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BiologyZoologyPeer-reviewed journal article

DNA Specimen Preservation using DESS and DNA Extraction in Museum Collections: A Case Study Report

Eri Ogiso‐TanakaiD, Daisuke ShimadaiD, Akito OgawaiD, Genki IshiyamaiD, Ken-ichi Okumura, Kentaro HosakaiD, Chikako Ishii, Kyung-Ok Nam, Masakazu HoshinoiD, Shûhei NomuraiD, Showtaro KakizoeiD, Yasuhide NakamuraiD, Isao NishiumiiD, Minako Abe ItoiD, Taiju KitayamaiD, Norio TanakaiD, Tsuyoshi HosoyaiD, Utsugi JinboiD

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Abstract

Recent advances in DNA research have increased the necessity for museums to preserve not only morphological specimens but also their DNA, leading us to maintain tissue samples linked to specimens at -80{degrees}C. DNA analysis has become an essential tool for taxonomic research and biodiversity assessment; however, freezer storage for all samples is impractical due to space limitations and operational costs. This creates a pressing need to develop more widely applicable DNA preservation methods. We investigated the comparative effects of traditional preservation methods versus DESS (DMSO/EDTA/saturated NaCl solution) preservation on both morphology and DNA integrity using museum specimens from various taxonomic groups. Our results demonstrated that DESS preservation maintained high-quality DNA fragments exceeding >15 kb at room temperature across all examined species, with nematode samples maintaining DNA integrity even after 10 years of storage. When preserving whole organisms, the optimal preservation solution conditions for maintaining both morphological features and DNA integrity varied among species. Notably, DNA integrity was maintained even after complete evaporation of the DESS solution. These findings suggest that DESS utilization for specimen DNA preservation is effective across many species, not only for long-term storage in environments without freezer facilities but also for temporary preservation until freezing. Simple SummaryRecent advances in DNA research have increased the necessity for museums to preserve not only morphological specimens but also their DNA, leading us to maintain tissue samples linked to specimens at -80{degrees}C. However, as freezer storage for all samples is impractical, there is a pressing need to develop more widely applicable DNA preservation methods. In this study, we investigated the effectiveness of traditional preservation methods versus DESS (DMSO/EDTA/saturated NaCl solution) preservation with regards to both morphology and DNA integrity using our museum specimens. Our results demonstrated that DESS preservation maintained high molecular weight DNA at room temperature across all examined species. When preserving whole organisms, the optimal preservation solution conditions for maintaining both morphological features and DNA integrity varied among species. Notably, DNA integrity was maintained even after complete evaporation of the DESS solution. These findings suggest that DESS utilization for specimen DNA preservation is effective across many species, not only for long-term storage in environments without freezer facilities but also for temporary preservation until freezing is possible.

In-depth summary

Claude Opus 5.5 · xhigh effort · 8 Nov 2026 · from the full text of version 2 (5 Apr 2025) · CC BY 4.0

DESS (DMSO/EDTA/saturated NaCl) kept DNA at room temperature in animals, seagrasses and a brown alga, even after evaporating from bird muscle, but dissolves gastropod shells and holothurian ossicles.

Keeping a −80°C tissue sample for every museum specimen is impractical, and ethanol or RNAlater dehydrate tissue and can spoil morphology; DESS was first developed for avian tissue and later shown to work in nematodes and other invertebrates. This case study compares DESS with conventional preservatives across taxa from the National Museum of Nature and Science (Tokyo) for morphology, DNA integrity, pH, evaporation and nondestructive barcoding from the preservative.

Key results

  1. ShownRoom-temperature DESS kept long genomic DNA in marine nematodes for up to a decade, and usable DNA in a brown alga and two seagrasses, though seagrass DNA was less intact than animal DNA. Nematode DNA quality was unrelated to storage time, which the authors attribute to each specimen's condition at collection.

    Nematodes stored 3 months to 10 years all kept fragments >10 kb, unrelated to collection year (longest >60 kb, sample 2012-1). Turbinaria ornata after 3 months: DIN (DNA Integrity Number) 5.3, peak 26.3 kb. Zostera marina and Phyllospadix iwatensis after 15 months in 50% or 100% DESS: DIN 2.9 to 4.9 vs 1.0 for Z. marina silica-dried for 1 month. · Nematodes; Seagrasses; Algae

  2. ShownDESS evaporates about half as fast as water and leaves salt crystals rather than an empty tube. Bird muscle kept its DNA after the DESS was evaporated off; muscle that had been in ethanol did not.

    Open tubes at room temperature (RT): DESS 30–40 mg/day vs water 60–80 mg/day; anhydrous ethanol gone in about 3 days. Closed tubes over 2 years: DESS lost about 10–20 mg at RT; at 55°C water and ethanol nearly fully evaporated, DESS substantially only in screw-cap tubes. Vacuum-dried muscle kept 10 days at 25°C: DNA degraded after ethanol, nearly unchanged after DESS. · 3.1.2. Rate of evaporation; Birds

  3. ShownThe EDTA in DESS dissolves calcareous structures. DESS therefore ruins sea cucumber and gastropod morphology, and it fragments DNA in gastropod soft bodies left in their shells. Soft bodies removed from their shells, and sea cucumber tissue, still gave good DNA.

    After 28 months in 100% DESS, ossicles of Peniagone sp. and Pseudostichopus sp. were badly degraded; an Echinolittorina radiata shell almost fully disintegrated in 4 months; shelled mollusks raised DESS pH by 0.5–1.2 units. Shell-free Sinotaia quadrata histrica DNA matched ethanol-stored tissue; sea cucumber tissue kept long DNA after 2 years except the largest specimen (DIN 3.9 and 5.5). · 3.1.1. The pH stability of the DESS solution; Sea cucumbers; Slugs and snails (Gastropoda)

  4. ShownCytochrome c oxidase subunit I (COI) barcoding from the DESS supernatant alone, which leaves the specimen intact, often worked in spiders and in the mysid Neomysis japonica. It was less reliable in insects, and a seagrass marker longer than 2 kb did not amplify.

    Spiders after 1 month in 25–100% DESS: 66/96 (68.8%) amplified, all confirmed as spider COI. Light-trapped Coleoptera and Membracidae: none after several days; after 2 years in 90% DESS, 9/20 (45%) with LCO1490/HCO2198 and 12/20 (60%) with the shorter mlCOIint/HCO2198 amplicon. N. japonica: all samples amplified with the short primers after 18 days in 50% DESS, and with both pairs after 2 years in about 90% DESS. · Spiders; Insects; Shrimp (Neomysis); Seagrasses

  5. ShownAdding EDTA to 70% ethanol (the strength many Japanese shippers accept) inhibited DNA degradation at room temperature in chicken muscle over 10 days and in spider legs over 6 months. It cost far less than DESS.

    Chicken breast at 25°C: 70% ethanol gave marked DNA fragmentation by day 10, prevented by 1 mM or 10 mM EDTA. Spider legs over 6 months: 70% ethanol + EDTA gave COI PCR yields comparable to DESS, whereas anhydrous or 75% ethanol often failed to amplify. Cost per tube: 2.4 yen vs 1.5 yen for 70% ethanol and 25 yen for DESS. · Spiders; Birds; 3.3.1. Cost-based selection of preservation…

Methods, data and reproducibility

Pilot comparisons of DESS (20% DMSO, 250 mM EDTA, saturated NaCl) and a Tris/sodium sulfite variant (DESS-NMNS) against ethanol, formalin, propylene glycol and DESS dilutions across museum taxa. Measured: preservative pH and evaporation (up to 2 years), morphology, genomic DNA integrity (Qubit, TapeStation DIN), and COI/ITS PCR from tissue or from the DESS supernatant.

  • Free-living marine nematodes collected in Japan (2012–2019 and 2022), stored in DESS at room temperature · nematodes (free-living marine)
  • Spider specimens collected across Japan 2016–2023, stored in DESS dilutions, ethanol or 70% ethanol + EDTA · spiders · n = Seventy-seven specimens of 35 species
  • Insects: legs of Prionus insularis split across 12 storage conditions; light-trapped Coleoptera and Membracidae placed in 100% DESS (Kiso Village, Nagano) · Prionus insularis; Coleoptera; Membracidae · n = 1 P. insularis individual (12 leg parts); 20 light-trapped specimens
  • Mysid Neomysis japonica from Lake Shinji preserved in DESS, 99% ethanol or 5% formalin · Neomysis japonica
  • Deep-sea holothurians trawled from the Kuril-Kamchatka and Japan trenches, whole bodies in 100% DESS or 99.5% ethanol · Pseudostichopus sp., Peniagone sp., Elpidia kurilensis · n = 3 species
  • Gastropods (Lottia kogamogai, Echinolittorina radiata, Nassarius siquijorensis, Sinotaia quadrata histrica) in DESS or 100% ethanol, with or without shells · gastropods (4 species) · n = 4 species; 4 S. quadrata histrica specimens
  • Bird muscle: supermarket chicken breast as a model tissue, plus muscle of three wild species kept 2 years in DESS · chicken; Otus lettia; Pellorneum ruficeps; Sturnia malabarica · n = 3 wild species plus chicken
  • Seagrasses Zostera marina and Phyllospadix iwatensis (Hokkaido), brown alga Turbinaria ornata (Hachijo Island), and Basidiomycota mushrooms in DESS-NMNS since 2010 · seagrasses; brown alga; fungi (Basidiomycota) · n = 2 seagrass species; 1 alga; 6 mushroom species
Methods & tools
Qubit dsDNA HS/BR assay (Qubit 2.0 fluorometer), Agilent TapeStation with Genomic DNA and D1000 ScreenTape, QIAGEN DNeasy Blood & Tissue Kit (modified, silica suspension), Boom silica extraction (diatomaceous earth, SiO2, Wakosil, Davisil silica gel), CTAB extraction, OmniPrep for Plant (G-Biosciences), Tks Gflex DNA Polymerase (Takara), EmeraldAmp MAX PCR Master Mix (TaKaRa), COI primers LCO1490/HCO2198 and mlCOIint/HCO2198, rDNA primers ITS5/ITS4, NS1/LR7, NS1/LR12, TissueLyser III (QIAGEN), HIDS biodegradable chelating agent (Nippon Shokubai)
Reproducibility gaps
No sequence accessions, data links or code are given; several comparisons are reported as data not shown, and sample sizes per condition are often unstated. Wet-lab protocols, reagent recipes and catalog numbers are described in detail.
Limitations (6)
  • The insect dilution comparison used leg segments from a single Prionus insularis; replicate conditions were hard to prepare, so the dilution that matches 100% DESS is still unknown. Storage in the dark meant the effect of light was not tested. · stated by the authors
  • The fungal comparisons may be confounded: years in high-salt DESS-NMNS could lower DNA extraction efficiency, and the amount of tissue per extraction was not standardized. · stated by the authors
  • DESS preserved DNA less well in aquatic plants than in animals. Seagrass DNA degraded during 8 further months at RT, so cool storage is advised. Turbinaria ornata DNA was not checked at collection, so its change during storage is unknown. · stated by the authors
  • Storage beyond 10 years, long-term pH stability, the durability of polypropylene tubes and the best DESS concentration for each taxon all still need testing. · stated by the authors
  • Most comparisons rest on one or a few specimens per condition, often from mixed species, with no statistical tests. · noted in this summary
  • The estimate that DESS would take 90–120 years to lose most of its water at RT is a simple extrapolation from 2-year tube experiments, and the 55°C acceleration is not calibrated against time at RT. · noted in this summary

Read this if you manage museum or field tissue collections and want freezer-free, room-temperature DNA preservation options, with taxon-specific caveats, costs and protocols for DESS, ethanol plus EDTA and barcoding from the supernatant.

Citations
8
FWCI
4.26
Field percentile
top 5%

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