Steady state and time resolved spectroscopic study of QD–DNA interaction

Abstract

Here, we report the preparation of bioconjugates between cationic polymer functionalized green emitting CdTe quantum dot (QD) and ethidium bromide (EB) intercalated double stranded DNA (dsDNA). Water soluble, high quantum yield of CdTe QDs have been prepared by one pot synthesis. Cationic polymer (CP) is being used for surface modification of QD to obtain strong electrostatic interaction with EB intercalated dsDNA. It is found that the energy transfer (41%) takes place between CP modified QD and EB dye and the measured distance between donor and acceptor is found to be 35.7 Å which is close to the estimated distance. Analysis suggests that cationic polymer prevents denaturation, condensation or other conformational change of biomolecules in QD conjugated DNA system.

Introduction

A significant attention has been paid on the quantum dot (QD) based Förster resonance energy transfer (FRET) due to their narrow emission and broad excitation spectra [1], [2]. A number of experimental studies exist on QD-based fluorescence resonance energy transfer for many potential applications [3], [4], [5], [6], [7], [8]. Medintz et al. reported the potential of luminescent semiconductor quantum dots for development of hybrid inorganic–bio receptor sensing materials [2]. They demonstrated the use of luminescent CdSe–ZnS QDs as energy donors in FRET-based assays with organic dyes as energy acceptors in QDs–dye-labeled protein conjugates. In most cases, the energy transfer in QD-bioconjugates is discussed as a FRET process. FRET occurs when the electronic excitation energy of a donor fluorophore is transferred to a nearby acceptor molecule and the transfer efficiency increases with increasing the spectral overlap between the donor emission and acceptor absorption [9]. The efficiency of FRET depends on the distance of separation between donor and acceptor molecules. FRET from QD to dye molecules is used for protein–protein binding assay [10]. Thakur et al. studied QD-protein interaction using resonance energy transfer process [11]. Again, the understanding of conformational changes of BSA protein using surface energy transfer has been reported [12]. Recently, Rotello et al. demonstrated that amino acid functionalized QD-protein interaction is the best mimic of protein–protein interaction because protein–protein interaction is basically interaction between amino acids [13]. Similarly, cationic surface charged nanoparticles–DNA interaction can be a mimic of protein–DNA interaction because histone protein binds with DNA by its cationic surface which regulates DNA transcription [14], [15], [16]. The nonspecific interaction between CdSe/ZnS core-shell QD and dye tagged DNA, had been investigated using ultrafast spectroscopy [16]. Rogach et al. have used quantum dot/dye-labeled DNA complexes for DNA hybridization detection [17]. Recently, the study of interaction between CdTe quantum dot and DNA has been reported [18], [19]. Very recently, He et al. demonstrated an interesting graphene based DNA–CdTe QD probe for sensing of hepatitis B virus [20].

Generally, spacer is being used to overcome nonspecific interaction between QD and DNA. Klenerman et al. have used tri (ethylene glycol) as spacer to prevent nonspecific interaction between QD and DNA [21]. Travas-Sejdic et al. used cationic polymer capped QD and dye-labeled single stranded DNA for nucleic acid detection [22]. Different capping agents such as mercaptopropanoic acid or thioglycolic acid [23], [24], [25], [26] have been used to prepare water soluble QD.

In this work, we have synthesized water soluble; green emitting thioglycolic acid (TGA) capped CdTe QD [27], [28], [29]. However, TGA capped QD do not interact with DNA because of their similar charges. Thus, we have modified TGA capped CdTe QD by tetra alkylated ammonium groups of cationic polymer (CP) which acts as spacer [30]. We have used ethidium bromide (EB) as an intercalating probe for double stranded DNA (dsDNA) [31]. Finally, CP modified QD interacts with negative charged DNA via an electrostatic force of attraction. Our aim of the present work is to study the interaction between CP modified QD and dsDNA using spectroscopy. Using FRET, we have measured the distance between QDs and interacting dsEB (EB intercalated in dsDNA or complex of EB and dsDNA) and correlate with the calculated distance. Such DNA–QD bioconjugates should have great potentials for optical-based molecular rulers and it could pave the way for designing new optical-based materials for the application in chemical sensing or biological imaging.