---
title: "FAST-MaP: Primer-less Sequencing Protocol for Per-Nucleotide RNA Structure Mapping"
id: "biorxiv-10-fast-map-chemical-mapping-of-rna-structures-using-primer-less-sequencing"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-10-fast-map-chemical-mapping-of-rna-structures-using-primer-less-sequencing"
content_type: "clinical_feed_article"
specialty: "General"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.09.22.753544v1?rss=1"
published_at: "2026-09-23T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# FAST-MaP: Primer-less Sequencing Protocol for Per-Nucleotide RNA Structure Mapping
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-10-fast-map-chemical-mapping-of-rna-structures-using-primer-less-sequencing
- **Specialty:** [General](https://medichelpline.com/clinical-feed/general.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.09.22.753544v1?rss=1)
- **Published At:** 2026-09-23T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- FAST-MaP (Fast and Accessible Sequencing Technology for Mutational Profiling) is a protocol for per-nucleotide **RNA structure** characterization that requires only standard molecular-biology equipment and no in-house sequencing or bioinformatics expertise. - The method chemically modifies RNA with orthogonal probes (reported probes: **2A3** and **DMS**), followed by reverse transcription and PCR to produce dsDNA amplicons for sequencing. - Sequencing is performed via a commercial **primer-less sequencing** service; returned FASTQ files are processed by a freely accessible web server to produce normalized reactivity profiles within minutes. - The complete workflow, from DNA template preparation to structural reactivity data, can be completed in approximately one week. - The authors demonstrate the workflow on a 659-nucleotide RNA and show how the protocol can test structure preservation across buffers and evaluate specific secondary and tertiary structure predictions from computational modeling or cryo-EM. - FAST-MaP is presented as accessible to users without sequencing infrastructure or bioinformatics training, lowering barriers to routine experimental RNA structure testing across fields such as structural biology, virology, and RNA therapeutics. - Authors disclosed an invention disclosure filed with Stanford University covering the protocol and analysis tools; additional competing interests were not reported. - Funding sources reported include the National Institute of General Medical Sciences (NIGMS) R35 GM122579 and the Howard Hughes Medical Institute; supplementary materials and data/code links are provided by the authors.
## Clinical Analysis & Structured Key Points
FAST-MaP: Chemical Mapping of RNA Structures Using Primer-less Sequencing | bioRxiv Skip to main content New Results FAST-MaP: Chemical Mapping of RNA Structures Using Primer-less Sequencing View ORCID Profile Jigyasa Verma , View ORCID Profile Hamish Milson Blair , View ORCID Profile Wipapat Kladwang , View ORCID Profile Rhiju Das doi: https://doi.org/10.64898/2026.09.22.753544 Jigyasa Verma Stanford University Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Jigyasa Verma Hamish Milson Blair Stanford University Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Hamish Milson Blair Wipapat Kladwang Stanford University Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Wipapat Kladwang Rhiju Das Stanford University Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Rhiju Das For correspondence: rhiju{at}stanford.edu Abstract Info/History Metrics Supplementary material Data/Code Preview PDF Abstract RNA structure governs the function of non-coding RNAs and influences mRNA stability and translation, making testing of models of experimental RNA structure relevant to fields spanning structural biology, virology, and molecular therapeutics. Here we present FAST-MaP (Fast and Accessible Sequencing Technology for Mutational Profiling), a protocol that enables per-nucleotide RNA structure characterization using standard molecular biology equipment and requiring no sequencing infrastructure or bioinformatics expertise. RNA is chemically modified with orthogonal probes (2A3 and DMS), reverse-transcribed, and PCR-amplified to produce dsDNA amplicons that are submitted directly to a commercial primer-less sequencing service. Returned FASTQ files are processed through a freely accessible web server to generate normalized reactivity profiles within minutes. The complete protocol, from DNA template to structural data, can be completed in approximately one week. We illustrate the workflow on a 659-nucleotide RNA, demonstrating how to test structure preservation across buffers, and how to test specific secondary and tertiary structure predictions of the RNA from computational modeling or cryo-electron microscopy. The protocol requires only standard molecular-biology skills and does not require sequencing or bioinformatics expertise. Competing Interest Statement J.V., H.M.B., and R.D. filed an invention disclosure with Stanford University covering the FAST-MaP protocol and associated analysis tools. The authors declare no other competing interests. Footnotes https://huggingface.co/spaces/daslab-stanford/cmuts Funder Information Declared National Institute of General Medical Sciences (NIGMS), National Institutes of Health , R35 GM122579 Howard Hughes Medical Institute 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 4.0 International license . Back to top Previous Next Posted September 23, 2026. Download PDF Supplementary Material Data/Code 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 FAST-MaP: Chemical Mapping of RNA Structures Using Primer-less Sequencing 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 FAST-MaP: Chemical Mapping of RNA Structures Using Primer-less Sequencing Jigyasa Verma , Hamish Milson Blair , Wipapat Kladwang , Rhiju Das bioRxiv 2026.09.22.753544; doi: https://doi.org/10.64898/2026.09.22.753544 Share This Article: Copy Citation Tools FAST-MaP: Chemical Mapping of RNA Structures Using Primer-less Sequencing Jigyasa Verma , Hamish Milson Blair , Wipapat Kladwang , Rhiju Das bioRxiv 2026.09.22.753544; doi: https://doi.org/10.64898/2026.09.22.753544 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 (8021) Biochemistry (18781) Bioengineering (14921) Bioinformatics (44492) Biophysics (22625) Cancer Biology (19761) Cell Biology (26945) Clinical Trials (138) Developmental Biology (13993) Ecology (21037) Epidemiology (2067) Evolutionary Biology (25473) Genetics (16185) Genomics (23535) Immunology (18725) Microbiology (42548) Molecular Biology (18095) Neuroscience (93601) Paleontology (701) Pathology (2987) Pharmacology and Toxicology (5104) Physiology (8127) Plant Biology (16020) Scientific Communication and Education (2097) Synthetic Biology (4572) Systems Biology (10251) Zoology (2393)
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