Chemical Trends in Sample Preparation for Nucleic Acid Amplification Testing (NAAT): A Review
Abstract
:1. Introduction
2. Cell Lysis
2.1. Chemical Cell Lysis
2.1.1. Detergents
2.1.2. Enzymatic Lysis
2.1.3. Alkaline Lysis
2.1.4. Chaotropic Lysis
2.1.5. New Reagents for Cell Lysis
2.2. Other Cell Lysis Methods
3. Nucleic Acid Extraction
3.1. Solid-Phase Extraction (SPE)
3.1.1. Reagents
Anionic Supports under Chaotropic Conditions
Solid Phase | Surface | Binding Buffer | Washing Buffer | Elution Buffer | Elution Volume | Target | Sample Matrix | Amplification | LOD | Ref. |
---|---|---|---|---|---|---|---|---|---|---|
MB | Silica | Ethanol | Kit | Kit | 10 µL | HPV virus | Synthetic DNA | qPCR | - | [19] |
MB | Silica | GuHCl | Mineral oil + GuHCl | Water | 10 µL | Bacteria | Liquid stool (clinical) | PCR | - | [41] |
Glass membrane | Whatman glass pad | 20 mM Tris-HCl, 4 M GuSCN, 1 mM DTT, pH 7.7 (lysis buffer) | Isopropanol, 15% v/v | Water | 5 µL | Animal | Mixed meat (minced) | qPCR | [42] | |
Paper/Disc | Cellulose | 1.5 M GuHCl, 50 mM Tris [pH 8], 100 mM NaCl, 5 mM EDTA, 1% Tween-20 | 10 mM Tris pH 8.0, 0.1% Tween-20 | Water | 10 µL | Viral gene in fish | Blood (fish) | PCR | 104 cells | [49] |
MB | Silica | GuHCl, TRIS, EDTA, NaCl in ethanol (50%) | Wash buffer I (GuHCl + 68% v/v ethanol) Wash buffer II (70% v/v ethanol) | 10 mM Tris, 0.1 mM EDTA pH 8 | 200 µL | Bacteria | Serum and saliva | RPA | - | [48] |
MB | Silica | GuSCN + Triton X-100 (pH 6.8) | Organogel (12-HAS) GuSCN (pH 6.8) Ethanol NaCl2 (pH 7.6) | 10 mM Tris, 0.1 mM EDTA pH 8 (TE buffer) | 100 µL | Virus | Spiked blood | qPCR | 5 particles | [50] |
MB | Silica | 4 M GuSCN, 10 mM MES (2-ethanesulfonic acid), 1% Triton X-100, with 1% ß-mercaptoethanol | oil immersed, Ethanol, 50% v/v, then water Water | None (on-bead amplification) | Virus | Nasopharyngeal swab | LAMP | 1–10 copies/µL | [51] | |
MB | Silica | 3 M GuHCl, protein kinase K, at elevated T | Isopropanol | 10 mM Tris, 0.1 mM EDTA pH 8 | 8 µL | Virus | Buccal swab | LAMP, qPCR | - | [45] |
MB + Steel wool | Silica | GuSCN + EDTA + Tris-HCl + Triton X-100 | GTIC Ethanol Tris-HCl + EDTA | 30 µL | Synthetic sputum + residual urine sample | qPCR | - | [52] | ||
MB | Silica | Isopropanol | Washing buffer 1 and 2 | Elution buffer | Virus | Cervical swab | PCR | 103 copies/mL | [112] | |
MB | Silica | 3.5 M GuSCN, isopropanol, 45% v/v, 2.5% Tween 20, 10 mM Tris pH 8.0, 1 mM EDTA | 3 M GuSCN isopropanol 30% v/v, 5% Tween 20, 40 mM Bis-Tris pH 6.0, 2 mM EDTA then 50 mM Tris pH 8.0 0.5 mM EDTA ethanol 80% v/v then ethanol, 100% v/v | human | Plasma | PCR | - | [113] | ||
GB | Glass for DNA, oligo(dT) functionalized for RNA | Ethanol | Fluorinated oil Buffer AW1/2 (DNA) or Tris-HCl (pH 7.5) + LiCl + EDTA (RNA) | DNA: Tris HCl, 10 mM, EDTA, 0.5 mM, pH 9/RNA, Tris-HCl (pH 7.5) | 100 µL | mRNA | THP-1 cell | qPCR/RT-qPCR | 10 cells | [110] |
MB | Selective recognition using NA probe | 100 mM phosphate, 150 mM NaCl, pH 6.0 | 10 mM Tris, 50 mM NaCl, pH 8.0 | 10 µL | Virus | Lab culture | Amplification-free | 0.021 pfu/mL | [114] | |
Membrane (kit, ground) | Silica | Buffer AW | Buffer AW1/2 | Kit | Virus | Lab culture | RT-LAMP | 25 copies | [115] | |
Porous silicon | Silica | 6 M GuSCN in 10 mM Tris, 1 mM EDTA (pH 8) with 1% Triton-X 100 (adjusted to pH 6.4) | Ethanol, 70% v/v in 10 mM NaCl | 10 mM Tris, 0.1 mM EDTA pH 8 (TE buffer) | 10 µL, 25 µL | [116] | ||||
Silica filter | Silica | Binding buffer | GuSCN,3 M 25% v/v, Ethanol, 75% v/v then Ethanol 96% v/v | Water | 50 µL | HPV 16 | Cervical specimens | NASBA | [117] | |
Paper | Polyether sulfone (PES) | GuSCN, NaCl, 1-butanol, glycoblue (coprecipitant) | Ethanol 70% v/v, then 100% v/v | LAMP mix | 12.5 µL | HPV 16 | Cervical specimens | LAMP | 1.2.105 copies | [118] |
Paper | Paper also polymer monolith | 2.6 M GuSCN, 300 mM NaCl, 35% v/v 1-butanol 45 μg glycoblue (co-precipitant) | Ethanol 70% v/v, then 100% v/v | Tris EDTA | 200 µL | Bacteria | Synthetic urine | Isothermal helicase-dependent amplification (tHDA) | [119] |
Non-Chaotropic Binding
Solid Phase | Surface Group | Binding Buffer | Washing Buffer | Washing Steps, Volume | Elution Buffer | Elution Volume | Target | Sample Matrix | Amplification | LOD | Kit vs. Assay | Ref. |
---|---|---|---|---|---|---|---|---|---|---|---|---|
MB | Fe3O4 nanoparticles | PEG + NaCl | Ethanol, 75% v/v | Water | 50 µL | Human saliva | PCR | n/a | Assay | [43] | ||
Glass filter | Glass | 200 mM NaOH with 1% SDS (=lysis buffer) | Isopropanol, 15% v/v | 1, 75 µL | Water | 2 µL | Bacteria (aerosol spiked) | Cultured | qPCR | 10 CFU | Kit | [34] |
MB | Silica | Lysis buffer (SDS and Protein Kinase K) | Washing buffer 1 and 2 | 2 | Low ionic strength elution buffer | 100 µL | K562, CHO-K1 cells | Culture media | PCR | 18 cells | Comparable but faster | [97] |
MB | Carboxyl (to compare with silanol) | PEG 8000 (18 wt%), NaCl, 1 M | Ethanol, 80% v/v | Water | Animal | Faecal swab | PCR | 35.53 ± 15.03 ng (faecal) 261.12 ± 390.08 ng (cloacal swab) 233.52 ± 142.83 (oral swab) 87.3 ± 7.2% N/A | [139] | |||
MB | Silica | 5% PEG8000, 0.5 M NaCl, and 3.5 mM KOH | Wash can be eliminated | On-bead amplification | - | Bacteria | Artificial saliva, sweat, urine | qPCR | 0.15 CFU/50 μL | Assay | [140] |
Cationic Supports
Solid Phase | Surface | Binding Buffer | Washing Buffer | Elution Buffer | Elution Volume | Target | Sample Matrix | Amplification | LOD | Ref. |
---|---|---|---|---|---|---|---|---|---|---|
Acrylonitrile butadiene styrene (ABS) device | (3-Aminopropyl)triethoxysilane (APTES) | Dimethyl suberimidate in TE-based lysis buffer | PBS | NaHCO3 10 mM, pH > 10 | Virus | Clinical | RPA | 10 copies | [31] | |
MB | Imidazole | Tris-HCl (pH3) | PBS | NaHCO3 (pH 10.6) | Bacteria | Human urine/milk | qPCR | 5 CFU/10 mL | [44] | |
PMMA | Histidine or polyhistidine | 0.5 M KAc, pH 5.0 | 0.5 M potassium acetate, pH 5.0 | NaHCO3 (pH 10.6) | 10 µL | Bacteria | Culture | PCR | <5000 cells | [141] |
Amine-functionalized diatomaceous earth | 3-aminopropyl(diethoxy)methyl silane | Dimethyl suberimidate in lysis buffer (Proteinase K, Tris-HCl [pH 8.0], EDTA, SDS, Triton X-100, lysozyme solution RNase-Free Dnase) | PBS | NaHCO3 10 mM, pH > 10 | 100 µL | PCR qPCR | [131] | |||
Fe3O4 | PDA | PEG, 20% v/v, 4 M NaCl | Ethanol, 70% v/v | 10 mM Tris-HCl, 1 mM EDTA, pH 8 | 50 µL | PCR | [142] | |||
Glass slide | APTES | Dimethyl adipimidate (DMA) | PBS | NaHCO3 (pH 10.6) | 150 µL | HRAS gene | Urine | PCR | - | [145] |
ABS chamber wall | APTES | Dimethyl pimelimidate (DMP) in 100 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% SDS, and 10% Triton X-100) with either proteinase K (for DNA) or proteinase K and DNase I (for RNA) | PBS | NaHCO3 pH < 10.6 | 50 µL/min | Viral/bacterial, cancer | Plasma | PCR | 1 CFU/mL (10 cells/100 µL for cancerous cells) | [53] |
MB | ChargeSwitch magnetic beads (commercial, + charge) | ChargeSwitch binding buffer, pH.5 | ChargeSwitch wash solution AP001 + Tween20 pH 7; silicone oil | Bacteria | Cultured | dPCR | [147] | |||
Glass beads | TEOS or APTES or GO | Acetate pH5 | Tris-HCl pH7 | Tris-HCl pH 9 | 200 µL | Bacteria + virus | Toilet seat | qPCR | 0.007 CFU/cm2 | [148] |
Membrane Polyvinylidene Fluoride (PVDF) | Amine-functionalized diatomaceous earth | Dimethyl pimelimidate dihydrochloride (DMP) | PBS | Elution buffer | 100 µL | Bacteria | Lab cultured | PCR qPCR | [149] | |
SOI wafer | APTES | Dimethyl adipimidate (DMA), 25 mg/mL | PBS | NaHCO3 10 mM, pH 10.6 | 50 µL | Methylated DNA | Blood, urine | PCR | [150] | |
Capillary | Poly-diallyl dimethylammonium chloride (PDDA) | None (thermal lysate) | no wash | No elution, in capillary amplification | - | Bacteria | Lab cultured | qPCR | 10 ng/µL | [151] |
MB | Chitosan | Tris, 10 mM; Triton X-100, 0.1% v/v, pH 8.5 | Tris, 10 mM; Triton X-100, 0.1% v/v, pH 8.5 | On-bead amplification | Virus | Whole blood | PCR | 5 copes/µg of particles | ||
Membrane | Tertiary amine | None | Direct amplification | Bacteria | LAMP |
3.1.2. Fluidics
Liquid Handling
Immiscible Phase | Bead Surface | Mechanism | Binding | Washing | Elution | Target | Sample Matrix | Amplification | LOD | Ref. |
---|---|---|---|---|---|---|---|---|---|---|
FC-40, silicone oil, mineral oil | Silica | Chaotropic | Kit | Kit | Kit | HIV virus | Plasma | qPCR | - | [164] |
FC40 | silica | Chaotropic lysis | 5 m GuHCl, pH 4.1 (citrate) with triton X OR Sarkoosyl OR Tween 20 | Carryover study | Carryover study | Carryover study | Carryover study | Carryover study | [159] | |
Silicone oil | Silica | Chaotropic | Kit | Kit | HBV virus | Spiked blood | qPCR | n/r | [121] | |
Silicone oil | Silica | Chaotropic lysis | 4 M GuSCN, 10 mM MES, 1% Triton X-100, with 1% ß-mercapto-ethanol | Oil immersed, Ethanol, 50% v/v, then water Water | None (on-bead amplification) | Virus | Nasopharyngeal swab | LAMP | 1–10 copies/μL | [51] |
Mineral oil | Silica | Chaotropic | GuHCl | GuHCl, 5 M | Water | Bacteria | Liquid stool (clinical) | PCR | - | [41] |
Mineral oil | Silica | Chaotropic | 5 M GuHCl, 0.005% TWEEN-20 | LAMP-CRISPR | [163] | |||||
Mineral oil | Silica | Chaotropic | lysis buffer: Tris-HCl, lysozyme, protein kinase K, SDS, EDTA, RNase | GuHCl, 6 M | Magnesium acetate | Bacteria | Spiked milk | dRPA | 10 cells | [29] |
Mineral oil | Silica | Chaotropic | 5 M GuHCl in 10 mM Tris-HCl 1 mM EDTA pH 8 | Ethanol, 70% v/v | Water | Animal identification | Dung | qPCR, LAMP | [162] | |
Mineral oil | Silica | Chaotropic | 3 M GuHCl | Plasmid | Cultured | dRPA | 1.7e5 CFU/mL | [161] | ||
Olive oil | Silica | Chaotropic | GuSCN, isopropanol and carrier RNA to facilitate nucleic acid precipitation | Aqueous low-salt solution | Virus | nasopharyngeal swab | RT-qPCR | 12.7 ± 4.6 ng/μL | [158] | |
Liquid wax | Silica | Chaotropic | Alcohol | HIV | Whole blood | qPCR | 1200 copies/mL (RNA) | [155] | ||
Organogel (12-HAS) | Silica | Chaotropic | GuSCN + Triton X-100 (pH 6.8) | GITC (pH 6.8) Ethanol NaCl2 (pH 7.6) | 10 mM Tris, 0.1 mM EDTA pH 8 (TE buffer) | HBV virus | Spiked blood | qPCR | 5 particles | [50] |
Olive oil (silicone and mineral also evaluated) | ChargeSwitch | Ionic (cationic surface) | ChargeSwitch binding buffer, pH 5 | [165] | ||||||
Silicone oil | ChargeSwitch | Ionic (cationic surface) | ChargeSwitch binding buffer, pH 5 | ChargeSwitch wash solution AP001 + Tween20 pH 7 | Direct amplification in LD Amplitaq Gold pH 8.3 | Bacteria | Cultured | dPCR | Only proof of concept provided | [147] |
Olive oil | ChargeSwitch | Ionic (cationic surface) | ChargeSwitch binding buffer, pH 5 | ChargeSwitch washing buffer with SDS and TWEEN-20 | [157] | |||||
FC-40 | ZrO | Zr−O−P coordination bond and hydrogen bond | Lysis buffer: 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA·1% Triton X-100, 0.1% Sodium Deoxycholate, 0.1% SDS, 140 mM NaCl | 10 mM PBS | Target DNA | Plasma | LAMP | [166] | ||
Castor oil | Cellulose | Chaotropic | kit | Kit | HPV plasmids | Transport medium | 10 copies/100 μL | [167] | ||
FC-40 | Silica | Chaotropic | Kit | Kit | HBV virus | Spiked plasma | dLAMP | 104 copies/ml | [120] | |
Mineral oil | (dT)coated | Chaotropic | 6 M GuHCl | 0.005% Tween-20 | On-bead amplification | Virus | Artificial sputum | LAMP | 470 copies/mL | [156] |
Liquid wax olive oil | Oligo-dT PMPs | Recognition | kit | Kit | Tris-HCl | Breast cancer cells | - | RT-qPCR | - | [160] |
FC-40 | Biotinylated oligo | Recognition | 20 mM Tris pH 7.5, 100 mM KCl, 5 mM MgCl2, and 0.3% Nonidet P-40/Igepal, 17U RNAseOUT™, and 2.5 μL of 100X Halt™ protease inhibitor cocktail | Diethyl pyrocarbonate in PBS | Diethyl pyrocarbonate in PBS | microRNA | Culture medium | RT-qPCR, dPCR, array | [168] |
Process Integration
Solid Phase | Surface | Primary Binding Principle | Elution = Amplification Mix | Volume | Target | Sample | Amplification | LOD | Reference | |
---|---|---|---|---|---|---|---|---|---|---|
Elution in amplification mix | MB | Silica | Chaotrope | LAMP mix | 10 μL | Bacteria | Food | LAMP | 50 cells per test, or 10 cells/μL | [172] |
Paper | Whatmann FTA | Ionic interaction | LAMP mix | 15.5 | Lambda DNA | Saliva | LAMP | 100 copies/mL | [178] | |
Paper | Polyether sulfone (PES) | Chaotropic | LAMP mix | 12.5 | HPV 16 | Cervical specimens | LAMP | 1.27.105 Copies | [118] | |
MB | ChargeSwitch magnetic beads (commercial, + charge) | Ionic interaction | Amplitaq Gold | Bacteria | Cultured | dPCR | [147] | |||
Elution-free | Paper | Whatmann FTA | Ionic interaction | On-paper amplification | Bacteria | Whole blood | LAMP | 10 CFU/mL | [179] | |
MB | Silica | Alkaline crowding | On-bead amplification | Bacteria | Artificial saliva, sweat, urine | qPCR | 0.15 CFU/50 µL | [140] | ||
MB | Chitosan | Ionic interaction | On-bead amplification | Virus | Whole blood | PCR | 5 copes/µg of particles | [180] |
3.2. Extraction Methods without Stationary Phase
Substrate/Method | Primary Extraction Principle | Extraction | Comment | Target | Sample Matrix | Amplification | LOD | Ref. |
---|---|---|---|---|---|---|---|---|
LLE | Preferential solubility | Various ILs and MILs | Thermal elution | White blood cells | White blood cells | qPCR | 500 pg DNA from 50 µL blood | [181] |
LLE | Preferential solubility | [P6,6,6,14+] [Ni(hfacac)3−] MIL, [P6,6,6,14+] [Co(hfacac)3−]+ Tris | Thermal elution | Plant | Plant | qPCR | 311.8 ng of A. thaliana DNA per mg sample | [54] |
Hydrogel | No binding, just physical exclusion of debris | In-gel amplification | Bacteria | Artificially infected fruits and vegetables | dLAMP | Single cell | [130] | |
Polyacrylamide gel | Electrophoresis | Free flow electrophoresis, followed by lysis | DNA migrates through gel after lysis | Phage | Culture medium | qPCR | 1 PFU/mL or 0.02 copies/µL | [186] |
ITP | Electromigration | LE 50 mM Tris HCl pH 8.2 TE 50 mM Tris HEPES pH 7.8 | Lambda DNA | Blood | PCR | 10 cells | [187] | |
ITP | Electromigration | LE 100 mM of Tris-HCl TE 100 mM Tris and 100 mM of HEPES | Hydrogel as immiscible interface | Cell-free DNA | Plasma | PCR | [188] | |
ITP | Electromigration | LE: 200 mM HCl with 400 mM Bistris as the LE solution TE: 10 mM Tricine with 20 mM Bistris | Paper to generate EOF counterflow, not for binding | Morpholino NA probes | - | Amplification-free detection | 5 pM after 10 min | [189] |
ITP | Electromigration | LE 250 mM HCl and 375 mM Tris pH 7.8; TE 25 mM serine and 25 mM Tris pH 8.7 | Virus | Whole blood (spiked DNA) | RPA | 1000 copies/mL | [190] | |
ITP | Electromigration | LE Tris HCl MgCl2, PEG1450, PVP, Triton X-100, and tetramethyl ammonium chloride pH 8.1 TE β-alanine, Tris, PVP, Triton X-100 pH 8.9–9.1 | Paper as carrier, also focuses RPA reagents | Synthetic viral DNA | Whole blood | RPA | 104 copies/mL | [191] |
4. Evaluation of Sample Preparation Method for NA-PONT Assays Based on the REASSURED Criteria
Environment Lysis Reagents | Environment Extraction and Device | Equipment-Free | Deliverable to End-Users | User-Friendly | Affordable | Equipment-Free | Ref. | |
---|---|---|---|---|---|---|---|---|
1. Centrifugal | Guanidium for lysis and binding | Plastic | Needs spinning | Relies on advanced instrumentation | All integrated/automated | Instrument expensive | Requires instrument | [45] |
2. Organogel as immiscible barrier | Guanidium for lysis, binding, and wash | Plastic | Only needs magnet | Yes, low reliance on equipment and skill | Can be operated after limited training | No instrumentation, simple device | Yes, other than a magnet | [50] |
3. Self-powered switch-controlled system | AL | Plastic device and manifold | Yes, powered by syringe (vacuum) | Yes, simple | Yes, easy to activate with gear and syringe | Simple device and tool | Syringe-powered | [145] |
4. Abridged solid-phase extraction with AP lysis (ASAP) | AL | Plastic tubes | Just needs magnet (and pipette in current form) | Needs training for manual pipetting | Few reagents, no wash but in its current form relies on manual handling | Affordable reagents, but still needs packaging in device/instrument | Not in device | [140] |
5. Paper-based ITP with on-paper RPA | Surfactant + enzyme | Electrolytes, paper | Membrane on paper | Paper devices easy to operate | Few reagents, all happens in electric field | Economic device, simple operation | Needs electrical power | [191] |
5. Summary and Future Perspectives
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
12-HAS | 12-Hydroxystearic Acid |
ADE | Amine-Functionalized Diatomaceous Earth |
AMPs | Antimicrobial Peptides |
AL | Alkaline Lysis |
AP | Alkaline polyethylene glycol-based lysis method |
APTES | 3-Aminopropyltriethoxysilane |
ASAP | Abridged solid-phase extraction with alkaline Poly(ethylene) glycol lysis |
BSA | Bovine Serum Albumin |
BAW | Bulk Acoustic Wave |
CAI | Centrifugation-Assisted Immiscible Fluid Filtration |
cdPCR | Chamber-Based Digital PCR |
cfDNA | Cell-Free DNA |
CFU | Colony-Forming Unit |
CMC | Critical Micellar Concentration |
CMV | Cucumber Mosaic Virus |
CIFF | Centrifugation-Assisted Immiscible Fluid Filtration |
CRISPR | Clustered Regularly Interspaced Short Palindromic Repeats |
CTAB | Cetyltrimethylammonium Bromide |
cSPE | Conventional Solid-Phase Extraction |
DMP | Dimethyl Pimelimidate |
DNA | Deoxyribonucleic Acid |
dNTP | Deoxynucleotide Triphosphate |
dMDA | Digital Multiple Displacement Amplification |
dPCR | Digital Polymerase Chain Reaction |
DI | Deionized |
DMS | Dimethyl Suberimidate |
DMA | Dimethyl Adipimidate |
DTT | Dithiothereitol |
E. coli | Escherichia coli |
EDTA | Ethylenediaminetetraacetic Acid |
EL | Electrical Lysis |
FC-40 | Fluorinert FC-40 |
Fe3O4 | Iron (II, III) oxide |
fg | Femtogram |
gDNA | Genomic DNA |
GFP | Green Fluorescent Protein |
GUSCN | Guanidinium Thiocyanate |
Gu | Guanidine |
GuHCl | Guanidine Hydrochloride |
HAdV | Human Adenovirus |
HBV | Hepatitis B Virus |
HCl | Hydrochloric acid |
HCV | Hepatitis C Virus |
HCN | Hydrogen Cyanide |
HEPES | 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid |
HGMS | High-Gradient Magnetic Separation |
HI | Homobifuctional Imidoester |
HPV | Human Papillomavirus |
hrs | Hours |
IA | Immunoassay |
ICP | Ion Concentration Polarisation |
ISM | Ion-Selective Membrane |
IL | Ionic Liquid |
ITP | Isotachophoresis |
IPA | Isopropyl Alcohol |
KCl | Potassium Chloride |
IFAST | Immiscible Phase Filtration Assisted by Surface Tension |
kb | kilo basepair |
LAMP | Loop-mediated Isothermal Amplification |
LLE | Liquid–Liquid Extraction |
LMOGs | Low-Molecular-Mass Organogelators |
LOD | Limit of Detection |
MB | Magnetic Bead |
MB-SPE | Magnetic Bead Solid-Phase Extraction |
MES | 2-ethanesulfonic Acid |
mL | Millilitre |
MILs | Magnetic Ionic Liquids |
Min | minutes |
MSIs | Magainin analogues (synthetic antimicrobial peptides) |
MTB | Mycobacterium tuberculosis |
mtDNA | Mitochondrial DNA |
NA | Nucleic Acid |
NAAT | Nucleic Acid Amplification Test |
NA-PONT | Nucleic Acid Pont-Of-Need Testing |
NA-SPE | Nucleic Acid Solid-Phase Extraction |
NaCl | Sodium Chloride |
NaHCO3 | Sodium Hydrogencarbonate |
NaOH | Sodium Hydroxide |
-NH2 | Amine group |
PCR | Polymerase Chain Reaction |
PDA | Polydopamine |
PDMS | Polydimethylsiloxane |
PEG | Polyethylene Glycol |
pg | Picogram |
PMPs | Paramagnetic Particles |
PONT | Point-of-Need Testing |
Q. saponaria | Quillaja saponaria |
qPCR | Quantitative Polymerase Chain Reaction |
RNA | Ribonucleic Acid |
RBCs | Red Blood Cells |
RT | Reverse Transcription |
RT-RPA | Reverse Transcription Recombinase Polymerase Amplification |
RPA | Recombinase Polymerase Amplification |
SARS-CoV-2 | Severe Acute Respiratory Syndrome Coronavirus 2 |
SAW | Surface Acoustic Wave |
SDS | Sodium Dodecyl Sulfate |
sec | Seconds |
SIO− | Silanol |
SPE | Solid-Phase Extraction |
SPRI | Solid-Phase Reversible Immobilization |
SSNES | Self-powered Switch-Controlled NA Extraction System |
STT | Sodium dodecyl sulphate, Tween 20, and Triton X-100 |
TE | Tris-EDTA |
TPW | Two-Phase Wash |
µL | Microlitre |
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Main Lysis Method | Secondary Lysis Method | Reagents | Time/Temp (min or h/°C) | Target | Sample Matrix | Amplification | Lysis Efficiency | Yield Recovery Rate LOD | Ref. |
---|---|---|---|---|---|---|---|---|---|
Detergent | BSA | 0.3% IGEPAL CA-630 0.1% BSA | 5 min/on ice | Mammalian | N/A | RT-qPCR | N/A | N/A N/A 10 cells | [26] |
Ethanol | 0.008% Q. saponaria 5% (w/v) NaCl 5% (v/v) ethanol | 48 h/55 °C | Yeast | N/A | N/A | 99.0% | N/A N/A N/A | [27] | |
Enzymatic | Lysozyme Proteinase + SDS | 1. 1 h/45 °C 2. 5 h/50 °C | Soil microbiome | Soil | N/A | N/A | ~24 µg/g N/A N/A | [28] | |
Enzymatic | 10 mg/mL Lysozyme 20 ng/mL Proteinase K 0.1% SDS 1 mM EDTA 10 mM Tris-HCl 1 µL RNase | 10 min/N/A | Bacteria | Milk (Spiked) | dRPA | N/A | ~20 ng/µL from 10 cells N/A 10 cells | [29] | |
Enzymatic | 0.5% SDS 1 mg/mL Proteinase K 10 mM Dithiothreitol | 15 min/65 °C | Virus | Serum (Spiked) | RT-RPA | N/A | N/A N/A 500 copies/mL | [30] | |
Enzymatic | 10 mM Tris-HCl (pH8) 10 mM EDTA 1% SDS 10% Triton X-100 Proteinase K DMS | 20 min/56 °C | Virus | Clinical | RPA | N/A | N/A 95% 10 copies | [31] | |
Alkaline | N/A | 1.10 mM NaOH 2. 1 mM HCl | 5 min/N/A | Mammalian | Blood buccal swabs, saliva, cigarette butts | qPCR | N/A | 21.8 ng/µL N/A N/A | [32] |
0.5 M NaOH 10 mM Na2EDTA (pH 8) | 1 min/N/A | Plant | Plant | RT-RPA | N/A | N/A N/A 20 copies | [33] | ||
Surfactant | 0.2 M NaOH 1% SDS (dried) | N/A | Bacteria | Aerosol (Spiked) | qPCR | N/A | N/A 10% 101 CFU | [34] | |
PEG | 60% PEG200 20 mM KOH (pH 13.3–13.5) | 15 min/RT | Human Animal Bacteria Plant | Raw samples | PCR | N/A | N/A N/A 10 pg | [35] | |
1.25% PEG 200 10% PEG 8000 5% (v/v) NaOH | 1. 3 min/RT 2. 10 min/70 °C | Virus | Whole blood (Spiked) | LAMP | 100% | N/A N/A 102 PFU/mL | [36] | ||
6% PEG 200 0.08% NaOH | 3 min/RT | Fungal | Strawberry (Spiked) | RPA | N/A | N/A N/A 100 fg | [37] | ||
6% PEG 200 0.08% NaOH | 3 min/RT | Oomycete | Leaf | RPA | N/A | N/A N/A 500 fg | [38] | ||
60% PEG 400 100 mM KOH | N/A | Human | Whole blood | PCR | N/A | N/A N/A N/A | [39] | ||
50 g/L PEG 4600 20 mM KOH (pH 13.5) | 2 min/N/A | Fungal (mycelium) | Plant | LAMP | N/A | N/A N/A 19.9 pg/µL | [40] | ||
Chaotropic | N/A | 5 M GuHCl | 5 min/RT | Bacteria | Liquid stool (clinical) | PCR | 50% (G−) 60% (G+) | Ave 109.5 ng/µL (3-chamber) Ave 59.3 ng/µL (5-chamber) ~60% N/A | [41] |
4 M GUSCN 20 mM Tris-HCl 1 mM DTT pH 7.7 | N/A | Animal | Mixed meat | qPCR | N/A | N/A N/A 0.1% | [42] | ||
Enzymatic | GuHCl, Proteinase K | 30 min/56 °C | Bacteria | Human saliva | PCR | N/A | 157.2–165 ng/µL 7.86–8.25 µg N/A | [43] | |
Proteinase K GUSCN | 10 min/56 °C | Bacteria | Human urine Milk | qPCR | N/A | N/A N/A 5 CFU/10 mL | [44] | ||
6 M GuHCl Proteinase K pH 6.1 | 10 min/56 °C | Virus | Buccal swab (spiked) | LAMP | N/A | N/A N/A N/A | [45] | ||
Detergent | 6 M GuHCl 2% Triton X-100 13 mM EDTA 10 mM NaCl 51 mM Tris (pH 5.5) | 5 min/RT | Virus | Serum (Spiked) | RT-PCR | N/A | 1.3–2.0 µg/100 µL N/A N/A | [2] | |
AMP (Melittin, Bombolitin III, MSI-78, or MSI-594) | 5 min/RT | Bacteria | N/A | qLAMP | 100% | N/A N/A N/A | [46] | ||
5 M GuSCN 100 mM EDTA 0.5% (v/v) Sarkosyl | 5–10 min/N/A | Bacteria | N/A | N/A | N/A | N/A N/A N/A | [47] | ||
6 M GuHCl 2% Triton X-100 13 mM EDTA 10 mM NaCl 51 mM Tris pH 5.5 | 5 min/RT | Bacteria | Serum Saliva (Spiked) | dRPA | N/A | 15–35 ng/µL 89.4%, 79.6% (saliva, serum) 1.1 × 108 copies/μL | [48] | ||
1.5 M GuHCl 50 mM Tris [pH 8] 100 mM NaCl 5 mM EDTA 1% Tween-20 | 10 s/RT | Fish | Blood (Fish) | PCR | N/A | N/A N/A 104 cells | [49] | ||
4.8% GuSCN 5% Triton X-100 (pH 6.8) | N/A | Virus | Spiked blood | PCR | N/A | N/A N/A 5 particles | [50] | ||
4 M GUSCN 1% Triton X-100 1% ß-mercaptoethanol 10 mM 2-Ethanesulfonic acid | 5 min/RT | Virus | Nasopharyngeal swab | LAMP | N/A | N/A N/A 1–10 copies/µL | [51] | ||
4 M GuSCN 10 mM Tris-HCl (pH 8) 1 mM EDTA (pH 8) 0.5% Triton X-100 300 µL Isopropanol 3 µL ß-mercaptoethanol 5.6 µg poly-A carrier RNA (For RNA) | 3 min/RT | Synthetic DNA | Synthetic sputum (Spiked) Residual urine sample | qPCR | N/A | N/A 10.2 ± 4.03%, 91.2 ± 7.46% (sputum, urine) N/A | [52] | ||
0.1 M Tris-HCl (pH8.0) 10 mM EDTA 1% SDS 10% Triton X-100 Proteinase K DNase I (RNA) | 10 min/RT (RNA) 20 min/56 °C (DNA) | Mammalian Bacteria | N/A | RT-qPCR qPCR | N/A | ~100 ng/µL N/A 103 CUF/mL, 101 cells/mL (DNA, RNA) | [53] | ||
MIL | Peptide Enzymatic Detergent | 6 µL [P6,6,6,14+] [Ni(HfAcAc)3−] | 1 h/N/A | Plant | Plant | qPCR | N/A | ~8 ng N/A N/A | [54] |
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Lee, S.M.; Balakrishnan, H.K.; Doeven, E.H.; Yuan, D.; Guijt, R.M. Chemical Trends in Sample Preparation for Nucleic Acid Amplification Testing (NAAT): A Review. Biosensors 2023, 13, 980. https://doi.org/10.3390/bios13110980
Lee SM, Balakrishnan HK, Doeven EH, Yuan D, Guijt RM. Chemical Trends in Sample Preparation for Nucleic Acid Amplification Testing (NAAT): A Review. Biosensors. 2023; 13(11):980. https://doi.org/10.3390/bios13110980
Chicago/Turabian StyleLee, Soo Min, Hari Kalathil Balakrishnan, Egan H. Doeven, Dan Yuan, and Rosanne M. Guijt. 2023. "Chemical Trends in Sample Preparation for Nucleic Acid Amplification Testing (NAAT): A Review" Biosensors 13, no. 11: 980. https://doi.org/10.3390/bios13110980