Exploration of 3D conformational space occupied by quadruplex DNA
DNA quadruplex structures are characterized by a high degree of structural diversity. To date, only human telomeric DNA has been extensively studied via NMR and X-ray crystallography. Structural information on quadruplex-prone oncogene promoter sequences alone or in complex with ligands is sparse. The first crystal structure of a quadruplex-ligand complex was determined only recently, in 2003. Since then, ~30 X-ray and ~10 NMR structures have been solved. The small number of reported structures limits existing drug discovery platforms which require detailed knowledge of quadruplex molecular architectures and potential drug binding sites. Driven by this gap in knowledge and inspired by our recent success in solving the structure of Tel22-NMM complex, we are in the process of crystallizing: 1) a variety of oncogene promoter quadruplexes in complex with ligands studied in our laboratory; 2) sequences with high quadruplex forming potential from the genome of D. discoideum. Solving structures of new quadruplexes and their complexes with ligands will provide insights into this important therapeutic target and will facilitate the discovery of new anticancer drugs that act via stabilization of quadruplexes.
Interaction of G-quadruplex DNA with water-soluble porphyrins
Water-soluble porphyrins have been shown to inhibit cancer growth, possibly due to their involvement in the binding, stabilization, and structural alteration of DNA in telomeres and oncogene promoters. Telomeres protect termini of eukaryotic chromosomes from degradation and fusion. Telomeres and the enzyme telomerase that is responsible for their maintenance play an important role in maintaining genomic stability and cell mortality, as evidenced by the 2009 Nobel Prize in Medicine. Porphyrins have the necessary pharmacological properties to be successful drugs. Knowledge of the molecular details of quadruplex - porphyrin interactions will be essential for improving the affinity and selectivity of quadruplex ligands as potential anticancer agents. Our efforts are centered on human telomeric DNA repeats, dAGGG(TTAGGG)3, that can fold into a variety of secondary structures, depending on specific buffer conditions and a variety of oncogene promoter sequences. Our favorite porphyrins include N-methylmesoporpyrin IX (NMM), 5,10,15,20-tetrakis(N-methyl-4-pyridyl) porphyrin (H2T4) and its metal derivatives, CuT4, ZnT4, and PtT4.
Cationic Porphyrins in Chirality Sensing
Porphyrins modified with lanthanides serve as nondestructive reporters for different DNA sequences and in chirality sensing of various biological substrates. Traditionally, these probes suffer from low solubility, poor resolution, weak binding and low selectivity. In response to these limitations, our lab has modified H2T4 and its neutral analogue with various Gd, Eu, and Yb β-diketonates. These complexes are currently being characterized by CD and NMR spectroscopy for binding to chiral amino acids, amino alcohols, and natural products. In the future, the molecular basis for chiral sensing will be investigated by NMR and X-ray. The results of structural and spectroscopic studies will guide the development of chiral sensors with improved sensitivity toward specific biological substrates.
Prof. John Trent (University of Louisville), Deondre Jordan '19,
Prof. Brad Chaires (University of Louisville), and Barrett Powell '18 at
the International Meeting on Quadruplex Nucleic Acids in Prague, June 2017
Joint group meeting with Dr. Eric Brown (far left) from the University of Pennsylvania
Deondre Jordan '19 and Amber Sheth '18 (center) with Dr. Amanda Reig
and student Brian Van Dyke from Ursinus College, visiting Swarthmore to learn
about and use our circular dichroism spectrometer
Thao Tran (IECB, Bordeaux), F. Brad Johnson (UPenn Med School)
Jack Nicoludis '12 and Liliya Yatsunyk at the Third International Meeting on
G-quadruplex DNA and G-assembly in Italy, Sorrento, July 2011
I have established productive collaborations with US and international scientists. I have spent the 2010-11 and 2014-15 academic years on sabbatical in the laboratory of Dr. Jean-Louis Mergny, at the European Institute of Chemistry and Biology (IECB) in France, where I and five of my students learned new biophysical, biological, and structural techniques for characterization of GQs and GQ-based higher order assemblies. I and one of my students, Jack Nicoludis, spent few weeks in the laboratory of Dr. J. Brad Chaires learning ITC and DSC calorimetric techniques. Locally, I have established collaborations with Dr. Veronika Szalai from NIST, with biologists Dr. F. Brad Johnson and Dr. Eric Brown from the University of Pennsylvania and Dr. Brett Kaufman from the University of Pittsburgh, Dr. Sharon Burgmayer from Bryn Mawr, and Dr. Mahrukh Azam from the Chemistry Department of West Chester University. Our other collaborators include Dr. Piotr Habdas from Saint Joseph's University, PA and a group of Dr. Roberto Purello from the University of Catania in Italy.
Most research is our laboratory is done by Swarthmore undergraduates. Students with interest in cancer research, especially those who want to pursue graduate studies or go to medical schools, are highly encouraged to apply. Based on background and interests, students will pursue independent projects or be teamed with senior students in the lab. Contact Professor Yatsunyk via e-mail or stop by our lab and talk to students about their experience.
- Camille and Henry Dreyfus Teacher-Scholar Award, Deciphering the structure and dynamics of quadruplex DNA and DNA-ligand complexes, 2016-2020
- Pennsylvania Department of Health, Formula Health Grant Understanding interactions between porphyrin ligands and G-quadruplex DNA. 01/15 - 12/17
- NSF MRI Acquisition of 400-MHz NMR Spectrometer, 08/13 - 07/16, Co-PI
- Swarthmore College Faculty Research Award Interaction of porphyrin ligands with G-quadruplex DNA. 12/07- 06/16
- Initiative d’Excellence de l’Université de Bordeaux (IdEx Bordeaux) Visiting professor Program. 03/15 - 05/15
- Université de Bordeaux Professeur invite Invited Professor Program. 09/14 - 10/14
- HHMI-supported summer research fellowship for Scott Taylor (summer 2008) and Erica Evans (summer 2009), Karan Ahluwalia (2010), Steven Barret (2011), Vienna Tran (2012), Navin Sabharwal (2013), Katherine Bredder (off campus HHMI 2013), Kara Bledsoe (2014)
- Summer Undergraduate Research Fellowship for David Kornfilt for 2008 and for Michelle Ferreira for 2013
- Dreyfus Foundation summer stipends for Jack Nicoludis (summer 2011) and Cole Harbeck (summer 2012)
- Research Corporation summer stipends for Jack Nicoludis (summer 2009 and 2010), Steven Barrett (summer 2010), and Amlan Bhattacharjee (summer 2009)
- Starfield Summer Research Fellowship for Navin Sabharwal (summer 2012)