Related papers: Structure of DNA-Functionalized Dendrimer Nanopart…
We study sequence dependent complexation between oligonucleotides (single strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by…
We present a comprehensive theoretical and experimental study of the solution phase properties of DNA-based family of nanoparticles - dendrimer-like DNA molecules (DL-DNA). These charged DNA dendrimers are novel macromolecular aggregates,…
Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic…
Using all atomistic molecular dynamics (MD) simulations we report the microscopic picture of the nanotube-dendrimer complex for PAMAM dendrimer of generation 2 to 4 and carbon nanotube of chirality (6,5). We find compact wrapping…
DNA interactions with polycations are not only important for our understanding of chromatin compaction but also for characterizing DNA-binding proteins involved in transcription, replication and repair. DNA is known to form several types of…
Using small-angle neutron scattering and liquid integral equation theory, we relate the structure factor of flexible dendrimers of 4th generation to their average shape. The shape is measured as a radial density profile of monomers…
We study the structure of carboxylic acid terminated neutral poly (propyl ether imine) (PETIM) dendrimer from generation 1 through 6 (G1-G6) in a good solvent (water) by fully atomistic molecular dynamics (MD) simulations. We determine as a…
Polyamidoamine (PAMAM) dendrimers, being protonated under physiological conditions, represent a promising class of nonviral, nano-sized vectors for drug and gene delivery. We performed extensive molecular dynamics simulations of a generic…
Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since…
Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure.…
We study the influence of mutual interaction on the conformation of flexible poly(propyleneamine) dendrimers of fourth generation in concentrated solution. Mixtures of dendrimers with protonated and deuterated end groups are investigated by…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
The aim of the present paper is the study of the entropic elasticity of the dsDNA molecule, having a cristallographic length L of the order of 10 to 30 persistence lengths A, when it is subject to spatial obstructions. We have not tried to…
We have performed fully atomistic classical molecular dynamics (MD) simulations to calculate the effective interaction between two polyamidoamine (PAMAM) dendrimers. Using the umbrella sampling (US) technique, we have obtained the potential…
The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon…
Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity.…
By resorting to the thick-chain model we discuss how the stretching response of a polymer is influenced by the self-avoidance entailed by its finite thickness. The characterization of the force versus extension curve for a thick chain is…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
The effect of polyvalent molecular cations, such as spermine, on the condensation of DNA into very well-defined toroidal shapes have been well studied and understood. However, a great effort has been made trying to obtain similar condensed…
When mixed together, DNA and polyaminoamide (PAMAM) dendrimers form fibers that condense into a compact structure. We use optical tweezers to pull condensed fibers and investigate the decondensation transition by measuring force-extension…