Spectrochimica Acta Part A 78 (2011) 1587–1591 Contents lists available at ScienceDirect Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy journal homepage: www.elsevier.com/locate/saa Mechanistic pathway for controlled extraction of guest molecule bound to herring sperm DNA using -cyclodextrin S. Syed Jaffer, Prasun Ghosh, Pradipta Purkayastha ∗ Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741252, WB, India article info Article history: Received 4 August 2010 Received in revised form 28 December 2010 Accepted 7 February 2011 Dedicated to the 65th birth anniversary of Professor Sanjib Bagchi. Keywords: Twisted intramolecular charge transfer Guest–DNA interaction Fluorescence Extraction -Cyclodextrin abstract trans-2-[4-(Dimethylamino)styryl]benzothiazole (DMASBT) is known to have dual emitting states where the locally excited (LE) state is responsible for fluorescence in less polar environment and in polar milieu fluorescence is from the twisted intramolecular charge transfer (TICT) state. This compound also under- goes minor groove binding to herring sperm DNA (hsDNA) evidenced by the absorption spectra before and after the binding process and an effect on DMASBT fluorescence by an anionic quencher. The binding occurs efficiently in a 1:1 manner, i.e. one guest molecule binds to one site on the hsDNA. Instead of following the DNA twist, the aromatic part seems to project outward. Thus, the bound molecule can be successfully extracted out from the DNA in a controlled way by the hydrophobic cavity of -cyclodextrin (-CD). The extraction starts even with a low concentration of -CD and increases as the concentra- tion is increased. Absorption, steady-state and time resolved fluorescence spectroscopic methods have been employed to explore the mechanistic pathway of binding of DMASBT to hsDNA. The mechanistic approach toward controlled extraction of the guest molecules from hsDNA by -CD is reported and is expected to serve a significant purpose in treatment of drug overdose. © 2011 Elsevier B.V. All rights reserved. 1. Introduction Drug molecules that target a particular DNA sequence can selec- tively inhibit or modulate gene expression and hence they are valuable for a variety of chemotherapeutic strategies [1,2]. The knowledge of the elementary steps of dynamics and the informa- tion about static molecular structures are essentially required for understanding the recognition process and drug action [3,4]. The development of effective therapeutic agents that help to control gene expression stems from the characterization of the interaction of small molecules with DNA [5]. Small molecules serve as ana- logues in studies of protein–nucleic acid recognition, as sensitive probes for monitoring nucleic acid structure, provide site-specific affinity for molecular biology and yield rationales for drug design [6]. The total DNA content of a cell is termed the “Genome”. The “Genome” is unique to an organism, and is the information bank governing all life processes of the organism, DNA being the form in which this information is stored [7]. Transcription and replication are vital to cell survival and proliferation as well as for smooth func- tioning of all body processes. DNA starts transcribing or replicating on receiving a signal, which is often in the form of a regulatory ∗ Corresponding author. Tel.: +91 33 25873121; fax: +91 33 25873020. E-mail addresses: ppurkayastha@iiserkol.ac.in, prad purk@yahoo.com (P. Purkayastha). protein binding to a particular region of the DNA. Thus, by mimick- ing the binding specificity and strength of this regulatory protein by a small molecule, the DNA function can be artificially modu- lated, inhibited or activated. This small molecule can act as a drug when activation or inhibition of DNA function is required to cure or control a disease. The non-covalently bound drugs, i.e., the minor groove binders are usually crescent shaped, which complements the shape of the groove and facilitates binding by promoting van der Waals interactions, whereas, intercalators introduce strong struc- tural perturbations in DNA [8]. In the ocean of research activities on drug-DNA binding, a few model DNAs are generally adopted to look through the out- comes. Among them calf thymus DNA (ctDNA) and herring sperm DNA (hsDNA) are used quite vividly [9]. Composition of isolated deoxyribonucleoproteins shows that about 14% of the total DNA in herring sperm nuclei is free from protamine and is bound with non-protamine proteins in the weight ratio of nonprotamine pro- teins to DNA of 0.25–0.30. The remaining 86% of the total DNA is combined mainly with protamine and a small amount of nonpro- tamine proteins; the weight ratios of protamine and nonprotamine proteins to DNA are 0.75 and 0.08, respectively [10]. Herring sperm DNA is used as a blocking agent in prehybridization and hybridiza- tion procedures to minimize non-specific binding of hybridization probe to membranes and in situ. We chose this DNA as our model medium to study its interaction with the guest molecule followed by extraction of the guest by a foreign agent. 1386-1425/$ – see front matter © 2011 Elsevier B.V. All rights reserved. doi:10.1016/j.saa.2011.02.005