title: Interaction of nucleic acids with carbon nanotubes and dendrimers.
abstract: Nucleic acid interaction with nanoscale objects like carbon nanotubes (CNTs) and dendrimers is of fundamental interest because of their potential application in CNT separation, gene therapy and antisense therapy. Combining nucleic acids with CNTs and dendrimers also opens the door towards controllable self-assembly to generate various supra-molecular and nano-structures with desired morphologies. The interaction between these nanoscale objects also serve as a model system for studying DNA compaction, which is a fundamental process in chromatin organization. By using fully atomistic simulations, here we report various aspects of the interactions and binding modes of DNA and small interfering RNA (siRNA) with CNTs, graphene and dendrimers. Our results give a microscopic picture and mechanism of the adsorption of single- and double-strand DNA (ssDNA and dsDNA) on CNT and graphene. The nucleic acid-CNT interaction is dominated by the dispersive van der Waals (vdW) interaction. In contrast, the complexation of DNA (both ssDNA and dsDNA) and siRNA with various generations of poly-amido-amine (PAMAM) dendrimers is  governed by electrostatic interactions. Our results reveal that both the DNA and siRNA form stable complex with the PAMAM  dendrimer at a physiological pH when the dendrimer is positively charged due to the protonation of the primary amines. The  size and binding energy of the complex increase with increase in dendrimer generation. We also give a summary of the current  status in these fields and discuss future prospects.
authors: Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560 012, India.
authors: Bidisha
authors: B
authors: Nandy
authors: Mogurampelly
authors: M
authors: Santosh
authors: Prabal K
authors: PK
authors: Maiti
mesh_terms: D000327:Adsorption; D020029:Base Pairing; D044704:DNA, A-Form / Q000737:chemistry; D059371:DNA, B-Form / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000737:chemistry; D050091:Dendrimers / Q000737:chemistry*; D000431:Ethanol / Q000737:chemistry; D006108:Graphite / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D056004:Molecular Dynamics Simulation; D037742:Nanotubes, Carbon / Q000737:chemistry*; D034741:RNA, Small Interfering / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D044704:DNA, A-Form; D059371:DNA, B-Form; D004277:DNA, Single-Stranded; D050091:Dendrimers; D037742:Nanotubes, Carbon; C104700:PAMAM Starburst; D034741:RNA, Small Interfering; D012997:Solvents; D014867:Water; D000431:Ethanol; D006108:Graphite