reduction of Off-Target Effects of Gapmer Antisense Oligonucleotides by Oligonucleotide Extension.

Mol Diagn Ther. 2022-1

[5]
Stapled β-Hairpins Featuring 4-Mercaptoproline.

J Am Chem Soc. 2021-9-22

[6]
Thiol-Mediated Uptake.

JACS Au. 2021-5-3

[7]
A naked antisense oligonucleotide with phosphorothioate linkages is taken up intracellularly more efficiently but functions less effectively.

Biochem Biophys Res Commun. 2021-10-8

[8]
Oligonucleotide Phosphorothioates Enter Cells by Thiol-Mediated Uptake.

Angew Chem Int Ed Engl. 2021-8-23

[9]
Directed evolution of cyclic peptides for inhibition of autophagy.

Chem Sci. 2021-1-13

[10]
The Challenges and Strategies of Antisense Oligonucleotide Drug Delivery.

Biomedicines. 2021-4-16

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