Atomic force microscopy and surface-enhanced Raman scattering detection of DNA based on DNA-nanoparticle complexes

Polymerase chain reaction - surface-enhanced Raman spectroscopy (PCR-SERS) method for gene methylation level detection in plasma

Gene promoter hypermethylation is a vital step in tumorigenesis. This paper set out to explore the use of polymerase chain reaction - surface-enhanced Raman spectroscopy (PCR-SERS) for the detection of gene methylation levels, with a focus on cancer diagnosis. Methods: PCR with methylation independent primers were used on DNA samples to amplify target genes regardless of their methylation states. SERS was used on the obtained PCR products to generate spectra that contained peak changes belonging to CG and AT base pairs. Multiple linear regression (MLR) was then used to deconvolute the SERS spectra so that the CG/AT ratios of the sample could be obtained. These MLR results were used to calculate methylation levels of the target genes. For protocol verification, three sets of seven reference DNA solutions with known methylation levels (0%, 1%, 5%, 25%, 50%, 75%, and 100%) were analysed. Clinically, blood plasma samples were taken from 48 non-small-cell lung cancer (NSCLC) patients and 51 healthy controls. The methylation levels of the genes p16, MGMT, and RASSF1 were determined for each patient using this method. Results: Verification experiment on the mixtures with known methylation levels resulted in an error of less than 6% from the actual levels. When applied to our clinical samples, the frequency of methylation in at least one of the three target genes among the NSCLC patients was 87.5%, but this percentage decreased to 11.8% for the control group. The methylation levels of p16 were found to be significantly higher in NSCLC patients with more pack-years smoked (p=0.04), later cancer stages (p=0.03), and cancer types of squamous cell and large cell versus adenocarcinoma (p=0.03). Prediction accuracy of 88% was achieved from classification and regression trees (CART) based on methylation levels and states, respectively. Conclusion: This research showed that the PCR-SERS protocol could quantitatively measure the methylation levels of genes in plasma. The methylation levels of the genes p16, MGMT, and RASSF1 were higher in NSCLC patients than in controls.

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.

Structural Changes Induced in Grapevine (Vitis vinifera L.) DNA by Femtosecond IR Laser Pulses: A Surface-Enhanced Raman Spectroscopic Study

In this work, surface-enhanced Raman spectra of ten genomic DNAs extracted from leaf tissues of different grapevine (Vitis vinifera L.) varieties, respectively, are analyzed in the wavenumber range 300–1800 cm⁻¹. Furthermore, structural changes induced in grapevine genomic nucleic acids upon femtosecond (170 fs) infrared (IR) laser pulse irradiation (λ = 1100 nm) are discussed in detail for seven genomic DNAs, respectively. Surface-enhanced Raman spectroscopy (SERS) signatures, vibrational band assignments and structural characterization of genomic DNAs are reported for each case. As a general observation, the wavenumber range between 1500 and 1660 cm⁻¹ of the spectra seems to be modified upon laser treatment. This finding could reflect changes in the base-stacking interactions in DNA. Spectral shifts are mainly attributed to purines (dA, dG) and deoxyribose. Pyrimidine residues seem to be less affected by IR femtosecond laser pulse irradiation. Furthermore, changes in the conformational properties of nucleic acid segments are observed after laser treatment. We have found that DNA isolated from Feteasca Neagra grapevine leaf tissues is the most structurally-responsive system to the femtosecond IR laser irradiation process. In addition, using unbiased computational resources by means of principal component analysis (PCA), eight different grapevine varieties were discriminated.

Detection of Gold Nanoparticles Aggregation Growth Induced by Nucleic Acid through Laser Scanning Confocal Microscopy

The gold nanoparticle (GNP) aggregation growth induced by deoxyribonucleic acid (DNA) is studied by laser scanning confocal and environmental scanning electron microscopies. As in the investigated case the direct light scattering analysis is not suitable, we observe the behavior of the fluorescence produced by a dye and we detect the aggregation by the shift and the broadening of the fluorescence peak. Results of laser scanning confocal microscopy images and the fluorescence emission spectra from lambda scan mode suggest, in fact, that the intruding of the hydrophobic moiety of the probe within the cationic surfactants bilayer film coating GNPs results in a Förster resonance energy transfer. The environmental scanning electron microscopy images show that DNA molecules act as template to assemble GNPs into three-dimensional structures which are reminiscent of the DNA helix. This study is useful to design better nanobiotechnological devices using GNPs and DNA.

SERS-based approaches toward genetic profiling

In the last decade surface-enhanced Raman scattering (SERS) has experienced an important resurgence, and as a consequence it has seen wide application in the biological field, especially for DNA identification. SERS-based DNA detection can be carried out directly and indirectly and, in the latter approach, it relies on the use of SERS tags, whose role is to indirectly prove the recognition and binding of a specific oligonucleotide sequence. Herein, the role of SERS tags is analyzed focusing specifically on the use of DNA identification for genetic profiling.

Subpicosecond surface dynamics in genomic DNA from in vitro-grown plant species: a SERS assessment

In this work the surface-enhanced Raman total half band widths of seven genomic DNAs from leaves of chrysanthemum (Dendranthema grandiflora Ramat.), common sundew (Drosera rotundifolia L.), edelweiss (Leontopodium alpinum Cass), Epilobium hirsutum L., Hypericum richeri ssp. transsilvanicum (Čelak) Ciocârlan, rose (Rosa x hybrida L.) and redwood (Sequoia sempervirens D. Don. Endl.) have been measured. We have shown that surface-enhanced Raman spectroscopy (SERS) can be used to study the fast subpicosecond dynamics of DNA in the proximity of a metallic surface. The dependencies of the total half band widths and the global relaxation times, on the DNA molecular subgroup structure and on the type of genomic DNA, are reported. In our study, the full widths at half-maximum (FWHMs) for the SERS bands of genomic DNAs from different leaf tissues are typically in the wavenumber range from 15 to 55 cm(-1). Besides, it can be observed that molecular relaxation processes studied in this work have a global relaxation time smaller than 0.71 ps and larger than 0.19 ps. A comparison between different ranges of FT-Raman and SERS band parameters, respectively, corresponding to DNA extracted from leaf tissues is given. It is shown that the interaction between DNA and a metallic surface has the potential to lead to a shortening of the global relaxation times, as compared with molecular dynamics in solution. We have found that the surface dynamics of molecular subgroups in plant DNA is, in some cases, about two times faster than the solution dynamics of nucleic acids. This can be rationalized in a qualitative manner by invoking the complex landscape of the interaction energy between the molecule and the silver surface.

Applications of surface-enhanced Raman scattering in advanced bio-medical technologies and diagnostics

In this review of the literature on surface-enhanced Raman scattering (SERS), we describe recent developments of this technique in the medical field. SERS has developed rapidly in the last few years as a result of the fascinating advancements in instrumentation and the ability to interpret complex Raman data using high-processional, computer-aided programs. This technique, has many advantages over ordinary spectroscopic analytical techniques - such as extremely high sensitivity, molecular selectivity, intense signal and great precision - that can be leveraged to address complex medical diagnostics problems. This review focuses on the SERS-active substrate, as well as major advances in cancer and bacteria detection and imaging. Finally, we present a perspective on anticipated future advancements in SERS techniques to address some of the most critical challenges in the areas of diagnostics, detection, and sensing.

Protein-directed approaches to functional nanomaterials: a case study of lysozyme

Using lysozyme as a model, protein-directed approaches to functional nanomaterials were reviewed, making rational materials design possible in the future.

Plasmonic imaging of brownian motion of single DNA molecules spontaneously binding to Ag nanoparticles

We find the spontaneous binding of single DNA molecules to uncoated silver nanoparticles (AgNPs) in aqueous solution with Mn(2+) (3 mM). From dark-field optical microscopic imaging of AgNPs bound to DNA molecules, we demonstrate analysis of the Brownian motion of single DNA molecules via plasmon resonance elastic light scattering. Our results provide that the plasmonic imaging technique is free from photobleaching and blinking and thus is useful in long-time observations of single-molecule DNA dynamics.

Direct observation of one-dimensional plasmon coupling in metallic nanofibers prepared by evaporation-induced self-assembly with DNA

Here we report a simple method for the preparation of highly aligned metallic nanofibers with anisotropic aggregates of silver nanoparticles (AgNPs) as well as a direct observation of localized plasmon field and its coupling in the prepared metallic nanofibers. Metallic nanofibers of several tens of nanometers wide and millimeters long were prepared. The preparation method, which is based on the process of evaporation-induced self-assembly with DNA and drying front movement, eliminates the need for lithography and an external field, and it is fast, cheap and easy. Dark-field scattering spectroscopy was used to study the strong plasmon coupling of AgNPs in the metallic nanofibers. We observed strong near-field coupling between neighboring nanoparticles, which results in red-shifted multipolar plasmon modes that are highly polarized along the fiber axis. The polarization dependence of plasmon coupling in the metallic nanofibers observed in this study was satisfactorily explained by the morphology of the metallic nanofibers, which was characterized by atomic force microscopy (AFM) and scanning electron microscopy (SEM). Furthermore, Raman spectra imaging of the metallic nanofibers revealed the existence of intense hot spots localized along their axes, which played a significant role in the intensity of surface enhanced Raman scattering (SERS) signals from DNA bases in the metallic nanofiber. Our results demonstrate the use of evaporation-induced self-assembly with DNA as a straightforward method to produce one-dimensional coupling of localized plasmons with a longer scale.

Base-stacking-determined fluorescence emission of DNA abasic site-templated silver nanoclusters

DNA-templated silver nanoclusters (Ag NCs) are emerging sets of fluorophores that are widely applicable because of high brightness, good photostability, and visible to near-infrared emissions tunable using the DNA sequence and length to change the NC size. We find that fluorescent Ag NCs can be size-selectively grown at DNA abasic sites (AP site) using a constrained duplex environment opposed by a cytosine and flanked by two guanines. The size of the AP site-grown Ag NCs is not affected by the increasing Ag(+) concentration. A Job's plot analysis shows that Ag(2) NCs are the species responsible for the observed emissions. Although varying the DNA sequence one base away from the AP site (i.e., the Ag NC growth site) does not alter the size of the fluorescent Ag NCs, the emissions of the formed Ag NCs are still gradually red shifted as the sequence changes from thymine (T) to cytosine (C), adenine (A), and guanine (G). Furthermore, this emission shift is strongly dependent on the base-stacking direction of the 3'-side sequence of the 5'-G stack exactly flanking the AP site, which exhibits a larger emission alteration than altering the 5'-side sequence of the 3'-G stack flanking the AP site on the other side of the site. The excited-state lifetimes of the Ag NCs are inversely proportional to the singlet energies (ΔE(0,0)) of the Ag NCs relative to their ground state and of the vertical ionization potentials of the guanines directly flanking the AP site as determined by the base stacking. All of these results support the conclusion that the Ag NC excited state becomes more stable by interacting with a guanine base because of the larger electronic dipole moment that can be modified by the stacked sequences. Additionally, the size of the formed Ag NCs seems to be dependent on the consecutive AP site number. Thus, the AP site design in this work provides an easy way to shed light on the role of DNA base stacking in the optical properties of Ag NCs.

Growth mechanisms of fluorescent silver clusters regulated by polymorphic DNA templates: a DFT study

The aggregation behaviors of silver atoms modulated by polymorphic DNA templates involving i-motif, G-quadruplex, and the Watson-Crick duplex, were investigated by using the density functional theory (DFT) calculations, combining with the experimental characterizations of CD, UV, fluorescence measurements and TEM, in order to understand the reason in the molecular level that polymorphic DNA templates affect the fluorescence emitting species of Ag nanomaterials. First, the affinity sites of silver ions on different DNA templates were analyzed by using DFT calculations, and the conformational variations of DNA templates caused by silver ions and atoms were disclosed. Second, the aggregation behaviors of silver atoms constrained by the polymorphic DNA templates were studied by DFT modeling, and distinct fluorescence property of nanosilvers templated by polymorphic DNA were evaluated using the time-dependent DFT calculations. It is illustrated that with the DNA template adopting i-motif or the duplex the silver atoms tend to aggregate inside the encapsulated spaces of nucleobases, and the formed silver nanoclusters are positively charged with high fluorescent spectral features; whereas with the template of the G-quadruplex the silver atoms are preferential to aggregate outside of the G-tetrad, which results in the formation of larger silver crystals without fluorescence property. The results obtained here are useful to explore the nucleation and growth mechanism of silver nanomaterials regulated by the structure-specific DNA templates, which is important to rational design of desirable fluorescent emitters for sensing in the field from biology to nanoscience.

Effects of multi-walled carbon nanotubes (MWCNT) under Neisseria meningitidis transformation process

Background

This study aimed at verifying the action of multi-walled carbon nanotubes (MWCNT) under the naturally transformable Neisseria meningitidis against two different DNA obtained from isogenic mutants of this microorganism, an important pathogen implicated in the genetic horizontal transfer of DNA, causing the escape of the principal vaccination measured worldwide by the capsular switching process.

Materials and methods

The bacterium receptor strain C2135 was cultivated and had its mutant DNA donor M2 and M6, which received a receptor strain and MWCNT at three different concentrations. The inhibition effect of DNAse on the DNA in contact with nanoparticles was evaluated.

Results

The results indicated an in increase in the transformation capacity of N. meninigtidis in different concentrations of MWCNT when compared with negative control without nanotubes. A final analysis of the interaction between DNA and MWCNT was carried out using Raman Spectroscopy.

Conclusion

These increases in the transformation capacity mediated by MWCNT, in meningococci, indicate the interaction of these particles with the virulence acquisition of these bacteria, as well as with the increase in the vaccination escape process.

Quantitatively probing the means of controlling nanoparticle assembly on surfaces

As a means of developing a simple, cost-effective, and reliable method for probing nanoparticle behavior, we have used atomic force microscopy to gain a quantitative 3D visual representation of the deposition patterns of citrate-capped Au nanoparticles on a substrate as a function of (a) sample preparation, (b) the choice of substrate, (c) the dispersion solvent, and (d) the number of loading steps. Specifically, we have found that all four parameters can be independently controlled and manipulated in order to alter the resulting pattern and quantity of as-deposited nanoparticles. From these data, the sample preparation technique appears to influence deposition patterns most broadly, and the dispersion solvent is the most convenient parameter to use in tuning the quantity of nanoparticles deposited onto the surface under spin-coating conditions. Indeed, we have quantitatively measured the effect of surface coverage for both mica and silicon substrates under preparation techniques associated with (i) evaporation under ambient air, (ii) heat treatment, and (iii) spin-coating preparation conditions. In addition, we have observed a decrease in nanoparticle adhesion to a substrate when the ethylene glycol content of the colloidal dispersion solvent is increased, which had the effect of decreasing interparticle-substrate interactions. Finally, we have shown that substrates prepared by these diverse techniques have potential applicability in surface-enhanced Raman spectroscopy.