{"id":20168,"date":"2025-07-01T08:30:53","date_gmt":"2025-07-01T12:30:53","guid":{"rendered":"https:\/\/news.etown.edu\/?p=20168"},"modified":"2025-06-23T10:03:00","modified_gmt":"2025-06-23T14:03:00","slug":"elizabethtown-college-scarp-series-preparation-of-novel-peptide-nucleic-acid-nucleobases-aimed-at-improving-pna-rna2-triplex-stability-for-rna-containing-pyrimidine-interruptions","status":"publish","type":"post","link":"https:\/\/news.etown.edu\/index.php\/2025\/07\/01\/elizabethtown-college-scarp-series-preparation-of-novel-peptide-nucleic-acid-nucleobases-aimed-at-improving-pna-rna2-triplex-stability-for-rna-containing-pyrimidine-interruptions\/","title":{"rendered":"Elizabethtown College SCARP Series: Preparation of triazole containing peptide nucleic acid nucleobases aimed at improving PNA-RNA2 triplex stability in double helical RNA"},"content":{"rendered":"

Chemistry majors Isabell Anderson \u201926 and Arianna Lepratto \u201928, along with Biochemistry and Molecular Biology major Jaqueline Hammond \u201928, are working to develop new synthetic tools that could improve how scientists target RNA-an essential molecule in the body\u2019s biology and disease processes as part of Elizabethtown College\u2019s <\/span>Summer Creative Arts and Research Program (SCARP)<\/span><\/a>.\u00a0<\/span><\/p>\n

Their study builds on a collaborative research project that dates back to the fall of 2015 between A. C. Baugher Professor of Chemistry Dr. James MacKay and Binghamton University professor Eriks Rozners, with Elizabethtown College’s focus primarily being on the synthesis of new molecules. The group of Blue Jays is working on synthesizing never-before-made molecular structures and improving synthetic methods, which could one day support the study of diseases and the discovery of new biological functions of RNA.<\/span> This research is a continuation of <\/span>previous SCARP research<\/span><\/a>.<\/span><\/p>\n

Title of Research<\/strong>
\n<\/b>\"\"Preparation of triazole containing peptide nucleic acid nucleobases aimed at improving PNA-RNA2<\/sub> triplex stability in double helical RNA<\/p>\n

Student Researchers<\/strong>
\n<\/b>Isabell Anderson \u201926 and Arianna Lepratto \u201928 (Chemistry)
\n<\/span>Jacqueline Hammond \u201928 (Biochemistry and Molecular Biology)<\/span><\/p>\n

Faculty Mentor<\/strong>
\n<\/b>Dr. James MacKay, A. C. Baugher Professor of Chemistry<\/span><\/p>\n

What are you researching?<\/strong><\/p>\n

Anderson:<\/strong> The ultimate goal of this research is to use a peptide nucleic acid (PNA) strand to form a triple helix with double-stranded, non-coding RNA, therefore recognizing the RNA. This triple helix is formed by way of Hoogsteen hydrogen bonds to the nucleobases on RNA. So far, recognition of RNA strands that have purine nucleobases has been successful. However, there have been difficulties when recognizing strands with a lot of pyrimidine nucleobases because they only form one hydrogen bond. My project centers around improving the recognition of pyrimidines by placing a purine-recognizing nucleobase with a triazole ring next to a pyrimidine-recognizing nucleobase on the PNA strand to enhance pi-stacking interactions and increase the stability of the triplex.<\/p>\n

Lepratto:<\/strong> My particular side of the project is in optimizing a reaction called an azide-alkyne cycloaddition, which forms the desired 1,2,3-triazoles mentioned in the title of the project. I am supposed to repeat the reaction many times and find the perfect conditions to maximize efficiency.<\/span><\/p>\n

Hammond:<\/strong> Arianna and I have been working on two different parts of making the acid-cleavable protecting group for 1,2,3-triazoles. My part has been focused on creating an alcohol through a Grignard reaction, and then converting that alcohol into a chloride, so the protecting group can be incorporated into the triazole yet be more easily removed after the PNA synthesis.<\/span><\/p>\n

Why did you choose this topic?<\/strong><\/p>\n

Anderson:<\/strong> I chose to do research in organic chemistry because I find this sub-discipline of chemistry the most interesting, and I really enjoy doing benchwork.<\/span><\/p>\n

Lepratto:<\/strong> I didn’t actually choose this topic; I was offered the position by Dr. MacKay, my mentor. I have expressed interest in organic chemistry research since my first month of school, and he has allowed me to join his research group and its meetings to learn what goes into the work. Once he got the opportunity to mentor a first-year student for this project, he reached out to me right away. I am very grateful for this opportunity.<\/span><\/p>\n

Hammond:<\/strong> Dr. MacKay contacted me regarding this research position, and I thought it would be a good opportunity to get accustomed to working in a research lab. I also thought the premise of helping create molecules that can deepen our understanding of the role of RNA in our bodies was interesting as well.<\/span><\/p>\n

What is the most interesting aspect of this research?<\/strong><\/p>\n

Anderson:<\/strong> The most interesting aspect of this research is that I’m getting to make new molecules that have never been made before.<\/span><\/p>\n

Lepratto:<\/strong> I am learning so much about chemistry, and just the hands-on lab work captures my awe and attention. Seeing what really goes into chemistry research in general is the best part of this project, as this is my dream career.<\/span><\/p>\n

Hammond:<\/strong> Dr. MacKay contacted me regarding this research position, and I thought it would be a good opportunity to get accustomed to working in a research lab. I also thought the premise of helping create molecules that can deepen our understanding of the role of RNA in our bodies was interesting as well.<\/span><\/p>\n

What are you hoping to accomplish through this research project?<\/strong><\/p>\n

Anderson:<\/strong> My big goal is to finish making the final nucleobase because I’ve been working on this since last summer, so it would be really great to be able to see if the nucleobase works in the way we intended it to. In general, I am just hoping to continue building my research skills and become a better researcher.<\/span><\/p>\n

Lepratto:<\/strong> Besides success in the project itself, I hope to gain valuable experience and knowledge on what will eventually be the career I dedicate my life to.<\/span><\/p>\n

Hammond:<\/strong> I hope to get a better understanding of how research is conducted in a lab environment and how to more effectively communicate with my peers, as I hope to one day have a career in research.<\/span><\/p>\n

Talk about working with your mentor. How have they helped you throughout this experience?<\/strong><\/p>\n

Anderson:<\/strong> Dr. Mackay has helped in this experience by being willing to answer any questions that I have, while also giving me the space to figure it out on my own if he knows that I can. He is also working directly beside us sometimes, so it is helpful to have him in the lab and see firsthand how he conducts research as well.<\/span><\/p>\n

Lepratto:<\/strong> Working with Dr. MacKay is great. Since I am only a first year, I haven’t been introduced to many of the reactions, mechanisms, vocabulary, and equipment, as I’ve only taken up to Ochem 1. Dr. MacKay has made working on this project very approachable and I have learned so much from him and his guidance, he is very patient with us and willing to answer any of our questions, and I already feel myself becoming more confident and independent when it comes to this type of work, and it’s only been a week!<\/span><\/p>\n

Hammond:<\/strong> My mentor, Dr. MacKay, has been very helpful in teaching me how to use instrumentation, communicate, set up reactions, and make me feel more confident in my abilities in the lab.<\/span><\/p>\n

Hear from the faculty mentor \u2013 Dr. James MacKay<\/strong><\/p>\n

\u201cI\u2019ve been doing SCARP for years because research is what makes science exciting. Probably <\/span>the most important goal and\/or outcome is simply that undergraduates are trained in the art of organic synthesis.<\/span><\/i> This is both what drives my research program but also my teaching. In the end, their presentation at a regional conference (Landmark) will set the stage for future opportunities where they will present their work on a broader stage. Given the goal of continued NSF support, we expect to publish and present at international conferences as we make more discoveries that relate to the fields of organic chemistry, biochemistry, RNA biology, etc. However, the timeline for publication is often quite slow, often 3 or more years from completion of the SCARP summer project.\u201d<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"

Chemistry majors Isabell Anderson \u201926 and Arianna Lepratto \u201928, along with Biochemistry and Molecular Biology major Jaqueline Hammond \u201928, are working to develop new synthetic tools that could improve how scientists target RNA-an essential molecule in the body\u2019s biology and disease processes as part of Elizabethtown College\u2019s Summer Creative Arts and Research Program (SCARP).\u00a0 Their […]<\/p>\n","protected":false},"author":157,"featured_media":20170,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_et_pb_use_builder":"","_et_pb_old_content":"","_et_gb_content_width":"","footnotes":""},"categories":[1338],"tags":[1123,1408,197,1350,195],"class_list":["post-20168","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-academics-and-research","tag-chemistry","tag-elizabethtown","tag-elizabethtown-college","tag-etown","tag-scarp","et-has-post-format-content","et_post_format-et-post-format-standard"],"_links":{"self":[{"href":"https:\/\/news.etown.edu\/index.php\/wp-json\/wp\/v2\/posts\/20168","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/news.etown.edu\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/news.etown.edu\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/news.etown.edu\/index.php\/wp-json\/wp\/v2\/users\/157"}],"replies":[{"embeddable":true,"href":"https:\/\/news.etown.edu\/index.php\/wp-json\/wp\/v2\/comments?post=20168"}],"version-history":[{"count":6,"href":"https:\/\/news.etown.edu\/index.php\/wp-json\/wp\/v2\/posts\/20168\/revisions"}],"predecessor-version":[{"id":20190,"href":"https:\/\/news.etown.edu\/index.php\/wp-json\/wp\/v2\/posts\/20168\/revisions\/20190"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/news.etown.edu\/index.php\/wp-json\/wp\/v2\/media\/20170"}],"wp:attachment":[{"href":"https:\/\/news.etown.edu\/index.php\/wp-json\/wp\/v2\/media?parent=20168"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/news.etown.edu\/index.php\/wp-json\/wp\/v2\/categories?post=20168"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/news.etown.edu\/index.php\/wp-json\/wp\/v2\/tags?post=20168"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}