  Atomistic molecular dynamics simulations have been carried out to reveal the
characteristic features of ethylenediamine (EDA) cored protonated poly amido
amine (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) that are
functionalized with single stranded DNAs (ssDNAs). The four ssDNA strands that
are attached via alkythiolate [-S (CH2)6-] linker molecule to the free amine
groups on the surface of the PAMAM dendrimers observed to undergo a rapid
conformational change during the 25 ns long simulation period. From the RMSD
values of ssDNAs, we find relative stability in the case of purine rich ssDNA
strands than pyrimidine rich ssDNA strands. The degree of wrapping of ssDNA
strands on the dendrimer molecule was found to be influenced by the charge
ratio of DNA and the dendrimer. As G4 dendrimer contains relatively more
positive charge than G3 dendrimer, we observe extensive wrapping of ssDNAs on
the G4 dendrimer. The ssDNA strands along with the linkers are seen to
penetrate the surface of the dendrimer molecule and approach closer to the
center of the dendrimer indicating the soft sphere nature of the dendrimer
molecule. The effective radius of DNA-functionalized dendrimer nanoparticle was
found to be independent of base composition of ssDNAs and was observed to be
around 19.5 {\AA} and 22.4 {\AA} when we used G3 and G4 PAMAM dendrimer as the
core of the nanoparticle respectively. The observed effective radius of
DNA-functionalized dendrimer molecule apparently indicates the significant
shrinkage in the structure that has taken place in dendrimer, linker and DNA
strands. As a whole our results describe the characteristic features of
DNA-functionalized dendrimer nanoparticle and can be used as strong inputs to
design effectively the DNA-dendrimer nanoparticle self-assembly for their
active biological applications.
