Periodic Reporting for period 1 - NAIL (Adsorption and Dynamics of Nucleic Acids on Surfaces in Ionic Liquid Environment)
Reporting period: 2018-03-01 to 2020-02-29
The current pool of pharmaceutical excipients is limited to a small number of sugars, amino acids, polymers, salts and detergents. This pool of stabilizing agents can receive a tremendous boost with the inclusion of ionic liquids (ILs). ILs have shown tremendous scope in increasing the stability of nucleic acids, even beyond conventional buffers. In addition ILs have unique properties like low volatility, large electrochemical window, biocompatibility which renders them desirable for applications in bioelectronics, biosensors, and microfluidic chips. To realize this tremendous potential of ILs, NAIL employs this unique combination of IL-DNA systems to understand the effect of IL on DNA adsorption on 2D surfaces. Scanning probe techniques have been used to understand the effect of various ions of the IL on the adsorption behavior of the DNA. The project also explored the role of specific interactions between the IL cation and the DNA bases on the overall persistence length and rigidity of the DNA. In addition to this, the project successfully demonstrates that by tuning the structure and concentration of the IL electrolyte the flexibility of the DNA chain can be controlled
A variety of IL-DNA systems were initially tested to identify the best combinations to address the objectives of the proposal. Imidazolium based ILs were identified as the most suitable ILs for investigation since the wide variety of anion-cation combinations possible with these ILs ensured that the adsorption of ILs on mica can be rendered negligible. In parallel, techniques like Tip Enhanced Raman Spectroscopy (TERS) and Fluorescence Lifetime Imaging Microscopy were tested for certain IL-DNA systems. This task proved to be challenging. However, the first phase of NAIL succeeded in establishing the required protocols in terms of sample preparation, sample treatment and technique development.
In the second phase we went a step further to understand the influence of various cations and anions of the ILs on the adsorption behavior of DNA. In particular, we were able to establish a clear correlation between the structure of cations of the IL and the rigidity of the DNA molecule. These studies were extended to also understand the influence of the IL anion on the rigidity of the DNA. These studies will be useful to develop IL assisted strategies to construct higher order nucleic acid architectures and more complex networks.
NAIL addressed the effect of concentration of ILs on the overall DNA network and also on the flexibility of the biopolymer. The project also clearly established the influence of ionic interactions and hydrogen bonding interactions on the flexibility of DNA strands. From the plethora of ILs, we judiciously identified certain specific ILs to unravel the role of specific interactions between the IL cation and DNA on the rigidity of the DNA molecules. The results point to the fact that specific hydrogen bonding interactions between the IL cation and the DNA molecule have a profound effect on the DNA flexibility
In the second phase we went a step further to understand the influence of various cations and anions of the ILs on the adsorption behavior of DNA. In particular, we were able to establish a clear correlation between the structure of cations of the IL and the rigidity of the DNA molecule. These studies were extended to also understand the influence of the IL anion on the rigidity of the DNA. These studies will be useful to develop IL assisted strategies to construct higher order nucleic acid architectures and more complex networks.
NAIL addressed the effect of concentration of ILs on the overall DNA network and also on the flexibility of the biopolymer. The project also clearly established the influence of ionic interactions and hydrogen bonding interactions on the flexibility of DNA strands. From the plethora of ILs, we judiciously identified certain specific ILs to unravel the role of specific interactions between the IL cation and DNA on the rigidity of the DNA molecules. The results point to the fact that specific hydrogen bonding interactions between the IL cation and the DNA molecule have a profound effect on the DNA flexibility
To the best of our knowledge, the NAIL project is the first of its kind that has tested the theoretical claims concerning IL-DNA systems. Moreover, the detailed DNA adsorption studies have helped in identifying the possible underlying mechanism by which complex salts can affect the persistence length of these biopolymers. Furthermore, theoretical and spectroscopic studies in this direction will provide the necessary support to propagate the hypothesis developed in this project. The IL-DNA systems will be further developed to construct higher order nucleic acid architectures that have direct applications in DNA based biosensors and nanodevices. Over the past two decades, ILs have found immense applications in a variety of fields. However, their foray into biological applications is still at its early stages. The knowledge developed in NAIL will be crucial to not only use existing ILs but also to synthesize new ILs with targeted functions. In essence the project not only identified key aspects governing the flexibility and adsorption of DNA molecules in the presence of ILs but also developed a holistic picture of DNA-IL systems.