DNA Sequencing
Genetic Sequencing
DNA sequencing refers to the general laboratory technique for determining the exact sequence of nucleotides, or bases, in a DNA molecule. The sequence of the bases (often referred to by the first letters of their chemical names: A, T, C, and G) encodes the biological information that cells use to develop and operate. Read more
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Both the "Ted-Ed" and "yourgenome" videos were very interesting and well explained in my opinion. I found it very intriguing in the "yourgenome" that the substance the DNA is placed in is heated to 96 degrees Celsius to separate the strands. Similarly, the substance is heated to 96 degrees Celsius again to detach the DNA strand from its opposite match that was created. I noticed some commonalities/overlaps of what Dr. Ojha explained during today's discussion and the videos such as how the matches of DNA strands are created by using the opposite bases (ex. A pairs with T), and that the bases are represented by specific colors. ~Cassina
ReplyDeleteFrom my knowledge DNA sequencing refers to laboratory technique used to determine the order of the four nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA. There are several different methods to sequencing but all include breaking down a DNA molecule and determining the order and determining the order of the bases in those fragments. A bit of history for sequincing starts in the 1970's and has evolved all the way till this day. Some methods include whole-genome sequencing and ChIP sequencing, yet all follow the basic common principles and help with " offering advantages in throughput and scale compared to capillary electrophoresis–based Sanger sequencing."
ReplyDeleteDNA sequencing can be accomplished through a variety of scientific methods that involve splicing and replication of DNA. The interpretation of the genome is accomplished through bioinformatic techniques to “stitch” back the sequence and determine what the DNA’s nucleotide sequence is. This allows us to understand an individual’s genome, but the applications of this method are not fully understood. I believe that while the scientific community has made great strides in achieving the sequencing of DNA, there needs to be an extended step that allows us to use this information and predict the basis for certain genetic diseases in humans. For example, we can use the sequence of DNA to develop new therapeutics that help to inhibit or stop certain diseases from a patient’s hereditary information and sequence of DNA. In this way, medical research will be able to be expanded further, and not limited to only sequencing DNA, but being able to critically use it to advance medicine.
ReplyDeleteWhat I found interesting is how you can use the color of the light reflected from the end of a base pair and put together an entire DNA sequence from it. I think this is very important because now scientists will be able to quickly read through and piece together large portions of DNA instead of having to manually piece together DNA sequences. I also found it interesting about how scientists are able to take out the organism of a DNA and artificially duplicate it. I think this is very important because it allows scientists to closer look at the DNA, test it, and eventually develop solutions and treatments catered specifically to the need of a a certain DNA type. This will help open up a new array of opportunities of how we look at solving gene-based diseases.
ReplyDeleteI found the yourgenome video to be interesting because it explains the different temperatures needed to sequence the DNA. The TED-Ed video does not mention temperature but uses a similar concept. In that video, it presents the uses of DNA sequencing and how it could affect our lives in the future. Although researchers have not found all the answers yet, they are looking at differences in the DNA sequence among humans to find how these differences give certain traits. The slides mentioned that there were different ways to sequence DNA, but the most used one is by breaking down the DNA into pieces to make it possible for the computer to analyze. After this step, the algorithm organizes the DNA in the order it was previously to give the DNA sequence.
ReplyDeleteDNA sequencing involves many steps. First, DNA must be cut up into smaller pieces and inserted into plasmid DNA, which is then isolated from bacteria and sequenced. Nucleotide bases, DNA polymerase, primers, and terminator bases are all added into the isolated DNA. The heating and cooling process helps produce many DNA strands that are of different lengths, and electrophoresis helps read the fragments of different lengths. DNA sequencing helps scientists understand different genes, which can potentially be useful in treating diseases that arise from mutations.
ReplyDeleteGenerally speaking I am fascinated by many things in this topic and I am sure there is a much more information I'll be surprised with as well. First of all I find it really interesting that humans and technology have evolved so much that we're able to distinguish and understand microscopic things such as DNA and be able to know it's exact structure. I also find it appealing that technologies such as BLAST allow us to compare and contrast different species. I can understand how this would be useful to scientists, because this automatic technology makes it efficient and less time consuming to formulate new ideas and discoveries. Also I really enjoyed learning about SNPs today and how they are NOT the same as mutations. From my understanding SNPs are a variation of DNA sequencing in which a nucleotide in the sequence is different and is found in at least 1% of the population. This is really useful especially for scientists involved with medicine because SNPs can help target specific genes associated with diseases.
ReplyDeleteI learned that in 2003, the first human genome was sequenced. In order to sequence, scientists have to break the long string of DNA into smaller pieces. They then use enzymes to make thousands of copies of genome pieces. Programs are then used to identify the nucleotides. Scientists still to this day are figuring out how to interpret DNA to its extent. I find it really interesting how humanity has advanced so far from ancient times to being able to know your identity through DNA sequencing.
ReplyDeleteI thought both videos provided really amazing visuals of how scientists conducted the Human Genome Project and sequenced the human genome in 2003. I find it really interesting that they were able to figure out that multiple copies of the DNA can be snipped into shorter pieces of different lengths, sequenced, then matched back together to get the entire DNA sequence. While I really appreciate this method, something that really stuck out to me was in the Ted-Ed video, when it was stated that in the future, DNA will be able to be sequenced in the matter of minutes. I find it fascinating that this is all still a work in progress, and I can't wait to see what the future holds for DNA sequencing! In addition, I very much enjoyed our discussion about SNPs today. It's so interesting how much time they can save for scientists or doctors if they are wondering whether to prescribe a treatment to a patient or are looking for a specific trait.
ReplyDeleteI learned DNA sequencing occurs when free DNA bases, DNA polymerase, DNA primer, and terminator bases are binded to single strands of DNA, they work together along with fluctuating temperatures to separate the new DNA from the original strand. Electrophoresis is used to allow the DNA to be moved through the gel by length in order for the terminator base to light up by laser, these colors indicate the different DNA bases, shortest to longest. Though, I was a bit familiar with this process already I found the video’s visuals to really improve my understanding. I also learned that a genome is all the genes that make up an organism, which make up DNA. Sequencing the first human genome took so long because its goal is to know all the possible letter sequences that make up a genome, and each fragment has to be sequenced individually. The sequences are interpreted differently causing the differences in looks, likes, immunity, responses, and actions among individuals.
ReplyDeleteWhen learning about DNA sequencing I was always curious about how researchers were able to keep track of and process so many chemical bases (ATGC). The Ted-Ed video stated how in the future, it could be done in a matter of minutes (I doubted this was even possible). Then I learned about how it took researchers 20 years to process a whole human genome which I was pretty impressed-- the computing technology in 2003 was pretty basic compared to the computers we have today. Another part that shocked me was how researchers used enzymes to make duplicates of the genome pieces. I thought enzymes were hard to manipulate and control, but it turns out it is possible to use them to make copies of genomes! Even now, scientists are still working on how to interpret DNA. Once society figures out how to interpret DNA, we are able to figure out clearly how certain medications respond to certain people and what physical characteristics some humans possess.
ReplyDeleteFrom my knowledge, DNA sequencing is the arrangement of many single DNA bases or nucleotides into their correct order. The reason that we break apart nucleotide bases only to rebuild them is because the large unbroken strings of DNA are too big for us to read and figure out. However, when we break them apart, they become a usable size for us and much easier to work with. Later, we stitch together the decoded pieces into one whole genome. In the past, people used methods to rebuild DNA that were expensive, time consuming, and difficult. However, now and in the future, DNA sequencing is getting less expensive and more efficient. I am really excited to see what the future is for DNA sequencing. Seeing how easy and cheap it is going to be in the future shows that we will be able to easily decode genomes and create medicines that will be able to help everyone no matter what their genes are. I also hope we will be able to help everyone understand their own bodies better so they will be able to live their lives safer and healthier.
ReplyDeleteI learned that DNA sequencing is the process of determining the precise order of the nucleotides in a DNA molecule. These nucleotides, also known as bases, are the building blocks of DNA and are made up of adenine (A), thymine (T), cytosine (C), and guanine (G). These bases and their sequence in a strand of DNA carries important genetic information that cells use to grow and function. DNA sequencing is useful for learning about the function of genes and other components of the genome. DNA sequencing involves using specialized techniques (ex: next-generation sequencing) and equipment, that are continuously being improved in order to make DNA sequencing faster, cheaper, and more accurate, in order to be able to read the sequence of base pairs in a DNA fragment. DNA sequencing is helpful for identifying genetic variations, diagnosing genetic disorders, determining ancestry, and many more.
ReplyDeleteDNA is made up of strings of nucleotides, and DNA sequencing is the process used to find the specific order of the nucleotides in a specific strand of DNA. We break large DNA strands into smaller ones because it is easier to analyze them. This is also used to analyze them faster because we can run multiple smaller samples at once rather than one larger one. DNA sequencing is used to identify patterns that code for specific proteins, which can be used to identify problems caused by discrepancies of said proteins. This technology is relevant in the current day and will continue to be relevant in the future because it can still be improved on.
ReplyDeleteFragments of the DNA that's being worked with is inserted into plasmid DNA. Then that's inserted into bacteria solely for the purpose of multiplying. Then the DNA is isolated from the bacteria and added to a plate for sequencing. The mixture in the play also includes extra DNA bases, polymerase, primer, and Terminator bases. What's stood out to me was that you need to keep a high temperature for the DNA to separate, low temperature for the primer to bind to the plasmid DNA, then an increase temperature for the polymerization enzyme to work, and then everything must be heated until the high temperature is reached
ReplyDeleteDNA Sequencing is the a laboratory technique for determining the exact sequence of nucleotides (A, T, C, and G) in a DNA strand. There are a variety of methods used to do this, but most involve the basic processes of splitting the strand into smaller segments, duplicating them, and analyzing them. This must be done because DNA strands are far too long to analyze without splitting them. These techniques for sequencing are constantly evolving, and although today they are time intensive, they may be less so in the future. DNA Sequencing has a wide variety of applications, from diagnosing medical problems to determining characteristics in a person.
ReplyDeleteThings that I took away from this video are:
ReplyDeleteComplimentary base pairs of mRNA to DNA.
How scientists sequence a genome. By using mRNA polymerase, lone bases and a DNA strand. Original DNA is split, then the strand is attached from which the polymerase starts making new enzymes with the lone bases provided by the scientists. Once all these extra proteins are made they are put in an electrophoresis machine which sorts them by length.
Questions I have: What is the significance of sorting them by length? What does that tell you?
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ReplyDeleteI am quite interested in the goals people are setting for DNA sequencing; I think their goals are almost unthinkable. The first human genome to ever be sequenced took decades to be completed, but people are trying to shorten that time to mere minutes at a significantly lower cost. People have to figure a faster way to break down the DNA into smaller pieces, increase the signal coming from each letter (one way is to use enzymes to duplicate the genome piece), create double stranded DNA, and finally read and understand the significance of the sequence of DNA. I think this will be a very difficult task for us in the future.
ReplyDeleteDNA Sequencing first requires that the original DNA must be split into separate pieces. These are inserted into plasmid DNA which leads to multiple copies of the DNA being produced through the replication of bacteria. The DNA isolated from the bacteria are placed in wells on a tray and a mix of free DNA bases, DNA Polymerase enzymes, DNA primers, and terminator bases. With the varying adjustment of temperatures from 96 degrees to 60 degrees, a new strand of DNA is synthesized by the DNA Polymerase enzyme until the fluorescent terminator base is added. When multiple strands are synthesized of different lengths are produced. A capillary tube is used to transfer the negatively charged DNA. Once the DNA strands approach the end of the tube, a laser is used to detect the terminator bases. These specific bases correspond to a specific color upon interaction with the laser. Since the shortest fragments will fluoresce first and the longer fragments will fluoresce afterwards, the DNA sequence is formed.
ReplyDeleteFrom my understanding, DNA is deoxyribose nucleic acid, also a polymer, that can sequence about three million nucleotides using technologies. This process includes DNA polymerase to change the lengths of chains in DNA. Later, Industrial Automation Sequencing occurred and had fluorescent dye to tag the nucleotide. This proves to be effective in which sequencing data made it cheaper and faster with the help of technology. Advanced can also improve and correct errors in human genomes such as 454 Sequencing and pyrosequencing, where the number of nucleotides are limited until DNA synthesis stops.
ReplyDeleteThe human genome is a massive amount of compressed information in a tiny space, merely attempting to read it requires a complex procedure to "amplify" the signals we can read off the DNA.
ReplyDeleteWith enzymes or bacteria, the extracted DNA is replicated, and then special "pairs" are added to the sequence. These special pairs, produce a specific color that can be read by machines.
However, the DNA strand must be only one of the chains instead of the double helix in order to have the special pairs added, so it is split by raising the temperature to 96 degrees. No information is lost because only A bases can link to T bases, same for G and C, this allows us to know what the bases on the other chain are.
After the new colored bases are added, a machine can attempt to read the light signatures and record the DNA sequence.
Esther:
ReplyDeleteThe first generation sequencing, dideoxy termination, also known as the Sanger process was used for the Human Genome Project. The idea is that during DNA synthesis, DNA polymerase can use ddNTP as the feedstock, but its reaction will stop when the ddNTP is added. Specific experiments are performed by PCR, but unlike normal PCR, it requires only one primer instead of a pair. Ordinary dNTP and four different ddNTPS were added to the four same reaction systems. So let's say we have ddATP, ddGTP, ddCTP and ddGTP and we call this A,G,C,T system, and each of these systems will stop reacting at the appropriate base, so we have A series of DNA fragments of varying lengths that end at A,G,C,T, For example, the pieces of DNA in system A, they all end in A. And then we take those pieces and we do a high resolution electrophoresis, and based on the electrophoresis, we can read the sequence. This was the case with the earliest methods of sequencing, but it was extremely time-consuming, requiring the DNA to be broken into countless small, suitable pieces and then pieced back together after the sequence was completed. This is why the Human genome project required so many countries and took so long. Of course, modern second-generation DNA sequencing technologies are already widely available, and they have the advantages of low cost, high throughput, and short time compared to first-generation sequencing technologies.
DNA is an incredibly dense storage medium, and current technology can not read the entire genome of a human at once requiring the DNA to be cut. Moreover, one needs to separate the double helix of DNA into a single strand. Sequencing the genome can tell us about which genes code for which the proteins, and can explain differences in protein structure that vary from person to person
ReplyDeleteBrady
I learned that DNA is very condensed and requires DNA to be cut with certain tools that we now have available thanks to technology. There are different types of ways to cut DNA and usually it gets cuts into one strand. It can help us tell which genes codes for different proteins and can help explain how people are different.
ReplyDeleteAllison Oh
DNA sequencing is used to figure out the sequence of the nucleotides in a strand of DNA. To complete this process, first the strand has to be spliced into smaller fragments and made into multiple copies. To do this, the strands can be inserted into a plasmid which a bacteria can take in and replicate. Then to summarize really quickly, the strands are isolated and put into the sequencing region with a mixture of ingredients. Then through a process of heating and cooling, strands of different lengths are produced determined by the terminator bases. Then the sizes are determined by electrophoresis. Then the sequence is determined by the the light emitted by each terminator. All the strands will be viewed in a computer to figure out the letter sequence.
ReplyDeleteDNA sequencing is the process of dictating the orders of the bases of a strand of DNA. These bases include A, T, C, and G. Before sequencing DNA, it must be split into smaller pieces as the entire strand would be too large to analyze. These smaller pieces are put into plasmid DNA which is then inserted into a bacterial cell. During the process of sequencing, various factors are involved such as terminator bases, DNA polymerase, DNA primers, and the four bases, A, T, C, G. When sequencing, the temperature is manipulated to split the DNA in half as well as allow DNA polymerase to bind to the strand of DNA to make more strands. After which, the strands are arranged by length during the process known as electrophoresis. These strands then travel through a capillary that at the end as a laser that reads and records the sequence of the new strands of DNA. DNA sequencing is very complex and scientists are still working on improving it today. When technology improves in the future, these process may become more efficient, allowing for us to get an even greater understanding of DNA.
ReplyDeleteDNA sequencing, the process of figuring out the order of bases in a gene, is crucial for biomedical research because it allows scientists to easily compare different sets of genes and figure out which types of genes cause certain problems or benefits. One way to figure out the DNA sequence is by first splitting the DNA into smaller pieces so that it is easier to process. Then you need to put the DNA into bacterial DNA so that when the bacteria duplicates, the DNA would duplicate as well, making it harder for the DNA to go missing because there are so many of them. Then you need to heat up the DNA strand so that the complementary strand is completely detached, which allows the DNA polymerase to come in and fit the bases back together. Because the surrounding free bases also includes terminator bases, after some free bases are integrated into the strand, there is a chance that a terminator base will be integrated, meaning that the DNA polymerase will stop. By heating up the area again, the newly created strand of DNA is detached. Repeating this process, there is now many new DNA strands with differing lengths due to the random chance that that a terminator base would be chosen. By using electric attraction, these DNA strands move toward a laser beam. Because of the differing sizes of these DNA strands, the shorter strands move faster and the longer slower, resulting in the shorter strands reaching the laser beam first. The laser beam detects the specific base type of the first terminator base, and longer DNA strands soon follow, which results in the laser beam detecting many terminator bases that is ordered by the length of the DNA strands. For example, the first shortest strand might have the terminator A. The next longer one might have G. Continuing this process, the laser beam results in a ordered DNA sequence of AG....
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