Corinne Hrnicek
Dr. Chapman
Phoenix College Stem Train program
18 March 2025
Project Backround
This topic was selected because it is the project stem train students are working on this semester. The DNA extraction kit was sitting on the desk for a long time and now we get to use it. This topic was also selected because it is fascinating and important for medicine, plants, biology, and science. Extracting Plant DNA is important because “It allows scientists to analyze specific genome regions that are conserved across species. It is important to learn more about this topic, because It forms the basis for many downstream applications in scientific research, conservation efforts, and agricultural advancements. It is important to conduct research in this area because It helps study trait inheritance, develop genetically modified organisms (GMOs), and preserve endangered plant species. It is crucial for a wide range of applications in plant biology. It helps identify interesting mutations in plant genes, which can improve or hinder their growth in specific conditions” (The DNA Connection 2024).
What is already known about this topic is that “DNA microarray and RNA sequencing (RNA-seq) techniques are advantageous for large-scale genome-wide studies….genomics tools cannot always provide precise information about protein levels and regulation”(Neuman 2021). Something else that we already know is that “Recent studies have shown MN patches to be a promising method for rapid DNA extraction, with applications for the detection of allergens in food matrices” (Selz 2023). Yet another reason that the research should be further explored is that it can help detect food allergens. We also know that “in vitro repair of DNA damage (depurinated sites, strand nicks and base modifications) increases the number of samples that amplify”(Skage 2007). I find it interesting that the number of samples increases when there is In vetro repair of DNA damage. In addition, while researching previous experiments relating to DNA extraction, I found that “Arabidopsis thaliana is widely used in the research of plant molecular biology, but RNA isolation from certain tissues is difficult” (Suzuki 2004). I do not know why Arabidopsis is more commonly used if it is more difficult to isolate from certain tissues. I came across a passage in one of the articles I cited that said“ Thousands of eukaryotic genes generate mature transcripts with covalently linked ends, including exonic circular RNAs and circular intronic RNAs”(Xiao 2019). I am not exactly sure what that means, but it was a fascinating article, and i look forwards to learning more about the different types of RNA.
“It is very important but usually difficult to extract high quality DNA from plants for molecular work since there exist a great deal of polysaccharides, hydroxybenzenes, esters and other secondary metabolities” (Jinlu 2022). Expanding on current knowledge is important so that we can further research and be more efficient as well as accurate in extracting DNA despite polysaccharides, hydroxbenzenes, esters and other secondary metabolites.
I will research the topic by observing how the DNA extraction tool works and experimenting with the Plant DNA extraction tool. This is my first time using the machine, so observing and experimenting will be a learning experience.
“Nowadays, handling time and cost are key factors in selecting the most suitable DNA extraction method”(Comparison 2013). Even in the experiment that I am working on, we have encountered issues with how expensive it would be to buy ddt vs buying a different kit and doing DNA purification instead of RNA purification. That is another reason why is important to further research this topic, to be more effective and cost efficient in DNA extraction.
Another reason it is important to further research this topic is because there is still so much to leran. “Scientists are only beginning to fully understand how microbial ecosystems form around plants and affect their growth. The plant microbiome can contain many thousands of different types of microorganisms, especially fungi and bacteria” (Doe 2021). If we are going to find out how microbial exosystems form around plants, we need to better understand and further research the thousands of different types of microorganisms. “Molecular phylogenetic serves as a “tool” to understand and describe the diversity of organism and reconstruct evolutionary relationship using molecular data such as DNA, RNA, and protein”(Hidayat 2016). This research can have an impact on medicine and we can use the information from DNA purification to better describe and understand the diversity of an organism. “Total DNA was extracted from fresh materials using a GeneJET Plant Genomic Purification Mini Kit”(Hidayat 2016).
The definition of DNA extraction is “DNA extraction is a method to purify DNA by using physical and/or chemical methods from a sample separating DNA from cell membranes, proteins, and other cellular components” (Gupta 2019).
Hypothesis
Hypothesis: The efficiency of DNA extraction from plant tissues varies significantly depending on the type of plant tissue used (e.g., leaves, stems, roots).
Research Question
Research Question: How does the type of plant tissue (leaves, stems, roots) affect the yield and purity of extracted DNA?
I expect to find results that support the hypothesis. The efficiency will vary based on the type of plant tissue. Each DNA sample will be a little different. I expect to learn more about DNA, plant extraction, and the tools used to extract the DNA.
References
Comparison of the efficiency of some of the most usual DNA extraction methods for woody
plants in different tissues of Vitis vinifera L. (2013). OENO One. https://doi.org/10.20870/oeno-one.2013.47.4.1559
Doe explains...the plant microbiome. Energy.gov. (n.d.). (2021)
https://www.energy.gov/science/doe-explainsthe-plant-microbiome#:~:text=The%20plant%20microbiome%20is%20an,living%20parts%20of%20their%20environment
Gupta N. DNA Extraction and Polymerase Chain Reaction. J Cytol.
2019 Apr-Jun;36(2):116-117. doi: 10.4103/JOC.JOC_110_18. PMID: 30992648; PMCID: PMC6425773.
Hidayat, T., & Priyandoko, D. (2016, March 18). Molecular phylogenetic screening of Withania
somnifera relative from Indonesia based on internal transcribed spacer region. HAYATI Journal of Biosciences. https://www.sciencedirect.com/science/article/pii/S197830191630016X
Jinlu Li, Shuo Wang, Jing Yu, Ling Wang, Shiliang Zhou. (2022) A Modified CTAB Protocol for Plant
DNA Extraction. Chinese Bulletin of Botany, 2013, 48(1): 72-78. https://doi.org/10.3724/sp.j.1259.2013.00072
Neuman, H. (n.d.). (2021) Wiley Online Library | Scientific Research Articles, journals, ... Wiley Online
Library. https://onlinelibrary.wiley.com/doi/10.1111/tpj.15410
Selz, J., Adam, N. R., Magrini, C. E. M., Montandon, F. M., Buerki, S., & Maerkl, S. J.
(2023). A field‐capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring. Applications in Plant Sciences, 11(3), e11529-n/a. https://doi.org/10.1002/aps3.11529
Skage, M., & Schander, C. (2007). DNA from formalin-fixed tissue: extraction or repair?
That is the question. Marine Biology Research, 3(5), 289–295. https://doi.org/10.1080/17451000701473942
Suzuki, Y. (2004, November). (PDF) RNA isolation from siliques, dry seeds, and other tissues of
Arabidopsis thaliana. Research Gate. https://www.researchgate.net/publication/8202391_RNA_isolation_from_siliques_dry_seeds_and_other_tissues_of_Arabidopsis_thaliana
The DNA connection: Understanding the significance of plant DNA extraction. Pure
Natural Plant Extracts Manufacturer - Over 19 Years. (2024, August 14). https://www.greenskybio.com/plant_extract/the-dna-connection-understanding-the-significance-of-plant-dna-extraction.html
Xiao, M.-S., & Wilusz, J. E. (2019). An improved method for circular RNA purification using.
RNase R efficiently removes linear RNAs containing G-quadruplexes or structured 3’ ends. Nucleic Acids Research, 47(16), 8755–8769. https://doi.org/10.1093/nar/gkz576
