BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: DNA Replication

CRISPR Quits Coronavirus Replication

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On March 22, 2022

In Student Post

The gene-editing CRISPR has now been utilized by scientists to prevent the replication of Coronavirus in human cells, which can ultimately become a new treatment for the contagious virus. However, since these studies were performed on lab dishes, this treatment can be years away from now.

Firstly, CRISPR is a genome-editing tool that is faster, cheaper, and more accurate than past DNA editing techniques whilst having a much broader range of use. The system works by using two molecules: Cas9 and guide RNA (gRNA). Cas9 is an enzyme that acts as “molecular scissors” that cuts two strands of DNA at a specific location. gRNA binds to DNA and guides Cas9 to the right location of the genome and ultimately makes sure that Cas9 cuts at the right point.

 

CRISPR'S Cas9 enzyme in action

CRISPR’S Cas9 enzyme in action

In this instance, CRISPR is used to allow the microbes to target and destroy the genetic material of viruses. However, they target and destroy the RNA rather than the DNA. The specific enzyme they use for this is Cas13b, which cleaves the single strands of RNA, similar to those that are seen in SARS-CoV-2. Once the enzyme Cas13b binds to the RNA, it destroys the part of the RNA that the virus needs to replicate. This method has been found to even work on new mutations of the SARS-CoV-2 genome, including the alpha variant.

COVID-19 vaccines are being distributed around the world, but an effective and immediate treatment for the virus is necessary. There are many fears that the virus will be able to escape the vaccines and become a bigger threat. Although this treatment is a step in the right direction for effective treatment of COVID-19, this technique will ultimately take a long time for the treatment to be publicly available.

CRISPR is greatly relevant to AP Bio, as seen through its use of enzymes in DNA replication. CRISPR utilizes Cas9, an enzyme that is similar to helicase. In DNA replication, the helicase untwists the DNA at the replication fork, which after the DNA strands are replicated in both directions. 

This article is fairly outdated since there have now been immediate treatments created for COVID-19. But, what do you think about the use of CRISPR for future viruses and pandemics? Personally, I believe that CRISPR will ultimately become a historical achievement in science due to its various uses. Thank you for reading and let me know what you think in the comments! 

 

Could Christmas Island rats make a comeback? Thanks to CRISPR gene editing, they might!

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On March 20, 2022

In Student Post

From climate change to overhunting by humans, there are many factors which contribute to the extinction of species in the animal kingdom. The Christmas Island rat, also known as Maclear’s rat, went extinct a century ago in what is believed to be the first and only case of extinction of a species due to disease. It has always been believed that once a species goes extinct, it is gone for good. That is until recently when scientists began experimenting with “de-extinction” efforts to bring back the Christmas Island rat.

Little does this rat know that his family reunions may be getting a whole lot bigger!

As published March 9 in the science journal, Current Biology, a team of paleo geneticists from the University of Copenhagen recently conducted a study into gene sequencing the Christmas Island rat, in order to estimate the possibilities of future gene editing experiments which could bring the species “back to life”. The process of genetic editing for de-extinction efforts, as explained by the research team in their abstract, consists of first identifying the genome of the species and then editing the genes of similar species to make it more similar to that of that extinct one. The team used frozen somatic cells of the extinct rats, cells with a 2n number of chromosomes which are made during the process of mitosis. The team was able to sequence the rats’ genome, aside from some small portions which remain missing. They then had to identify the modern species which they could gene edit. Their findings established that the Christmas Island rat shares around 95% of DNA with the modern Norway brown rat. At this point, it

Now that the rat’s genome has been sequenced to the best of the team’s ability and a similar species has been identified, the gene editing possibilities are endless, especially with CRISPR technologies and techniques. “CRISPR” stands for Clustered Regularly Interspaced Short Palindromic Repeats in DNA sequencing. This system was discovered by a group of scientists, led by Dr. Emmanuelle Charpentier. CRISPR uses Cas9, an enzyme which cuts DNA at specified sections as guided by RNA. There are three different types of edits drone with CRISPR technology: disruption, deletion, or correction/insertion. Disruption editing is when the DNA is cut at one point and base pairs are either added or removed to inactivate a gene. Deletion editing is when the DNA is cut at two points and a larger sequence of pairs is removed. Correction/insertion editing is when a new gene is added into a sequence using homology directed repair.

Thomas Gilbert, the lead scientist on the team, says that he would like to conduct CRISPR gene editing experiments on living species of rats before attempting to replicate the DNA of an extinct species. For example, attempting to mutate the DNA of the Norway brown rat into that of the common black rat. Once this experiment is conducted, the possibilities of reviving the Christmas Island rat will be more clear. Until then, we can only hope! Do you think it’s possible to see the Christmas Island rat revived anytime soon?

New research further advances the understanding of DNA repair

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On March 16, 2022

In Student Post

In a study recently published in Nature Cell Biology, there’s been a discovery that alters our understanding of how the body’s DNA repair process works and may lead to new chemotherapy treatments for cancer and other disorders. Because DNA is the repository of genetic information in each living cell, its integrity and stability are essential to life. DNA, however, is not inert. Rather, it is a chemical entity subject to abuse from the environment and any resulting damage, if not repaired, will lead to mutation and possibly disease.

File:DNA polymerase.png

DNA Polymerase

The fact that DNA can be repaired after it has been damaged is one of the great mysteries of medical science, but pathways involved in the repair process vary during different stages of the cell life cycle. In one of the repair pathways known as base excision repair (BER), the damaged material is removed, and a combination of proteins and enzymes work together to create DNA to fill in and then seal the gaps. In addition to genetic insults caused by the environment, the very process of DNA replication during cell division is prone to error. The rate at which DNA polymerase adds incorrect nucleotides during DNA replication is a major factor in determining the spontaneous mutation rate in an organism.

Researchers discovered that BER has a built-in mechanism to increase its effectiveness, it just needs to be captured at a very precise point in the cell life cycle. In BER, an enzyme called polymerase beta (PolyB) fulfills two functions: It creates DNA, and it initiates a reaction to clean up the leftover chemical waste. Through five years of study, scientists learned that by capturing PolyB when it is naturally cross-linked with DNA, the enzyme will create new genetic material at a speed 17 times faster than when the two are not cross-linked. This suggests that the two functions of PolyB are interlocked, not independent, during BER.

Cancer cells replicate at high speed, and their DNA endures a lot of damage. When a doctor uses certain drugs to attack cancer cells’ DNA, the cancer cells must cope with additional DNA damage. If the cancer cells cannot rapidly fix DNA damage, they will die. Otherwise, the cancer cells survive, and drug resistance appears. This research examined naturally cross-linked PolyB and DNA, unlike previous research that mimicked the process. Prior to this study, researchers had identified the enzymes involved in BER but didn’t fully understand how they work together. This research improves the understanding of cellular genomic stability, drug efficacy, and resistance associated with chemotherapy, which, as previously stated, can lead to new chemotherapy treatments for cancer and other disorders.

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