Probing the Competition between Duplex, G-Quadruplex and i-Motif Structures of the Oncogenic c-Myc DNA Promoter Region. 2023

Akanksha Pandey, and Sarupa Roy, and Seergazhi G Srivatsan
Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India.

Development of probe systems that provide unique spectral signatures for duplex, G-quadruplex (GQ) and i-motif (iM) structures is very important to understand the relative propensity of a G-rich-C-rich promoter region to form these structures. Here, we devise a platform using a combination of two environment-sensitive nucleoside analogs namely, 5-fluorobenzofuran-modified 2'-deoxyuridine (FBF-dU) and 5-fluoro-2'-deoxyuridine (F-dU) to study the structures adopted by a promoter region of the c-Myc oncogene. FBF-dU serves as a dual-purpose probe containing a fluorescent and 19 F NMR label. When incorporated into the C-rich sequence, it reports the formation of different iMs via changes in its fluorescence properties and 19 F signal. F-dU incorporated into the G-rich ON reports the formation of a GQ structure whose 19 F signal is clearly different from the signals obtained for iMs. Rewardingly, the labeled ONs when mixed with respective complementary strands allows us to determine the relative population of different structures formed by the c-Myc promoter by the virtue of the probe's ability to produce distinct and resolved 19 F signatures for different structures. Our results indicate that at physiological pH and temperature the c-Myc promoter forms duplex, random coil and GQ structures, and does not form an iM. Whereas at acidic pH, the mixture largely forms iM and GQ structures. Taken together, our system will complement existing tools and provide unprecedented insights on the population equilibrium and dynamics of nucleic acid structures under different conditions.

UI MeSH Term Description Entries

Related Publications

Akanksha Pandey, and Sarupa Roy, and Seergazhi G Srivatsan
June 2018, Organic & biomolecular chemistry,
Akanksha Pandey, and Sarupa Roy, and Seergazhi G Srivatsan
February 2022, Biophysical chemistry,
Akanksha Pandey, and Sarupa Roy, and Seergazhi G Srivatsan
February 2001, The Journal of biological chemistry,
Akanksha Pandey, and Sarupa Roy, and Seergazhi G Srivatsan
September 2020, Chembiochem : a European journal of chemical biology,
Akanksha Pandey, and Sarupa Roy, and Seergazhi G Srivatsan
December 2011, International journal of biological macromolecules,
Akanksha Pandey, and Sarupa Roy, and Seergazhi G Srivatsan
December 2015, Physical chemistry chemical physics : PCCP,
Akanksha Pandey, and Sarupa Roy, and Seergazhi G Srivatsan
December 2023, Organic & biomolecular chemistry,
Akanksha Pandey, and Sarupa Roy, and Seergazhi G Srivatsan
August 2007, Journal of the American Chemical Society,
Akanksha Pandey, and Sarupa Roy, and Seergazhi G Srivatsan
August 2013, Nucleic acids research,
Akanksha Pandey, and Sarupa Roy, and Seergazhi G Srivatsan
July 2014, Journal of molecular biology,
Copied contents to your clipboard!