Surface-enhanced Raman study of the interactions between tripodal cationic polyamines and polynucleotides

Surface-enhanced Raman spectroscopy for studying the interaction of N-propyl substituted imidazole compound with salmon sperm DNA

BACKGROUND

Surface Enhanced Raman Spectroscopy (SERS) is a very promising and fast technique for studying drugs and for detecting chemical nature of a molecule and DNA interaction. In the current study, SERS is employed to check the interaction of different concentrations of n-propyl imidazole derivative ligand with salmon sperm DNA using silver nanoparticles as SERS substrates.

OBJECTIVES

Multivariate data analysis technique like principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) are employed for the detailed analysis of the SERS spectral features associated with the mode of action of the imidazole derivative ligand with DNA.

METHODOLOGY

Silver nanoparticles were used as a SERS substrate in DNA-drug interaction. Five different concentrations of ligands were interacted with DNA and mix with Ag-NPs as substrate. The SERS spectra of were acquired for all seven samples and processed using MATLAB. Additionally, PCA and PLS-DA were used to assessed the ability SERS to differentiate interaction of DNA-drug.

RESULTS

Differentiating SERS features having changes in their peak position and intensities are observed including 629, 655, 791, 807, 859, 1337, 1377 and 1456 cm^-1. These SERS features reveal that binding of ligand with DNA is electrostatic in nature, and have specificity to major groove where it forms GC-CG interstrand cross-linking with the DNA double helix.

CONCLUSIONS

SERS give significant information regarding to Drug-DNA interaction mechanism, SERS spectra inferred the mode of action of anticancer compound that are imidazole in nature.

Mg2+-induced DNA compaction, condensation, and phase separation in gene delivery vehicles based on zwitterionic phospholipids: a dynamic light scattering and surface-enhanced Raman spectroscopic study

Despite the significant efforts towards applying improved non-destructive and label-free measurements of biomolecular structures of lipid-based gene delivery vectors, little is achieved in terms of their structural relevance in gene transfections. Better understanding of structure-activity relationships of lipid-DNA complexes and their gene expression efficiencies thus becomes an essential issue. Raman scattering offers a complimentary measurement technique for following the structural transitions of both DNA and lipid vesicles employed for their transfer. This work describes the use of SERS coupled with light scattering approaches for deciphering the bioelectrochemical phase formations between nucleic acids and lipid vesicles within lipoplexes and their surface parameters that could influence both the uptake of non-viral gene carriers and the endocytic routes of interacting cells. As promising non-viral alternatives of currently employed risky viral systems or highly cytotoxic cationic liposomes, complexations of both nucleic acids and zwitterionic lipids in the presence of Mg²⁺ were studied applying colloidal Ag nanoparticles. It is shown that the results could be employed in further conformational characterizations of similar polyelectrolyte gene delivery systems.

Unraveling the Interaction of Silver Nanoparticles with Mammalian and Bacterial DNA

The focus of this study was to understand and unravel the interaction of silver nanoparticles (AgNPs) with different types of Deoxyribonucleic acid (DNA), mammalian and bacterial, having different base pair compositions. Binding of spherical silver nanoparticles (AgNPs) to Calf thymus (CT) DNA, Escherichia coli (EC) DNA and Micrococcus lysodeikticus (ML) DNA has been studied to gain insights into their mode of interaction and specificity. Interaction of AgNPs with synthetic DNA has also been carried out. On the basis of absorption, thermal melting, isothermal calorimetry and viscosity studies, we could establish the mode of binding and specificity of the synthesized silver nanoparticles with mammalian and bacterial DNA. Thermal melting (Tm) studies indicated a decrease in the Tm of all the DNAs, confirming the destabilization of DNA stacks on interaction with AgNPs. Comparative interaction studies with single stranded (ss) and double stranded (ds) DNAs further confirmed the specificity of the particles toward ds DNA. On the basis of the results we could confirm that the synthesized AgNPs could be used for selective detection of DNA through their DNA binding mechanism. In addition, the AgNPs-DNA complexes exhibited distinct differences in the SERS spectra making it an interesting SERS platform for identifying ds DNA. The optical and physical properties of AgNPs help in differentiating the DNAs of different base pair compositions through their binding affinity and specificity.

Distinguishing binding modes of a new phosphonium dye with DNA by surface-enhanced Raman spectroscopy

SERS spectroscopy provided structural data on binding of a dye as monomer and dimer within minor groove of adenine–thymine polynucleotides.

Adsorption mechanisms of RNA mononucleotides on silver nanoparticles

Surface-enhanced Raman scattering (SERS) of four RNA mononucleotides (AMP, GMP, CMP and UMP) has been studied on the citrate-reduced silver colloid aggregated with sodium sulfate. Concentration dependent spectra in the range of 1×10(-7)-1×10(-4) mol dm(-3) were obtained, assigned and interpreted according to the surface selection rules. For purine mononucleotides, AMP and GMP, adsorption onto the silver nanoparticles through the six-membered ring of the nitrogenous base was suggested. Concentration dependent splitting of the ring breathing band in the spectra of AMP indicated coexistence of two species on the silver surface, which differed in contribution of the adenine N1 atom and the exocyclic NH2 group in binding. Unlike the AMP spectra, the spectra of GMP implied only one mode of adsorption of the molecules onto the silver nanoparticles, taking place through the guanine N1H and C=O group. Weak SERS spectra of pyrimidine mononucleotides, CMP and UMP, pointed to involvement of carbonyl oxygen in adsorption process, whereby the molecules adopted the position on the nanoparticles with ribose close to the metal surface. Intense bands in the low wavenumber region, associated with stretching of the formed Ag-N and/or Ag-O bonds, supported chemical binding of the RNA mononucleotides with the silver surface.

Identification of virulence determinants in influenza viruses

To date there is no rapid method to screen for highly pathogenic avian influenza strains that may be indicators of future pandemics. We report here the first development of an oligonucleotide-based spectroscopic assay to rapidly and sensitively detect a N66S mutation in the gene coding for the PB1-F2 protein associated with increased virulence in highly pathogenic pandemic influenza viruses. 5'-Thiolated ssDNA oligonucleotides were employed as probes to capture RNA isolated from six influenza viruses, three having N66S mutations, two without the N66S mutation, and one deletion mutant not encoding the PB1-F2 protein. Hybridization was detected without amplification or labeling using the intrinsic surfaced-enhanced Raman spectrum of the DNA-RNA complex. Multivariate analysis identified target RNA binding from noncomplementary sequences with 100% sensitivity, 100% selectivity, and 100% correct classification in the test data set. These results establish that optical-based diagnostic methods are able to directly identify diagnostic indicators of virulence linked to highly pathogenic pandemic influenza viruses without amplification or labeling.

SERS study on adenine using a Ag/poly(t-butylacrylate) nanocomposite

Enhancement of Raman signals of the nucleobase adenine on an Ag based composite was studied using the 1064 nm laser line. The composite comprise emulsions of Ag nanoparticles encapsulated in poly(t-butylacrylate) (PtBA) beads that act as substrate for the Surface-Enhanced Raman Scattering (SERS) of adenine. For this system, Raman enhancement was observed for the ring-stretching vibrational mode of adenine after aggregation of the Ag/poly(t-butylacrylate) emulsion and isolation of the solid composite. This is a convenient and alternative analytical approach to SERS monitoring of solutions of adenine over the more common use of pure Ag colloids. As a consequence, this research contributes to develop innovative studies on DNA fragments using polymeric platforms that can act as highly sensitive SERS substrates.