Milton Academy's Science Journal Winter 2020
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The Mechanism of Evidence of a Ninth Good Will Hunting Stress pp. 6 & 7 Planet? pp. 14 & 15 Math pp. 16 &17 MiltonHelix Academy’s Science Journal Winter 2020 Page 1 Contents No More DSBs? How Base Editing Takes CRISPR to a New Level 3, 4, & 5 by Anna Yang The Stress Mechanism 6 & 7 by Miriam Zuo Bayes’ Theorem 8 & 9 by Nikhil Pande Photography 10 & 11 Quantum Dots: Tiny Crystals Brightening Today’s Technologies 12 & 13 by Wilder Crosier A Ninth Planet in our Solar System!? 14 & 15 by Luca Mostofi Solving the Good Will Hunting Problem 16, 17, & 18 by Madeleine Cesaretti Rising Through the Thrilling Haze (Poem) 19 by Anna Yang Helix Editorial Board 2019-2020 Co-heads Miriam Zuo Kiran Biddinger Wilder Crosier Senior Editors Zaki Alaoui Nikhil Pande Maya Geyling Faculty Advisor Mr. Sando Special Thanks to. Mr. Edgar, Dr. Richards, Mr. Reilly, Ms. Pedersen, Mr. Kernohan, and Ms. Lockwood Page 2 No More DSBs? vides a gene editing technique called base editing that di- How Base Editing Takes CRISPR to a New Level rectly and irreversibly con- by Anna Yang ‘23 verts a base pair into anoth- Gene editing is a process of initiate one of two responses, er, increasing the accuracy modifying DNA to correct non-homologous end joining and efficiency of HDR while or induce mutations. It has (NHEJ), or homology direct- suppressing indel formation the potential of curing many ed repair (HDR). NHEJ is from NHEJ. They synthe- genetic diseases such as Sick- initiated when a homologous sized an enzyme capable of le-cell anemia, color blind- strand is absent. Random in- in situ converting a C into a ness, Tay-Sachs disease, and sertions and deletions (in- U, which has the same base some types of cancer. These dels) were formed in the locus pairing property of a T. By in- diseases are caused by point where the sugar-phosphate activating the protein Cas-9 mutations, which are muta- backbone was broken by the (dCas-9) through Asp10Ala tions in the DNA sequence Cas-9 protein, disrupting or and His840Ala mutations (2), that involves a change in a sin- inactivating the gene. The cell the enzyme loses the ability to gle base pair. Consequently, uses the mechanism of HDR induce DSBs, but retains its point mutations may alter the when a homologous strand is DNA binding ability in con- amino acid sequence of the present, which uses an intact junction with a guide RNA translated polypeptides and homologous strand as a tem- that locates the target gene. impact its functioning. Cur- plate to complete the missing Then, dCas-9 is linked to a rently, the existing genom- bases. Although CRISPR is the cytidine deaminase, which ic editing technologies, such most widespread genome ed- directly converts the C into a as the CRISPR-Cas9 system, iting technique available, this U by atomic rearrangement edit the DNA base sequence method may lack in efficiency of the nucleotide. Under the through an engineered nu- and specificity. When NHEJ tested conditions, the enzyme clease. CRISPR, for exam- and HDR compete for DSB rat APOBEC1 shows the most ple, was originally a defense repair, indel formation always promising deamination ac- mechanism used by bacteria occur to some extent (1). This tivity compared to other cyt- against foreign pathogens, leads to gene disruption or in- idine deaminase enzymes (3). but was engineered in recent activation. To prevent the ran- years for targeted gene edit- dom insertion and deletion The G:U discrepancy in the ing. The enzyme Cas-9 acts as of nucleotides in response to target locus can be perma- a nuclease, and was associated a DSB, the target base must nently converted to the A:T Maya Geyling with a guide RNA that locates be directly converted with- pairing through the innate cel- the target sequence. Nucleas- out cleavage of the DNA lular function of DNA repair es such as Cas-9 induce dou- strand. This goal was achieved and replication. DNA repair ble-stranded breaks (DSB) by the recently developed is a process where a protein in the sugar-phosphate back- technology of base editing. complex recognizes a mis- bone of DNA as the first step match in base pairing, which to correcting mutations. DSBs A study by Komor et al. pro- is then corrected by a poly- Page 3 merase enzyme and sealed by gy has a significantly higher of successful C:G→A:T repair, DNA ligase. The maximum efficiency than Cas-9 medi- showing the highest efficiency efficiency of this method is ated HDR (see Fig.1b), with with the BE3 base editor (3). 50% yield of conversions (3), substantially fewer indels. By avoiding double-stranded and this suboptimal efficien- Fig.1: a) BE3 redirects the pref- breakages, base editing im- cy was a result of the cellular ered repair mechanism of cel- proved in efficiency and -re response of eukaryotic mis- match repair (MMR), which tends to repair the newly synthesized strand by recog- nizing its nicks before being sealed by DNA ligase (4). To prevent the MMR process from converting the edited U back to a C, the enzyme BE3 (5) was introduced to nick the unedited strand to simulate the newly synthesized strand for a higher probability of MMR repair (see Fig.1a). By inducing nicks, BE3 is used to manipulate MMR to target the original strand, thereby completing the substitution. With MMR favoring the un- edited G, the C:G point mu- tation could be corrected to A:U. The A:U base pair is then permanently converted to A:T, the desired outcome, through DNA repair and rep- lication. This method of nick- ing the target strand produces the base editor protein com- Fig.1: a) BE3 redirects the prefered repair mechanism of cellular base-excision repair plex (BE3, APOBEC–XTEN– by nicking the target strand, resulting in the desired outcome of base editing. b) Percentages of successful C:G→A:T repair, showing the highest efficiency with the BE3 dCas9(A840H)–UGI), base editor (3). augmenting the efficiency six- lular base-excision repair by duced indel formation rate in fold, while resulting in a mere nicking the target strand, re- the repair of point mutations. 1.1% average indel formation sulting in the desired outcome It has the potential to be uti- rate (6). Results confirm that of base editing. b) Percentages lized in a clinical setting to this base editing technolo- Page 4 cure genetic diseases caused affinity for oxygen. If an in- discoveries are in progress in by a single point mutation of dividual contains both copies the field of genetic engineer- A:T→C:G. Many inherited of the mutated gene, sickle ing. One recent breakthrough diseases resulting from a sin- cell disease occurs, with many is prime editing (7), which gle T→C point mutation ex- medical implications on the takes the concept of base ed- perienced advancement due organismal level. Base editing iting (the direct conversion to base editing. For example, already shows a significant of nucleotides without dou- sickle cell anemia was caused advancement in the treat- ble-stranded cleavage) and by a point mutation in the he- ment of sickle cell anemia and develops a safer and more ef- moglobin gene substituting a many similar diseases, by cor- ficient alternative. The poten- glutamic acid with valine in recting the underlying point tial of gene editing techniques the beta-globin polypeptide. mutation. This technology of such as base editing are end- Effects on the protein level are base editing was one of the less in the scientific and hemoglobin molecules that many newly developed meth- medical fields. What do you form clumps; this leads to de- ods of direct base editing that think the next step would be? formed red blood cells with a took the CRISPR technology sickle shape, and a decreased to a new level. Many more Sources Cited (1) Zaboikin, Michail, et al. “Non-Homologous End Precision Chemistry on the Genome and Transcriptome Joining and Homology Directed DNA Repair Frequen- of Living Cells.” Nature Reviews Genetics, vol. 19, no. cy of Double-Stranded Breaks Introduced by Genome 12, 2018, pp. 770–788., doi:10.1038/s41576-018-0059-1. Editing Reagents.” Plos One, vol. 12, no. 1, 2017, doi:10.1371/journal.pone.0169931. (7) Anzalone, Andrew V., et al. “Search-and-Replace Genome Editing without Double-Strand Breaks or (2) Komor, Alexis C., et al, “Improved Base Excision Donor DNA.” Nature, vol. 576, no. 7785, 2019, pp. Repair Inhibition and Bacteriophage Mu Gam Protein 149–157., doi:10.1038/s41586-019-1711-4. Yields C:G-to-T:A Base Editors with Higher Efficiency and Product Purity.” Science Advances, vol. 3, no. 8, (8) Ranzau, Brodie L., and Alexis C. Komor. “Genome, 2017, doi:10.1126/sciadv.aao4774. Epigenome, and Transcriptome Editing via Chemical Modification of Nucleobases in Living Cells.” Biochem- (3) Komor, Alexis C., et al., “Programmable Editing of a istry, vol. 58, no. 5, 2018, pp. 330–335., doi:10.1021/acs. Target Base in Genomic DNA without Double-Strand- biochem.8b00958. ed DNA Cleavage.” Nature, vol. 533, no. 7603, 2016, pp. 420–424., doi:10.1038/nature17946. (9) Cohen, Jon. “‘Base Editors’ Open New Way to Fix Mutations.” Science, vol. 358, no. 6362, 2017, pp. (4) Modrich, Paul. “Mechanisms in Eukaryotic Mis- 432–433., doi:10.1126/science.358.6362.432. match Repair.” Journal of Biological Chemistry, vol. 281, no. 41, 2006, pp. 30305–30309., doi:10.1074/jbc. (10) Pankaj, Radhika, and Yoshihisa Matsumoto. r600022200. “DNA Double-Strand Break Repair Through Non-Ho- mologous End-Joining: Recruitment and Assembly of (5) Eid, Ayman, et al.