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.[Nandy B, Santosh M and Maiti PK 2012 Interaction of nucleic acids with carbon nanotubes and dendrimers.

Determination of spectral markers of cytotoxicity and genotoxicity using in vitro Raman microspectroscopy: cellular responses to polyamidoamine dendrimer exposure

“…Atomic simulations of dendrimer-nucleic acid interactions have been conducted by Nandy et al and the study showed the formation of stable DNA and siRNA complexes with PAMAM dendrimers at a physiological pH based on electrostatic interaction. 40 The strong binding affinity of PAMAM dendrimers to the RNA has also been shown in computational and experimental designs by 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Pavan et al 41 The dose and time dependent changes on the nucleolus of the A549 cells upon PAMAM-G5 exposure are also evaluated in order to clarify mechanism of action of PAMAM-G5 dendrimers with RNA. The scatter plots of PCA of nucleolus of PAMAM-G5 exposed A549 cells and corresponding controls are provided in Supplementary Figure S9 and S10 for dose dependent and time dependent responses, respectively.…”

Electrical sensing of DNA-hybridization using two-port network based on suspended carbon nanotube membrane

“…As mentioned in previous literatures (Zheng et al 2003;Nandy et al 2012;Murmu and Adhikari 2012), DNA are non-covalently adsorbed on the carbon nanotube surfaces The red-shift of resonance frequency versus time after the probe DNA solution was dropped on the top surface of the device through hydrophobic, π-π stacking, and electrostatic interactions. Since the surface of CNT and DNA are both negatively charged, As a proof-of-concept of the proposed bio-sensing method, a terminal NH2 DNA was chosen as the capture DNA probe in this experiment in order to realize a stronger DNA-CNT binding by making the probe DNA a little bit positive charged.…”

“…Previous studies showed that the interaction of carbon nanotube (CNT) with single-stranded DNA produced stable negative charges because the phosphate groups on the DNA backbones were deprotonated (Zheng et al 2003;Nandy et al 2012;Murmu and Adhikari 2012). Based on this phenomenon, the electrical detection methods for DNA hybridization were explored using CNT transistors to directly sense the conductance shift of the CNT channel induced by CNT-DNA interaction (Sorgenfrei et al 2011;Martínez et al 2009;.…”

Gene delivery using dendrimer/pDNA complexes immobilized in electrospun fibers using the Layer-by-Layer technique

“…95 PBS solution (pH= 7.4) was always used to prepare these solutions. Complex solutions were vortexed and allowed to incubate for 20 minutes at room temperature prior to experiments.…”