Sequence-specific recognition of DNA minor groove by an NIR-fluorescence switch-on probe and its potential applications.
In molecular biology, understanding the functional and structural aspects of DNA requires sequence-specific DNA binding probes. Especially, sequence-specific fluorescence probes offer the advantage of real-time monitoring of the conformational and structural reorganization of DNA in living cells. Herein, we designed a new class of D2A (one-donor-two-acceptor) near-infrared (NIR) fluorescence switch-on probe named quinone cyanine-dithiazole ( QCY-DT: ) based on the distinctive internal charge transfer (ICT) process for minor groove recognition of AT-rich DNA. Interestingly, QCY-DT: exhibited strong NIR-fluorescence enhancement in the presence of AT-rich DNA compared to GC-rich and single-stranded DNAs. We show sequence-specific minor groove recognition of QCY-DT: for DNA containing 5'-AATT-3' sequence over other variable (A/T)4 sequences and local nucleobase variation study around the 5'-X(AATT)Y-3' recognition sequence revealed that X = A and Y = T are the most preferable nucleobases. The live cell imaging studies confirmed mammalian cell permeability, low-toxicity and selective staining capacity of nuclear DNA without requiring RNase treatment. Further, Plasmodium falciparum with an AT-rich genome showed specific uptake with a reasonably low IC50 value (<4 µM). The ease of synthesis, large Stokes shift, sequence-specific DNA minor groove recognition with switch-on NIR-fluorescence, photostability and parasite staining with low IC50 make QCY-DT: a potential and commercially viable DNA probe.
Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, India.
Nagarjun
N
Narayanaswamy
New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India.
Shubhajit
S
Das
Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India.
Pralok K
PK
Samanta
Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.
Khadija
K
Banu
School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
Guru Prasad
GP
Sharma
School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
Neelima
N
Mondal
Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.
Suman K
SK
Dhar
New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India.
Swapan K
SK
Pati
Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, India tgraju@jncasr.ac.in.
T
T
Govindaraju
D020856:AT Rich Sequence; D020029:Base Pairing; D052160:Benzothiazoles / Q000737:chemistry* / Q000378:metabolism / Q000633:toxicity; D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry* / Q000378:metabolism / Q000633:toxicity; D006367:HeLa Cells; D006801:Humans; D061986:MCF-7 Cells; D008856:Microscopy, Fluorescence; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010963:Plasmodium falciparum / Q000187:drug effects / Q000378:metabolism; D019265:Spectroscopy, Near-Infrared
D052160:Benzothiazoles; D005456:Fluorescent Dyes; C000604690:QCy-DT compound; D004247:DNA