---
title: "gRNA truncation as a tunable method to modulate base editing and reduce bystander edits"
id: "biorxiv-4-guide-rna-truncation-as-a-tunable-approach-for-modulating-base-editing-outcomes"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-4-guide-rna-truncation-as-a-tunable-approach-for-modulating-base-editing-outcomes"
content_type: "clinical_feed_article"
specialty: "General"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.09.10.749999v1?rss=1"
published_at: "2026-09-13T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# gRNA truncation as a tunable method to modulate base editing and reduce bystander edits
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-4-guide-rna-truncation-as-a-tunable-approach-for-modulating-base-editing-outcomes
- **Specialty:** [General](https://medichelpline.com/clinical-feed/general.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.09.10.749999v1?rss=1)
- **Published At:** 2026-09-13T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- The study assessed **guide RNA (gRNA) truncation** as a strategy to modulate nucleotide-level outcomes of **base editing**, using ABE8e in HUDEP-2 cells and other contexts reported by the authors. - Truncated gRNAs maintained measurable editing activity down to **15-nucleotide** lengths, though activity varied strongly with **target sequence**, **gRNA length**, and **delivery method**. - Shortening gRNAs changed editing efficiencies at individual positions within the canonical editing window, allowing selective reduction of **bystander editing** while preserving intended on-target conversion at several loci, including a therapeutically relevant **HbE** target. - At short gRNA lengths, large deletions at homologous globin loci were not detectable, consistent with loss of **Cas9 nickase** activity when gRNAs are sufficiently shortened. - Similar length-dependent effects were observed with **cytosine base editors**, PAM-relaxed ABE8e variants, and in primary **hematopoietic stem and progenitor cells (HSPCs)**, although the optimal truncated gRNA length differed across contexts. - The authors conclude that **gRNA length** is an actionable tuning parameter to adjust nucleotide-level base editing outcomes and reduce undesired bystander edits, with context-specific optimization required.
## Clinical Analysis & Structured Key Points
Guide RNA truncation as a tunable approach for modulating base editing outcomes | bioRxiv Skip to main content New Results Guide RNA truncation as a tunable approach for modulating base editing outcomes View ORCID Profile Anila George , View ORCID Profile Kirti Prasad , Poornasree Sadanandan , View ORCID Profile Srujan Marepally , View ORCID Profile Saravanabhavan Thangavel , View ORCID Profile Kumarasamypet Murugesan Mohankumar doi: https://doi.org/10.64898/2026.09.10.749999 Anila George Centre for Stem Cell Research (A unit of BRIC - inStem, Bengaluru), Christian Medical College Campus, Bagayam Vellore, India. Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Anila George Kirti Prasad Centre for Stem Cell Research (A unit of BRIC - inStem, Bengaluru), Christian Medical College Campus, Bagayam Vellore, India. Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Kirti Prasad Poornasree Sadanandan Centre for Stem Cell Research (A unit of BRIC - inStem, Bengaluru), Christian Medical College Campus, Bagayam Vellore, India. Find this author on Google Scholar Find this author on PubMed Search for this author on this site Srujan Marepally Centre for Stem Cell Research (A unit of BRIC - inStem, Bengaluru), Christian Medical College Campus, Bagayam Vellore, India. Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Srujan Marepally Saravanabhavan Thangavel Centre for Stem Cell Research (A unit of BRIC - inStem, Bengaluru), Christian Medical College Campus, Bagayam Vellore, India. Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Saravanabhavan Thangavel Kumarasamypet Murugesan Mohankumar Centre for Stem Cell Research (A unit of BRIC - inStem, Bengaluru), Christian Medical College Campus, Bagayam Vellore, India. Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Kumarasamypet Murugesan Mohankumar For correspondence: mohankumarkm{at}cmcvellore.ac.in Abstract Info/History Metrics Supplementary material Preview PDF Abstract Base editing enables programmable nucleotide conversion but can be limited by bystander editing and unintended genomic alterations. Here, we investigated guide RNA (gRNA) truncation as a strategy to modulate base editing outcomes. On editing across multiple genomic loci using ABE8e in HUDEP-2 cells, we found that truncated gRNAs retained measurable editing activity at lengths as short as 15 nucleotides, although activity depended strongly on target sequence, gRNA length, and delivery method. Importantly, truncation altered editing efficiencies at individual nucleotides within the editing window, enabling selective reduction of bystander editing while preserving on-target conversion at several loci, including a therapeutically relevant HbE target. Truncated gRNAs also eliminated detectable large deletions at homologous globin loci, consistent with loss of Cas9 nickase activity at short gRNAs lengths. Similar length dependent effects were observed with cytosine base editing, PAM relaxed ABE8e, and in primary hematopoietic stem and progenitor cells (HSPCs), although the optimal gRNA length varied between contexts. Together, these findings establish gRNA length as an additional parameter for tuning nucleotide level base editing outcomes and reducing bystander editing. Competing Interest Statement The authors have declared no competing interest. Funder Information Declared Wellcome Trust/DBT India Alliance, https://ror.org/04reqzt68 , IA/TSG/22/1/600410 Indian Council of Medical Research, https://ror.org/0492wrx28 , EM/EM/dev/CAR-2024-01-0113/F2/2024(228287) Anusandhan National Research Foundation , CRG/2022/00606 Department of Biotechnology , BT/PR45683/MED/31/465/2022 Council of Scientific and Industrial Research, https://ror.org/021wm7p51 , Senior Research Fellowship - Anila George Indian Council of Medical Research , Senior Research Fellowship - Kirti Prasad Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Back to top Previous Posted September 13, 2026. Download PDF Supplementary Material Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. You are going to email the following Guide RNA truncation as a tunable approach for modulating base editing outcomes Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website. Your Personal Message CAPTCHA This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. Share Guide RNA truncation as a tunable approach for modulating base editing outcomes Anila George , Kirti Prasad , Poornasree Sadanandan , Srujan Marepally , Saravanabhavan Thangavel , Kumarasamypet Murugesan Mohankumar bioRxiv 2026.09.10.749999; doi: https://doi.org/10.64898/2026.09.10.749999 Share This Article: Copy Citation Tools Guide RNA truncation as a tunable approach for modulating base editing outcomes Anila George , Kirti Prasad , Poornasree Sadanandan , Srujan Marepally , Saravanabhavan Thangavel , Kumarasamypet Murugesan Mohankumar bioRxiv 2026.09.10.749999; doi: https://doi.org/10.64898/2026.09.10.749999 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Areas All Articles Animal Behavior and Cognition (7983) Biochemistry (18684) Bioengineering (14804) Bioinformatics (44278) Biophysics (22531) Cancer Biology (19650) Cell Biology (26810) Clinical Trials (138) Developmental Biology (13915) Ecology (20940) Epidemiology (2067) Evolutionary Biology (25400) Genetics (16132) Genomics (23443) Immunology (18640) Microbiology (42360) Molecular Biology (17992) Neuroscience (93155) Paleontology (695) Pathology (2974) Pharmacology and Toxicology (5075) Physiology (8087) Plant Biology (15944) Scientific Communication and Education (2094) Synthetic Biology (4546) Systems Biology (10202) Zoology (2381)
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