---
title: "Chaotropic salt–silica protocols yield high recovery of filamentous phage ssDNA"
id: "biorxiv-9-purification-of-filamentous-phage-ssdna-genomes-using-chaotropic-salt-silica"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-9-purification-of-filamentous-phage-ssdna-genomes-using-chaotropic-salt-silica"
content_type: "clinical_feed_article"
specialty: "General"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.10.21.760820v1?rss=1"
published_at: "2026-10-23T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Chaotropic salt–silica protocols yield high recovery of filamentous phage ssDNA
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-9-purification-of-filamentous-phage-ssdna-genomes-using-chaotropic-salt-silica
- **Specialty:** [General](https://medichelpline.com/clinical-feed/general.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.10.21.760820v1?rss=1)
- **Published At:** 2026-10-23T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- Investigators developed and optimized two silica column protocols for purifying **ssDNA** from filamentous phages, using guanidine hydrochloride and potassium iodide as chaotropic salts. - The methods were applied to phages **M13KO7** and **Pf4** and achieved reported recoveries ranging from 60% to 100%. - Recovery compared favorably to the Monarch Spin gDNA Extraction and DNeasy Blood and Tissue kits, with equal or higher yields. - Purified DNA showed similar A260/280 and A260/230 ratios to commercial kits, intact banding on agarose gels, and no detectable host genomic DNA by PCR. - The authors observed that recovery depended critically on the presence of the chaotropic salts and on ethanol; lowering pH did not increase yield. - The data were interpreted using a water-exclusion model, in which hydrophobic interactions and hydrogen bonding dominate ssDNA binding to silica over electrostatic effects. - The study team reported phage-specific differences in recovery, indicating that some phages may need protocol optimization; the protocols are fully customizable to permit such tuning. - Comparison of virion **ssDNA** and double-stranded replicative form (RF) DNA revealed genome variants in both phages, including a shorter **M13KO7** variant lacking the kanamycin resistance–p15A insert. - The paper is a preprint and has not undergone peer review; the abstract did not report detailed stepwise reagent concentrations or the full protocol parameters in the section provided here.
## Clinical Analysis & Structured Key Points
Purification of filamentous phage ssDNA genomes using Chaotropic salt/silica methods | bioRxiv Skip to main content New Results Purification of filamentous phage ssDNA genomes using Chaotropic salt/silica methods View ORCID Profile Saumel Perez Rodriguez , View ORCID Profile Arya Khosravi , View ORCID Profile Carlos Milla , View ORCID Profile Paul Bollyky doi: https://doi.org/10.64898/2026.10.21.760820 Saumel Perez Rodriguez Stanford University Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Saumel Perez Rodriguez Arya Khosravi Stanford University Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Arya Khosravi Carlos Milla Stanford University Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Carlos Milla Paul Bollyky Stanford University Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Paul Bollyky For correspondence: pbollyky{at}stanford.edu Abstract Info/History Metrics Supplementary material Data/Code Preview PDF Abstract Filamentous phages play important roles in molecular biology and bacterial pathogenesis. There is therefore great interest in the genomes of the phages, including M13 and Pf, which infect Escherichia coli and Pseudomonas aeruginosa, respectively. However, efficient methods for purifying single-stranded DNA (ssDNA) from filamentous phages are scarce and rely mainly on repurposed commercial kits developed for dsDNA. These kits yield variable amounts of ssDNA, varying considerably from one phage to another, their solutions are proprietary and troubleshooting, and customizing the protocol to improve purification is not possible. Here, we developed and optimized two protocols based on ssDNA binding to silica columns in the presence of guanidine hydrochloride and potassium iodide chaotropic salts, for filamentous phages M13KO7 and Pf4. The protocols achieved 60 to 100% recovery, equal to or higher than the Monarch Spin gDNA Extraction and DNeasy Blood and Tissue kits, with similar A260/280 and A260/230 ratios, intact DNA in agarose gels, and no detectable host genomic DNA by PCR. Recovery depended critically on the chaotropic salts and on ethanol, and did not increase at lower pH, consistent with a water-exclusion model in which hydrophobic interactions and hydrogen bonding dominate over electrostatic repulsion. Phage-specific differences in recovery indicate that optimization may be needed for some phages, which the fully customizable nature of these protocols facilitates. Comparing the virion ssDNA with the double-stranded replicative form (RF) revealed genome variants in both phages, including a shorter M13KO7 form lacking the kanamycin resistance-p15A insert, and illustrates the value of analyzing both RF and ssDNA forms to study filamentous phage biology. Implementing these protocols in routine filamentous phage workflows should facilitate their characterization and engineering. Competing Interest Statement The authors have declared no competing interest. Footnotes https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1538112 Funder Information Declared Stanford Maternal and Child Health Research Institute , Postdoctoral Fellowship Cystic Fibrosis Research Institute (CFRI) , Elizabeth Nash Memorial Fellowship National Institutes of Health , K08 AI190313 , R01 HL148184-01 , R01 AI12492093 , R01 DC019965 , K24 AI166718 , P01AI1960471 Cystic Fibrosis Foundation, https://ror.org/00ax59295 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-ND 4.0 International license . Back to top Previous Next Posted October 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 Purification of filamentous phage ssDNA genomes using Chaotropic salt/silica methods 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 Purification of filamentous phage ssDNA genomes using Chaotropic salt/silica methods Saumel Perez Rodriguez , Arya Khosravi , Carlos Milla , Paul Bollyky bioRxiv 2026.10.21.760820; doi: https://doi.org/10.64898/2026.10.21.760820 Share This Article: Copy Citation Tools Purification of filamentous phage ssDNA genomes using Chaotropic salt/silica methods Saumel Perez Rodriguez , Arya Khosravi , Carlos Milla , Paul Bollyky bioRxiv 2026.10.21.760820; doi: https://doi.org/10.64898/2026.10.21.760820 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 (8164) Biochemistry (19027) Bioengineering (15171) Bioinformatics (45323) Biophysics (22958) Cancer Biology (20106) Cell Biology (27293) Clinical Trials (138) Developmental Biology (14142) Ecology (21393) Epidemiology (2067) Evolutionary Biology (25782) Genetics (16342) Genomics (23827) Immunology (19017) Microbiology (43178) Molecular Biology (18335) Neuroscience (95039) Paleontology (712) Pathology (3031) Pharmacology and Toxicology (5197) Physiology (8278) Plant Biology (16266) Scientific Communication and Education (2115) Synthetic Biology (4643) Systems Biology (10382) Zoology (2426)
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