Co-Extraction of DNA and RNA from Candida albicans Using a Chemical Method in Conjunction with Silicon Carbide with Few Cells
<p>Nucleic acid integrity analysis in 1% agarose gel. M: DNA Ladder 1 kb Plus—exACTGene Fischer BioReagent; (<b>A</b>) samples 1 to 10, method 1; (<b>B</b>) method 2; (<b>C</b>) method 3.</p> "> Scheme 1
<p>Nucleic acid purification and precipitation process. Source: Prepared by the author on the Biorender platform.</p> ">
Abstract
:1. Introduction
2. Materials and Methods
2.1. Preparation of Materials
2.2. Obtaining and Preparing Fungal Samples
2.3. Purification of Nucleic Acids
2.4. Integrity Analysis
2.5. Quantification and Purity of Isolated Nucleic Acids
3. Results
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Performance (ng/μL) | Purity | ||||||
---|---|---|---|---|---|---|---|
(A260/A280) | |||||||
Cultivation | Sample | Average Aliquot (mL) | No. cells/mL (× 106 CFU) | DNA | RNA | DNA | RNA |
Method 1 (BHI) | 1 | 0.1 | 0.025 | - | - | - | - |
2 | 0.5 | 0.075 | - | - | - | - | |
3 | 1.0 | 0.115 | - | - | - | - | |
4 | 1.5 | 0.115 | - | - | - | - | |
5 | 2.0 | 0.160 | 24.8 | - | 1.3 | - | |
6 | 2.5 | 0.260 | - | - | - | - | |
7 | 3.0 | 0.270 | 59.3 | 26.0 | 1.4 | 1.2 | |
8 | 3.5 | 0.295 | 72.4 | 36.1 | 1.4 | 1.2 | |
9 | 4.0 | 0.405 | 57.7 | 25.6 | 1.3 | 1.13 | |
10 | 4.5 | 0.595 | 61.9 | 31.1 | 1.4 | 1.1 | |
Method 2 (Sabouraud) | 1 | 0.2 | 0.816 | 7.9 | 50.7 | 1.0 | 1.3 |
2 | 0.4 | 1.632 | 86.9 | - | 1.4 | - | |
3 | 0.6 | 2.448 | 126.1 | 84.0 | 1.5 | 1.4 | |
4 | 0.8 | 3.264 | 102.3 | 61.9 | 1.6 | 1.4 | |
5 | 1.0 | 4.080 | 93.9 | 49.0 | 1.6 | 1.4 | |
6 | 1,2 | 4.896 | 263.7 | 231.4 | 2.1 | 2.2 | |
7 | 1.4 | 5.712 | 325.2 | 288.2 | 2.2 | 2.2 | |
8 | 1.6 | 6.528 | 165.9 | 145.5 | 2.1 | 2.1 | |
9 | 1.8 | 7.344 | 354.9 | 302.8 | 2.1 | 2.2 | |
10 | 2.0 | 8.160 | 569.8 | 477.6 | 2.2 | 2.2 | |
Method 3 (Sabouraud) | 1 | 0.2 | 0.622 | 35.2 | 29.3 | 2.0 | 2.0 |
2 | 0.4 | 1.244 | 47.5 | 40.4 | 1.8 | 1.7 | |
3 | 0.6 | 1.867 | 49.8 | 42.4 | 2.0 | 2.0 | |
4 | 0.8 | 2.489 | 97.7 | 83.4 | 2.1 | 2.1 | |
5 | 1.0 | 3.112 | 126.5 | 108.1 | 2.1 | 2.1 | |
6 | 1,2 | 3.734 | 202.0 | 171.9 | 2.2 | 2.2 | |
7 | 1.4 | 4.356 | 209.6 | 177.1 | 2.2 | 2.2 | |
8 | 1.6 | 4.979 | 228.9 | 190.4 | 2.2 | 2.2 | |
9 | 1.8 | 5.601 | 220.2 | 185.7 | 2.2 | 2.2 | |
10 | 2.0 | 6.224 | 384.2 | 312.6 | 2.2 | 2.2 |
Adapted Method | |||
---|---|---|---|
Steps | Oliveira et al. [15] | Methods 1 and 2 | Method 3 |
Cell sedimentation | 2 min/10,000× g (4th) | 5 min/3500 rpm * | 5 min/3500 rpm * |
Homogenized by inversion | 10 s | 10 s | 10 s |
Vortex homogenization | 1 h (200 rpm) | 1 min * | 2 min * |
Homogenized by inversion | 10 s | 10 s | 10 s |
Vortex homogenization | 1 h (200 rpm) | 1 min * | 2 min * |
Homogenized by inversion | 10 min | 5 min * | 5 min * |
Centrifugation | 15 min/10,000× g (4th) | 15 min/15,000 rpm * | 15 min./15,000 rpm * |
Homogenized by inversion | 10 min | 5 min * | 5 min * |
Centrifugation (4th) | 10 min/10,000× g (4th) | 15 min/15,000 rpm * | 15 min/15,000 rpm * |
Precipitation | 3 h at −20 °C | 30 min at −20 °C * | 30 min at −20 °C * |
Centrifugation | 10 min/10,000× g (4th) | 15 min/15,000 rpm * | 15 min/15,000 rpm * |
Centrifugation | 5 min/7000× g (4th) | 5 min/10,000 rpm * | 5 min/10,000 rpm * |
Drying | 30 min | 30 min | 30 min |
Solubilized in 50 μL of water | ------- | ------- | ------ |
Execution time | 06 h 50 min 06 s | 02 h 10 min 50 s | 02 h 12 min 50 s |
DNA/RNA Extraction—Mechanical Method (Silicon Carbide) | By Sample | ||
---|---|---|---|
Reagents | Grams/mL Per Sample (0.5 mL) | Mark | BRL |
Tris (hydroxymethyl)aminomethane | 0.06056 gold | LGC 250 g | 0.094 |
Disodium salt EDTA (2H2O) PA | 0.01861 gold | Neon 500 g | 0.0041 |
Sodium chloride PA | 0.01957 gold | Neon 500 g | 0.00087 |
Cetyltrimethylammonium bromideSHOVEL | 0.001 gold | Dynamic 100 g | 0.0009 |
Sodium Dodecyl Sulfate (SDS) | 0.003 gold | Dynamic 500 g | 0.00096 |
Phenol 90% | 0.6 mL | Dynamics 1 L | 0.064 |
Chloroform PA | 1.2 mL | Dynamics 1 L | 0.216 |
Isoamyl alcohol PA | 0.024 mL | Dynamics 1 L | 0.0036 |
Sodium acetate PA | 0.0073 gold | Dynamic 500 g | 0.0008 |
Ethanol PA | 1.8 mL | Dynamics 1 L | 0.090 |
Diethylpyrocarbonate (DEPC) | 0.015 mL | Sigma-Aldrich-25 mL | 0.462 |
By sample | - | - | 0.937 |
DNA/RNA electrophoresis | |||
Reagents | TAE 1X (300 mL) | Mark | BRL |
Tris PA | 1.452 g | LGC 250 g | 2.26 |
EDTA PA | 0.124 gold | Neon 500 g | 0.021 |
Acetic acid | 0.34 mL | Dynamics 1 L | 0.061 |
Diethylpyrocarbonate | 0.3 mL | Sigma-Aldrich 25 mL | 9.24 |
Agarose PA | 0.30 gold | KASVI 100 g | 1.476 |
IntercalatingBlue Green Loading Buffer Dye I (0.6 mL) | 0.0006 mL (0.6 μL) | 0.17 | |
DNA Ladder 1 kb plus (0.5 mL) | 0.0008 mL (8 μL) | LGC Biotechnology | 1.696 |
Total (per gel) | - | - | 14.92 |
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Freitas, E.C.V.d.; Santos, F.A.d.; Lopes, M.R.V.; Sousa Júnior, D.L.d.; Yafawi, T.T.A.; Araújo, A.C.F.; Freitas, P.R.; Menezes, I.R.A.d.; Coutinho, H.D.M.; Leandro, M.K.d.N.S. Co-Extraction of DNA and RNA from Candida albicans Using a Chemical Method in Conjunction with Silicon Carbide with Few Cells. DNA 2024, 4, 417-426. https://doi.org/10.3390/dna4040029
Freitas ECVd, Santos FAd, Lopes MRV, Sousa Júnior DLd, Yafawi TTA, Araújo ACF, Freitas PR, Menezes IRAd, Coutinho HDM, Leandro MKdNS. Co-Extraction of DNA and RNA from Candida albicans Using a Chemical Method in Conjunction with Silicon Carbide with Few Cells. DNA. 2024; 4(4):417-426. https://doi.org/10.3390/dna4040029
Chicago/Turabian StyleFreitas, Elizabeth Cristina Vieira de, Francisca Alves dos Santos, Maria Raíssa Vieira Lopes, Dárcio Luiz de Sousa Júnior, Tássia Thaís Al Yafawi, Ana Carolina Ferreira Araújo, Priscilla Ramos Freitas, Irwin Rose Alencar de Menezes, Henrique Douglas Melo Coutinho, and Maria Karollyna do Nascimento Silva Leandro. 2024. "Co-Extraction of DNA and RNA from Candida albicans Using a Chemical Method in Conjunction with Silicon Carbide with Few Cells" DNA 4, no. 4: 417-426. https://doi.org/10.3390/dna4040029
APA StyleFreitas, E. C. V. d., Santos, F. A. d., Lopes, M. R. V., Sousa Júnior, D. L. d., Yafawi, T. T. A., Araújo, A. C. F., Freitas, P. R., Menezes, I. R. A. d., Coutinho, H. D. M., & Leandro, M. K. d. N. S. (2024). Co-Extraction of DNA and RNA from Candida albicans Using a Chemical Method in Conjunction with Silicon Carbide with Few Cells. DNA, 4(4), 417-426. https://doi.org/10.3390/dna4040029