DNA Extraction in Homelabs

DNA extraction at CUBE HomeLab. Join whenever n discussion in Context2curriculm group and in Chatshaala.Photo shared by @Arunan sir .

A great discussion about the extraction of DNA from Chicken brain to Strawberry .Thanks to @⁨Sakshi⁩ @⁨~Akanksha Joshi⁩ @purva @Shahin @⁨Amirtha CUBE⁩ @⁨Chithra Mam⁩ and others.

What was the logic behind using soap to wash hands during Covid times ?

Can we do complex DNA Extraction Procedure in homelabs?

How soap helping in breaking the cell membrane of Corona virus@⁨~Akanksha Joshi⁩ @⁨Sakshi⁩ @purva and others?

Can we extract DNA from Strawberry ? or any other common things you can think of @⁨Sakshi⁩ @⁨~Akanksha Joshi⁩ @⁨Himanshu Joshi⁩ @⁨Chithra Mam⁩ and others.How about trying an attempt to extract DNA in our Homelabs? @⁨Abhijeet CUBE⁩ @⁨Amirtha CUBE⁩ @⁨Sakshi⁩ and others.

With only a few household items, you can extract DNA from strawberries just about anywhere! Extracting DNA from strawberries is super easy, allowing you to learn about genomics. Join NHGRI Director Eric Green and social media specialist Jenny Montooth as they show you step-by-step how to extract DNA from strawberries using materials available in your kitchen!"

https://www.genome.gov/about-genomics/teaching-tools/strawberry-dna-extraction#:~:text=With%20only%20a,in%20your%20kitchen!


A fruit with seeds outside like strawberry :strawberry: Date - 06/02/24, Time - 9:21, location - Delhi , Data collecter - Thikan sahu from chaitanya college pamgarh.Photo shared by @Thikan .

"“Simple, good old-fashioned soap and water is exceptionally effective at removing the coronavirus from your hands - more so than harsh chemicals or disinfectants that can also damage the skin,” adds Dr Corbett. "
How soap kills the COVID-19 virus | Coronavirus (COVID-19) | Queen's University Belfast

““In the case of the virus, this coat is actually a bilayer – consisting of two layers of these phospholipids with tails facing in, and heads facing out. When we wash our hands with soap and water, the tails of the soap molecules start to look for an area where there isn’t any water, and as they do so, they start to surround the virus particles.”
How soap kills the COVID-19 virus | Coronavirus (COVID-19) | Queen's University Belfast.

ISOLATION OF DNA from Chicken Brian ?? Why @⁨Sakshi⁩ and others are interested in chicken brain to isolate DNA !? Why not chicken muscle/blood !? @⁨Enas CUBE⁩ @⁨Amirtha CUBE⁩ @⁨Sakshi⁩ @⁨~Akanksha Joshi⁩ &others

Why soap came in picture in COVID times? Why are we using soap to wash out hands? @⁨Enas CUBE⁩ @⁨~Charvi⁩ @⁨Amirtha CUBE⁩ @⁨Chithra Mam⁩ @⁨Sakshi⁩ @⁨~Akanksha Joshi⁩ & others

How to isolate DNA ? How to break cell membrane and nuclear membrane? @⁨Sakshi⁩ @⁨Enas CUBE⁩ @⁨Amirtha CUBE⁩ & others

What is the function of soap in cleaning oils from hand !? @⁨Enas CUBE⁩ @⁨~Charvi⁩ @⁨Amirtha CUBE⁩ & others

https://www.youtube.com/watch?v=d2IBcOI22uI.

Follow up discussion:
[07/02, 12:44 pm] Enas CUBE: Dische’s diphenylamine reagent consists of diphenylamine, glacial acetic acid, sulfuric acid, and ethanol.[1]

When heated with DNA, it turns blue in the presence of DNA. A more intense blue color indicates a greater concentration of DNA.

[07/02, 12:46 pm] Enas CUBE: Can we think of any alternative to confirm the presence of DNA? @⁨Arunan sir :smiling_face:⁩ @⁨Theertha⁩ @⁨Sakshi⁩ @⁨shalini CUBE⁩ @⁨~Charvi⁩ @⁨Chithra Mam⁩ mam @⁨Batul Ma’am⁩ @amritha @⁨~Akanksha Joshi⁩
[07/02, 4:17 pm] Theertha: What may be the function of each of the components in Dische’s reagent ? How may these components detect DNA?

[07/02, 4:18 pm] Theertha: The acid converts deoxyribose to a molecule that binds with diphenylamine to form a blue substance.
All acids can convert deoxyribose to a molecule that binds with diphenylamine?? @⁨Enas CUBE⁩ @⁨Amirtha CUBE⁩ & others

The reagent does not interact with RNA, so can be used to distinguish DNA from RNA.

The muscle cell, also known as the myocyte is the smallest subunit of all muscular tissues and organs throughout the body. It is here in the myocyte, where the physiological steps of muscle contraction and where the pathophysiology of numerous muscular diseases takes place. https://www.ncbi.nlm.nih.gov/books/NBK544225/#:~:text=The%20muscle%20cell%2C%20also%20known,numerous%20muscular%20diseases%20takes%20place.

[07/02, 9:49 pm] Theertha: Multinucleation is one mechanism adopted by cells to generate and sustain large cell sizes. Muscle cells are one of the largest cell types, which are formed by fusion of mononucleated myoblasts and contain up to several tens (invertebrates) to several hundred (vertebrates) nuclei. Myonuclei are typically positioned at the cell’s periphery, and are distributed to maximize internuclear distance.
Mechanical positioning of multiple nuclei in muscle cells - PMC.

[07/02, 9:49 pm] Theertha: At higher salt concentrations, protein solubility usually decreases, leading to precipitation; this effect is termed salting-out ((Green and Hughes, 1955). Salts that reduce the solubility of proteins also tend to enhance the stability of the native conformation. In contrast, salting-in ions are usually denaturants.salt precipitation of proteins - Google Search

Extraction of DNA in Homelabs: can we extract DNA from banana? How are we going to do this @⁨Abhijeet CUBE⁩ @⁨Amirtha CUBE⁩ @⁨Enas CUBE⁩ @⁨Chithra Mam⁩ @⁨Himanshu Joshi⁩ @⁨Sakshi⁩ & others .

@⁨Sakshi⁩ did you extracted DNA from Chicken Brian? @⁨Sakshi⁩ @⁨~Akanksha Joshi⁩ @purva and others ? Why are we not interested in chicken muscle to extract DNA?@⁨Abhijeet CUBE⁩ @⁨Enas CUBE⁩ @⁨Aditya Joshi⁩ @⁨Amirtha CUBE⁩ & others

Following summary written by @Enas

@⁨Sunitha Mam⁩ mam has given introduced the CUBE in a meeting and about various model organism.
From Covid-19 to nowadays journey.

• A cell ( animal ) has 2 barrier: cell membrane and nuclear membrane when we have To isolate DNA out of it we have to break these two barrier.

• How can we break these barriers? Using detergent example SDS ( sodium dodecyl sulphate).

• Meaning of Hydrophilic and hydrophobic.

• What is covalent bond and non-covalent bond?

• What a detergent and cell membrane is made of ? ( hydrophobic(lipid part) and hydrophilic(inorganic or charged molecules)) .

• When we mix oil in water what happens and why so ?
• When glucose mixed with what happes? Does glucose molecules polar?

What will happen if a phospholipid monolayer is been kept in water?
How phospholipid bilayer of cell membrane is formed?
@⁨Arunan sir :smiling_face:⁩ @⁨Theertha⁩@⁨Sakshi⁩@⁨Sunitha Mam⁩ mam @⁨Chithra Mam⁩ mam @⁨~Dhanraj⁩

https://www.scienceabc.com/humans/why-is-dna-white.html


Amrita’s plan is to extract DNA from Banana.

• What things are common between plant and animal cell?
• What is the colour of DNA? If white what could be the reason ?

We saw a vedio regarding DNA extraction from strawberry.
Strawberry have 8 copies of each chromosome. So it’s a Octapoloid.
• What is polypoloidy ?
• what could be the reason of polypoloidy?
How octapoloidy occurs in strawberry?
• What is genome and subgenome ?

Then disscussed about mitosis and meiosis.
• tetrapoloidy can occur when protein which are participating in cell cycle is basically gets mutated which then may cause the diplod gametes to be formed which give rise to tetrapoloidy.

What is apomixis?
⁩ @⁨Chithra Mam⁩ mam @⁨Theertha⁩ @Amritha @⁨Himanshu Joshi⁩ sir

Polypoloidy is more found in plants example strawberry and wheat etc but in animals case it is less common. In case of drosophila the salivary gland is only polypoloid and not who organism is polypoloid , what could be the reason?
@⁨Theertha Cube⁩ @⁨~Batul Pipewala⁩ mam @⁨~Chitra⁩ mam @⁨~Abhijeet Singh⁩ @⁨~Himanshu Joshi⁩ sir

Today’s discussion was between Enas(Bsc. student from AND college), *who is going to extract DNA in Homelabs," and Itika (Bsc. Student from IIS Jaipur) who extracted DNA from Home

The interesting thing was that both the *procedures explained by Enas & Itika were the same.

The only difference is Enas planning to take 2 teaspoons of detergent, while Itika took 3 teaspoons.

Does that matter?
Please describe the setup @⁨Enas CUBE⁩ @itika

Procedure:

Chosen fruit: Banana
:low_brightness:Smashing using a plastic cover.
:low_brightness:Adding 1 teaspoon of salt, 2 teaspoons of detergent, and a small amount of water.
:low_brightness:Filter using cotton cloth.
:low_brightness:The filtrate is now treated with sanitizer.

Result:
White cloudy DNA can be seen. @⁨Aditya Joshi⁩ @⁨Enas CUBE⁩ @⁨Chithra Mam⁩ @⁨Himanshu Joshi⁩ & others .

Later, we came to the details of each step: @⁨Enas CUBE⁩ @⁨Chithra Mam⁩ @⁨Himanshu Joshi⁩ @⁨Aditya Joshi⁩ @itika & others

Why detergents:
Detergents can break down the cell membrane and nuclear membrane of plant cells.

Why salt:
Salt neutralizes the charges on the phosphate backbone of DNA molecules. Salt is NaCl; when in contact with water, it ionizes to Na+ and Cl-. Water molecules bond with Na+ and Cl-. These Na+ ions can bind to the phosphate backbone of DNA. As a result, the DNA molecules tend to clump together with salt, preventing precipitation. But at the same time, proteins are getting precipitated.
How? Any comments?
What concentration of salt can cause the precipitation of proteins?@⁨Aditya Joshi⁩ & others

Why alcohol:
Alcohol can remove water molecules from the surroundings of DNA and leads to aggregation/precipitation.

How can we explain each ingredient of our DNA Extraction method by asking why and how?
@⁨Enas CUBE⁩ @⁨Aditya Joshi⁩ @⁨shalini CUBE⁩ @⁨Abhijeet CUBE⁩ & others

https://www.youtube.com/watch?v=gnhUh6qVD5Y. Video shared by @⁨Himanshu Joshi⁩ . What we meant by Salt in & Salt out?
Is Salt in/Salt out applicable in DNA extraction methods?@⁨Aditya Joshi⁩ @⁨Enas CUBE⁩ & others

DNA EXTRACTION IN HOMELAB by Amritha .

[12/02, 12:11 pm] Amirtha CUBE: DNA EXTRACTION FROM GRAPES.

REQURIMENTS:1.one glass of water.
2. Two steel bowl.
3.salt.
4.dish wash.
5.plastic cover.
6.one spoon.
Amritha.k sn college alathur.
Time:12:00pm.
Place:Palakkad.
Date:12.2.24.

Video from Amritha,about the Extraction of DNA in Homelab.

Congratulations @⁨Amirtha CUBE⁩ for made an attempt to extract DNA from your homelabs.

Do you happy about the result?

Do you think we can improve? @⁨Amirtha CUBE⁩ ?

Why are we adding detergents into the DNA extraction method?

How detergents works @⁨Amirtha CUBE⁩ @⁨Aditya Joshi⁩ @⁨Abhijeet CUBE⁩ @⁨Chithra Mam⁩ @⁨Himanshu Joshi⁩ & others .

Eric D. Green, M.D., Ph.D., is the director of the National Human Genome Research Institute (NHGRI) at the U.S. National Institutes of Health (NIH). Dr. Green’s relationship with the Institute began long before his appointment as director. He served as the Institute’s scientific director (2002 - 2009), chief of the NHGRI Genome Technology Branch (1996 - 2009) and founding director of the NIH Intramural Sequencing Center (1997 - 2009). Prior to that, he played an integral role in the Human Genome Project.Eric D. Green, M.D., Ph.D., is the director of the National Human Genome Research Institute (NHGRI) at the U.S. National Institutes of Health (NIH). Dr. Green’s relationship with the Institute began long before his appointment as director. He served as the Institute’s scientific director (2002 - 2009), chief of the NHGRI Genome Technology Branch (1996 - 2009) and founding director of the NIH Intramural Sequencing Center (1997 - 2009). Prior to that, he played an integral role in the Human Genome Project. - Google Search

Strawberry DNA Strawberry DNA Extraction

The average glass of wine contains about 11 percent to 13 percent alcohol, but bottles range from as little as 5.5 percent ABV to as much as around 20 percent ABV. 1 When tasting wine, you’ll notice alcohol comes through as heat in the back of your mouth or throat. Wine Alcohol Content Guide for Every Type of Wine.

Follow up discussion in Context to curriculum group:

[12/02, 10:07 pm] Khushi: detergents disrupt the cell membrane thus does cell lysis so that dna will come out of cell
[12/02, 10:34 pm] Himanshu Joshi:
What is this medium and how did you prepare this?
[12/02, 10:36 pm] Himanshu Joshi: How does detergent get to know that it has reached the cell membrane of a cell and disrupted only that?
What about Nuclear membrane? @⁨~Khushi⁩
[12/02, 10:37 pm] Khushi: so it interacts with the phospholipid memrane …
[12/02, 10:41 pm] Himanshu Joshi: How does this interaction take place, I mean when a soap solution comes in contact with cell membrane, what interaction of soap with phospholipid membrane take place and why?
[12/02, 10:42 pm] Khushi: so its hyphophobic and hydrophilic interaction between lipid membrane and detergent
[12/02, 10:44 pm] Himanshu Joshi: Okay, lipid membranes have hydrophilic and hydrophobic ends. Where does the detergent bind and why?

Khushi :Detergent monomers solubilize membrane proteins by partitioning into the membrane bilayer. With increasing amounts of detergents, membranes undergo various stages of solubilization. The initial stage is lysis or rupture of the membrane. https://r.search.yahoo.com/_ylt=AwrKBWxKUsplJ2UGaXDnHgx.;_ylu=Y29sbwMEcG9zAzEEdnRpZAMEc2VjA3Nj/RV=2/RE=1707786955/RO=10/RU=https%3A%2F%2Fwww.thermofisher.com%2Fus%2Fen%2Fhome%2Flife-science%2Fprotein-biology%2Fprotein-biology-learning-center%2Fprotein-biology-resource-library%2Fpierce-protein-methods%2Fdetergents-cell-lysis-protein-extraction.html%23%3A~%3Atext%3DDetergent%2520monomers%2520solubilize%2520membrane%2520proteins%2520by%2520partitioning%2520into%2Cstage%2520is%2520lysis%2520or%2520rupture%2520of%2520the%2520membrane./RK=2/RS=Os5PBvieDYrpuYMK37MlrPnG3gI-

[13/02, 6:38 am] Chithra Ma’am: Detergents can be denaturing or non-denaturing with respect to protein structure. Denaturing detergents can be anionic such as sodium dodecyl sulfate (SDS) or cationic such as ethyl trimethyl ammonium bromide. These detergents totally disrupt membranes and denature proteins by breaking protein-protein interactions.
https://www.google.com/search?q=does+detergent+denature+proteins&rlz=1CDGOYI_enIN944IN944&oq=does+detergent+denature+proteins&gs_lcrp=EgZjaHJvbWUyCQgAEEUYORiABDIICAEQABgWGB4yCAgCEAAYFhgeMgoIAxAAGA8YFhgeMggIBBAAGBYYHjIICAUQABgWGB4yCAgGEAAYFhgeMggIBxAAGBYYHjIICAgQABgWGB4yDQgJEAAYhgMYgAQYigXSAQkxNTk0OGowajeoAgCwAgDiAwQYASBf&hl=en-GB&sourceid=chrome-mobile&ie=UTF-8
[13/02, 6:39 am] Chithra Mam: So detergents can also denature proteins and create gaps in membranes, ultimately breaking it down.