Interaction of G-quadruplex DNA with Water-soluble Porphyrins

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 telomeres. 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.

G-rich telomeric sequences can fold into non-canonical four-stranded DNA structures called G-quadruplexes. They require K+ or Na+ for stability, but are stabilized even further by particular ligands, like porphyrins. Porphyrins have the necessary pharmacological properties to be successful drugs. Knowledge of the molecular details of G-quadruplex - porphyrin interactions will be essential for improving the affinity and selectivity of G-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. 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.


Thao Tran, F. Brad Johnson, Jack Nicoludis, and Liliya Yatsunyk

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

We are collaborating with the laboratory of Jean-Louis Mergny, European Institute of Chemistry and Biology in Bordeaux, where our group will spend summer 2013. We are collaborating with the laboratory of Dr. F. Brad Johnson from the University of Pennsylvania School of Medicine on GQ-based telomere capping in Saccharomyces cerevisiae. My lab is carrying out biophysical characterization of yeast telomeric DNA fragments and their interactions with Stm1, a yeast GQ binding protein, and RQC, a DNA binding domain of a RecQ Helicase.

In addition, we are working with the laboratory of Dr. Mahrukh Azam from the Chemistry Department of West Chester University on characterizing interactions between (dT4G4)4 and (dT4G4T)4 and various cationic porphyrins. The goal of this work is to obtain a clear differentiation between various modes of porphyrin binding to GQ DNA. Our other collaborators include Dr. Piotr Habdas from Saint Joseph's University, PA and a group of Roberto Purello from the University of Catania in Italy. We continue collaboration with Sharon Burgmayer from Bryn Mawr who supplies us with octahedral ruthenium complexes. We just started a collaboration with Brett Kaufman from the University of Pennsylvania School of Medicine on mitochondrial DNA with quadruplex forming potential. We are looking forward to exciting results.

Undergraduate research

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.


  • Hangerford grant to attend Third International Meeting on G-quadruplex and G-assembly in Sorrento, Italy (June28 - July 1 2011, $1160); for a visit to Dr. B. Chaires lab at Brown Cancer Center, University of Louisville (January 2010, $600); to cover publication of research publication in an open-access journal, Nucleic Acids research (January 2011, $1,665).
  • Mellon Seed Grant in support of a Scholarly Community of Tri-College Faculty and Students Investigating Bioinorganic Chemistry for 2009/2010 ($1500), 2010/2011 ($1500), and 2011/2012 ($2300).
  • Research Corporation Cottrell College Science Award for 2008-2009
  • Camille and Henry Dreyfus Foundation Faculty Start-up Award for 2007-2011
    Swarthmore Start-up Fund
  • Swarthmore College Research Grant for 2007-2009 and 2009-2011.

Student Funding

  • 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)
  • 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)