Dear summer, it’s been fun…

CurChem is delighted to welcome Dr. Liliya Yatsunyk back to our front page for her second and final installment. In this piece, Liliya reflects on the summer research season. The summer has flown by, but there is much to celebrate and look forward to!


Dear summer, where are you?

“…ten weeks of intense and highly focused research have passed … with lightning speed.”

It is time to write the second (and final) blog about my lab’s summer research. It means that ten weeks of intense and highly focused research have passed … with lightning speed. The students worked frantically during the past two weeks, knowing well that their uninterrupted research time is over and soon it will be shared with classes, student clubs, sports, field trips, and other activities which populate student lives. The same is true for me, and I will greatly miss this summer time. But we are not at the end of our research journey, quite the opposite, the lab has made huge progress toward establishing X-ray crystallography as our principal structural method for studying unusual DNA structures and atomic details of their interactions with small molecule ligands. In this respect, our journey has just begun.

“…we are not at the end of our research journey”

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Our lab on the way to pizza after lab cleaning – Linda, Allan, Barrett, Liliya, Samantha, and Deondre

Our accomplishments

Writing this blog makes me reflect on all the things we planned to do during this summer. While the progress on some projects was slow and others did not get done at all, I would like to start with the list our major accomplishments.

First and foremost, as we hoped, we succeeded in hiring an amazing research assistant, Samantha Nyovanie. She is a recent graduate of Amherst College, an excellent chemist, and a wonderful person. She started on July 15th and by now has fully integrated into the lab and has been trained in all techniques vital to our research.

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Our new Research Assistant Samantha Nyovanie working on her project

Another important accomplishment is submitting the paper. Well, we did not submit the paper, it was our collaborators, Prof Eric Brown and his postdoctoral researcher, Nishita Shastri, from the University of Pennsylvania, who submitted the paper. We have collaborated on this work for three years, the paper has been in writing for about two years (and at the time it felt like it will never be submitted), but finally the button was pressed about two weeks ago and the paper was sent to Molecular Cell. The work focuses on tandem DNA sequences which cause replication stress and subsequent cancer mutations. We have completed all the biophysical work for the project, and my student Deondre Jordan spent a good portion of the summer finalizing and repeating some of the key data. Deondre Jordan, Barrett Powell and Jessica Chen (who graduated this year and is currently a Research Assistant at a University of Pennsylvania neuroscience laboratory) are all coauthors on this work. All of us were delighted when the paper was finally sent out. We hope that the reviewers will like our work as much as we do and that their comments will be fair and helpful.

We hope that the reviewers will like our work as much as we do and that their comments will be fair and helpful.

Now, the crystals. In the first blog I reported that Linda got beautiful pink crystals and Barrett was not that far from solving his structure. Both students were working on solving the phase problem by growing crystals with heavy atom derivatives or soaked with heavy atoms salts. By the end of the summer, both Barrett and Linda were able to grow brominated derivatives of their DNA as well as soaked their crystals in Ba(II) and Co(III). Both perfected their skills of freezing the crystals and learned a lot about data collection and processing. We sent our crystals to the APS synchrotron in Chicago and collected a variety of high resolution data. In addition, Allan has started on crystallization project (abandoning his NMM dimerization work) and after thorough screening and brief optimization obtained beautiful crystals of c-myc oncogene promoter DNA alone and in complex with small molecule ligands. His crystals are not pink but just as beautiful in their simplicity and colors created by polarized light.

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Allan’s new and beautiful crystals of c-myc oncogene promoter DNA

 

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Linda’s crystals. The first one is of brominated DNA. Believe it or not, but it did diffract to 3.2 A.

Deondre and Samantha have started on their crystallization adventures, although they are still waiting for crystals to grow. Officially, everybody in my lab has their own big crystallization project, and while collectively and recently, we did not yet solve a crystal structure, our hopes are high and our prospects are good. What I have learned from my postdoctoral experience is that if one poses a good scientific question, works very hard toward its solution, s/he eventually will reach the goal. All that is needed is to be patient and keep up the hard work.

“…if one poses good scientific question, works very hard toward its solution, s/he eventually will reach the goal.”

Lastly, the department has acquired two new instruments vital to our research. The Isothermal Titration Calorimeter will arrive in September and a Crystallization robot will arrive sometimes soon with our new biochemist, Daniela Ferra. Currently we are using a robot at Penn but a demo instrument has been installed at Swarthmore two weeks ago and my students are already trained to use it without supervision. No crystal yet from this new machine, but we have set many trays.

Things that did not work

While my students made impressive progress on X-ray crystallography, a few projects in the lab did not get done, either because of the mere nature of research, inefficient use of our time, or poor decisions. You live and you learn and, as I said in my previous blog – undergraduate researchers are the best people when it comes to failing. They are optimistic and as ready to restart the experiment as they are to do it for the first time.

We learned that growing crystals of DNA is not hard; growing good crystals is a challenge which we did not meet yet.

This summer we got many crystals, but some of them diffracted to 3.0 A others to 8.0, and yet others did not diffract at all. The phase problem remains an unsolved challenge. We learned that growing crystals of DNA is not hard; growing good crystals is a challenge which we did not meet yet.

I made a big progress on our main lab writing project – the paper describing the structure of tandem repeat DNA implicated in replication stress – the work which will follow the paper, submitted by Prof Eric Brown. My hope was to get this paper to the stage close to submission, and that did not happen.

“…a few projects did not get done either because of the mere nature of research, inefficient use of our time, or poor decisions.”

Allan’s project on the oligomerization of NMM, our favorite lab ligand, did not move pass the point it was at the beginning of the summer – Allan and I got carried away by the beautiful crystals of his oncogene promoter DNA. And needless to say that the paper on this project was not even started.

Linda’s beautiful crystals diffracted to 3.0 A at the beginning of our summer. They still diffract to that resolution, the space group is unclear, and anomalous signal from Bromine is too weak.

Looking into the future

The summer research semester has ended with Allan and Linda writing final papers on their projects; Deondre and Barrett wrote a chapter each for their theses. Barrett will be a senior this fall and his thesis is shaping up nicely. We cleaned the lab and according to the lab tradition, had pizza right after.

It is sad that the summer is over, and that the research will return to its secondary place as compared to teaching and taking classes.

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Barrett making meat crepes during our end-of-the summer lab dinner

We all cooked for our last lab dinner – we made lasagna, famous Sam’s chicken, crepes with pork, and carrots stuffed with muffins (well, they were supposed to be muffins stuffed with carrots but we added too many carrots). We reorganized the lab to accommodate more people and ordered consumables and DNA we need for the start of the semester. Barrett and Deondre, prepared and practiced their talks for the National American Chemical Society meeting which will take place in DC on August 20-24. Linda and Allan started on their posters for the same meeting. Sam is fully trained and mostly independent. It is time for a break for some and more lab work for others (Deondre and Allan are staying on and will be working for hourly pay using my NIH money). I need to prepare a new seminar course on assembly of DNA-based nanomaterials and nanomachines. It is sad that the summer is over, and that the research will return to its secondary place as compared to teaching and taking classes. But Sam will be working in the lab full time and force; I will have five research students for the semester (Irene, my other student, is coming back from the summer of investment banking on Wall street); I am looking forward to meeting my new freshmen students in the Honors General Chemistry course, and all of us are looking forward to coming back to our loved projects and an excitement of new research discovery.

 

 

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