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  • 1.
    Banerjee, Debapriya
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Vovusha, Hakkim
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Pang, Yanhong
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Oumata, Nassima
    Sanyal, Biplab
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Sanyal, Suparna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Spectroscopic and DFT studies on 6-Aminophenanthridine and its derivatives provide insights in their activity towards ribosomal RNA2014In: Biochimie, ISSN 0300-9084, E-ISSN 1638-6183, Vol. 97, 194-199 p.Article in journal (Refereed)
    Abstract [en]

    6-Aminophenanthridine (6AP), a plant alkaloid possessing antiprion activity, inhibits ribosomal RNA dependent protein folding activity of the ribosome (referred as PFAR). We have compared 6AP and its three derivatives 6AP8Cl, 6AP8CF3 and 6APi for their activity in inhibition of PFAR. Since PFAR inhibition requires 6AP and its derivatives to bind to the ribosomal RNA (rRNA), we have measured the binding affinity of these molecules to domain V of 23S rRNA using fluorescence spectroscopy. Our results show that similar to the antiprion activity, both the inhibition of PFAR and the affinity towards rRNA follow the order 6AP8CF3 > 6AP8Cl > 6AP, while 6APi is totally inactive. To have a molecular insight for the difference in activity despite similarities in structure, we have calculated the nucleus independent chemical shift using first principles density functional theory. The result suggests that the deviation of planarity in 6APi and steric hindrance from its bulky side chain are the probable reasons which prevent it from interacting with rRNA. Finally, we suggest a probable mode of action of 6AP, 6AP8CF3 and 6AP8Cl towards rRNA.

  • 2.
    Vovusha, Hakkim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Sanyal, Biplab
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    DFT and TD-DFT studies on the electronic and optical properties of explosive molecules adsorbed on boron nitride and graphene nano flakes2015In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 5, no 6, 4599-4608 p.Article in journal (Refereed)
    Abstract [en]

    The adsorption characteristics of explosive molecules: RDX, TATP, HMTD, TNT, HMX and PETN with boron nitride (BN) and graphene (G) flakes have been investigated using first principles density functional theory (DFT). It has been found that the binding between BN flakes and the explosive molecules is stronger than that with G flakes due to higher charge transfer in the BN-complexes. The energy decomposition analysis indicates that the dispersive interaction is the most dominant one. The optical properties and the nature of electronic transitions of BN and G-explosive complexes are studied by time dependent DFT (TD-DFT). It is observed that the strong interaction with BN flakes quenches the optical spectra by a significant amount whereas the graphene flakes leave the spectra almost unperturbed. Our findings of differential characteristics of 2D flakes will be useful for the designing of nanomaterials for the detection of aromatic and nonaromatic explosive molecules.

  • 3.
    Vovusha, Hakkim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Sanyal, Suparna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Sanyal, Biplab
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Interaction of Nucleobases and Aromatic Amino Acids with Graphene Oxide and Graphene Flakes2013In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 4, no 21, 3710-3718 p.Article in journal (Refereed)
    Abstract [en]

    In this work, we have studied interactions of nucleobases and aromatic amino acids with graphene (G) and graphene oxide (GO) flakes by ab initio density functional theory (DFT). It is evident from the results that GO complexes are stabilized by hydrogen bonding interactions whereas G complexes are stabilized by pi-pi interactions, leading to enhanced binding energies for GO complexes compared to G complexes. Moreover, time-dependent DFT (TD-DFT) calculations for the optical properties reveal that the GO nanoflakes and GO-nucleobase composite absorb visible light in the range of 400-700 nm, which may be useful for light-emitting devices. The insights obtained from our study will be useful to understand the role of GO flakes as carriers in targeted drug delivery and biosensors.

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