Gapmer ASO Designer - Yunnan University

About Clin ASO Designer

Platform Overview

Gapmer ASO Designer is an Antisense Oligonucleotide (ASO) design platform developed by the Bioinformatics team at Yunnan University. The platform utilizes advanced algorithms to provide high-efficiency, precise ASO design solutions.

Analysis Pipeline

1. Gene Sequence Acquisition → 2. Target Site Prediction → 3. Specificity Validation → 4. Off-target Effect Assessment → 5. Result Optimization → 6. Report Generation

Gapmer ASO Mechanism

reference: Roberts, T.C., Langer, R. & Wood, M.J.A. Advances in oligonucleotide drug delivery. Nat Rev Drug Discov 19, 673–694 (2020). https://doi.org/10.1038/s41573-020-0075-7 Antisense oligonucleotides (ASOs) bind to target RNA through complementary base pairing. This binding event recruits RNase H1 enzyme, which cleaves the target RNA, thereby preventing protein translation and reducing target gene expression.

Antisense oligonucleotides (ASOs) bind to the target RNA via complementary base pairing

Recruit intracellular RNase H1 enzyme

RNase H1 catalyzes hydrolysis of the RNA strand in the RNA-DNA heteroduplex

Degradation of target RNA blocks protein translation

Gapmer ASO Design Submission

Target Species

Gene Name Gene symbol

ASO Length The most commonly used parameters are cEt 16nt, MOE 20nt.

Select Homologous Species

MaxGC Content Value must be between 0.35 and 0.7

Number of ASOs to Design Number of ASO sequences to generate

Selection Priority Priority for filtering ASO sequences

Email Address

Investigate ASO Homology

Investigating the compatibility of ASO across different species (Based on RNAhybrid v2.12).

Gene Name

ASO Sequence

Species

Email Address

Investigate SNP in ASO

SNP157

Off-Target Effect Analysis

Target Gene

ASO Sequence

Genome Database

Email Address

Citation & Contact Information

Developer & Contact

👤

Principal Investigator

Yunkun Dang,Fan Lai

School of Life Sciences

Yunnan University

👤

ShunKai Chen

School of Life Sciences

Yunnan University

📧

Email

chenshunkai@stu.ynu.edu.cn

📱

Phone

+86 18725174715

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Address

School of Life Sciences

Yunnan University

Kunming, Yunnan Province, China

Available Tools

ASO Design Tool

Design gapmer ASOs with optimized parameters

Homology Analysis Tool

Analyze ASO compatibility across species

SNP Analysis Tool

Evaluate SNP effects on ASO binding

Off-Target Analysis Tool

Predict potential off-target effects

License & Source Code

⭐ View on GitHub

ClinASO is licensed under the MIT License

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.