# Unravelling the noncanonical extracellular DNA structures in biofilm and NETosis

**Authors:** Tevriz Dilan Demir, Satoe Azechi-Ogawa, Nikhil Ram-Mohan, Samuel Yang

PMC · DOI: 10.1093/nar/gkaf1505 · Nucleic Acids Research · 2026-01-09

## TL;DR

This paper explores the role of noncanonical DNA structures in biofilms and NETs, suggesting they may influence disease and immunity.

## Contribution

The paper advocates for investigating noncanonical extracellular DNA structures in dynamic environments for their impact on microbial and immune processes.

## Key findings

- Noncanonical DNA structures are found in biofilms and NETs, contributing to structural stability and antimicrobial activity.
- These structures may influence microbial behavior, immune responses, and host-pathogen interactions.
- Targeting these DNA structures could lead to new therapeutic strategies for diseases involving biofilms and NETs.

## Abstract

Noncanonical secondary structures of DNA have been well characterized in vitro for their catalytic and sensory functions, as well as in vivo for their regulatory functions in the genome. However, their presence and functional significance in the extracellular DNA (eDNA), particularly within biofilms and neutrophil extracellular traps (NETs), have only recently begun to be appreciated and have yet to be fully understood. Emerging studies have identified these atypical DNA conformations as integral components that contribute to the structural stability of biofilms and antimicrobial activity of NETs. In this personal view, we advocate for a comprehensive investigation of these unconventional DNA structures within extracellular contexts, where their distinct physiochemical properties are exposed to dynamic and unpredictable microenvironments, with the potential to profoundly influence microbial behaviour, immune responses, and host–pathogen interactions. Considering the broad spectrum of diseases associated with biofilm and NETs, targeting noncanonical eDNA structures may offer novel therapeutic avenues and shed light on mechanisms of immune tolerance and dysregulation.

Graphical Abstract

## Full-text entities

- **Genes:** DNASE1L3 (deoxyribonuclease 1L3) [NCBI Gene 1776] {aka D3, DHP2, DNAS1L3, LSD, SLEB16}, TNF (tumor necrosis factor) [NCBI Gene 7124] {aka DIF, IMD127, TNF-alpha, TNFA, TNFSF2, TNLG1F}, ERCC2 (ERCC excision repair 2, TFIIH core complex helicase subunit) [NCBI Gene 2068] {aka COFS2, CXPD, EM9, TFIIH, TTD, TTD1}, TLR9 (toll like receptor 9) [NCBI Gene 54106] {aka CD289}, AIM2 (absent in melanoma 2) [NCBI Gene 9447] {aka PYHIN4}, OGG1 (8-oxoguanine DNA glycosylase) [NCBI Gene 4968] {aka HMMH, HOGG1, MUTM, OGH1}, PRTN3 (proteinase 3) [NCBI Gene 5657] {aka ACPA, AGP7, C-ANCA, CANCA, MBN, MBT}, CGAS (cyclic GMP-AMP synthase) [NCBI Gene 115004] {aka C6orf150, D4, MB21D1, h-cGAS}, MPO (myeloperoxidase) [NCBI Gene 4353], IL6 (interleukin 6) [NCBI Gene 3569] {aka BSF-2, BSF2, CDF, HGF, HSF, IFN-beta-2}, IFNA1 (interferon alpha 1) [NCBI Gene 3439] {aka IFL, IFN, IFN-ALPHA, IFN-alphaD, IFNA13, IFNA@}, ZBP1 (Z-DNA binding protein 1) [NCBI Gene 81030] {aka C20orf183, DAI, DLM-1, DLM1}, PIF1 (PIF1 5'-to-3' DNA helicase) [NCBI Gene 80119] {aka C15orf20, PIF}, CAMP (cathelicidin antimicrobial peptide) [NCBI Gene 820] {aka CAP-18, CAP18, CRAMP, FALL-39, FALL39, HSD26}, F2 (coagulation factor II, thrombin) [NCBI Gene 2147] {aka PT, RPRGL2, THPH1}
- **Diseases:** diabetic (MESH:D003920), inflammation (MESH:D007249), haemolysis (MESH:D006461), SLE (MESH:D008180), organ dysfunction (MESH:D009102), autoimmune conditions (MESH:D001327), NETs (MESH:C536657), hemin toxicity (MESH:D064420), immune disorders (MESH:D007154), COVID-19 (MESH:D000086382), biofilm infections (MESH:D007239), viral infections (MESH:D014777), neutropenia (MESH:D009503), neutrophil (MESH:C564275), RA (MESH:D001172), thrombosis (MESH:D013927), chronic (MESH:D002908), PANoptosis (MESH:D065703), tissue damage (MESH:D017695), systemic (MESH:D015619)
- **Chemicals:** guanines (MESH:D006147), carbon (MESH:D002244), TMPyP4 (MESH:C021096), nitrogen (MESH:D009584), quinolines (MESH:D011804), phenazine (MESH:C000598831), phosphate (MESH:D010710), salt (MESH:D012492), chitosan (MESH:D048271), acridines (MESH:D000166), hydroxyl radical (MESH:D017665), Hemin (MESH:D006427), BRACO19 (MESH:C454064), vitamin C (MESH:D001205), adenine (MESH:D000225), oligonucleotide (MESH:D009841), spermine (MESH:D013096), iron (MESH:D007501), cytosine (MESH:D003596), G4 (MESH:D004003), carbohydrates (MESH:D002241), TRL1068 (MESH:C000627168), 8-oxo-guanine (MESH:C024829), heme (MESH:D006418), CpG (MESH:C015772), sodium (MESH:D012964), potassium (MESH:D011188), phosphatidylethanolamine (MESH:C483858), H2O2 (MESH:D006861), porphyrin (MESH:D011166), BioRender (-), CpG oligonucleotide (MESH:C408982), Chloroquine (MESH:D002738), ROS (MESH:D017382), calcium (MESH:D002118), magnesium (MESH:D008274), spermidine (MESH:D013095), hydrogen (MESH:D006859), OH (MESH:C031356), poly(dG-dC (MESH:C019530), NMM (MESH:C035596), lipid (MESH:D008055), polyamines (MESH:D011073)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Pseudomonas aeruginosa (species) [taxon 287], Aspergillus fumigatus (species) [taxon 746128], Streptococcus mutans (species) [taxon 1309], Staphylococcus epidermidis (species) [taxon 1282], Homo sapiens (human, species) [taxon 9606]

## Full text

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## References

177 references — full list in the complete paper: https://tomesphere.com/paper/PMC12784952/full.md

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Source: https://tomesphere.com/paper/PMC12784952