DNA sequence motifs for structure-specific recognition and separation of carbon nanotubes.

Single-walled carbon nanotubes (SWNTs) are a family of molecules that have the same cylindrical shape but different chiralities. Many fundamental studies and technological applications of SWNTs require a population of tubes with identical chirality that current syntheses cannot provide. The SWNT sorting problem-that is, separation of a synthetic mixture of tubes into individual single-chirality components-has attracted considerable attention in recent years. Intense efforts so far have focused largely on, and resulted in solutions for, a weaker version of the sorting problem: metal/semiconductor separation. A systematic and general method to purify each and every single-chirality species of the same electronic type from the synthetic mixture of SWNTs is highly desirable, but the task has proven to be insurmountable to date. Here we report such a method, which allows purification of all 12 major single-chirality semiconducting species from a synthetic mixture, with sufficient yield for both fundamental studies and application development. We have designed an effective search of a DNA library of approximately 10(60) in size, and have identified more than 20 short DNA sequences, each of which recognizes and enables chromatographic purification of a particular nanotube species from the synthetic mixture. Recognition sequences exhibit a periodic purine-pyrimidines pattern, which can undergo hydrogen-bonding to form a two-dimensional sheet, and fold selectively on nanotubes into a well-ordered three-dimensional barrel. We propose that the ordered two-dimensional sheet and three-dimensional barrel provide the structural basis for the observed DNA recognition of SWNTs.

Prevalence of Herpesvirus and Correlation with Clinical Parameters in Indian Subjects with Chronic Periodontitis.

OBJECTIVE: The identification of new uncultured species and viruses supports the possibility of combination of the herpes-virus-bacterial periodontal infection for periodontitis. The paucity of data and studies with larger sample size in Indian subjects provides an unclear picture of the presence of the herpesvirus in this population. MATERIALS AND METHODS: This was a cross-sectional study consisting of 100 each in the healthy group and chronic periodontitis (CP) group. The subgingival plaque was collected and polymerase chain reaction was performed post deoxyribonucleic acid (DNA) extraction by using specific primers for human cytomegalovirus (HCMV) and Epstein-Barr virus (EBV). The data were analyzed using Fisher's exact test, Mann-Whitney U test and Spearman's coefficient correlation. RESULTS: Human cytomegalovirus and EBV viruses were significantly higher in the CP group as compare to the healthy group. A higher percentage of those with CMV positive had EBV also positive (28.3%) compared to only 9.1% of CMV negative being EBV positive in the CP group. When both the healthy and CP group in total was compared, there was a significant correlation with all clinical parameters. CONCLUSION: Both the viruses dominated in disease as compared to health were similar to the earlier findings. The CP group had higher pocket depth and clinical attachment loss in the virus positive subjects. These findings could suggest that virus serves as a prelude to the disease and the combination of the two viruses could play a role in the pathogenesis.

Polymerase chain reaction-based identification of various serotypes of Streptococcus mutans in adults with and without dental caries.

Background: Dental caries is a multistep process which initiates the development of plaque' defined as a structured biofilm containing microbial communities. Teeth provide unique surfaces for bacterial colonization. Serotypes of Streptococcus mutans implicate the development of dental caries. Aim: The aim of the study was to determine the prevalence and association of serotypes of S. mutans in groups with and without dental caries. Materials and Methods: One hundred and fifty adults aged between 18 and 35 years were included in the study. Supragingival plaque samples were collected, followed by deoxyribonucleic acid extraction. Polymerase chain reaction was performed to identify S. mutans and its serotypes. Proportions of S. mutans and its serotypes were correlated with caries-active (CA) and caries-free (CF) groups. Results: CA group showed 66.7% positivity for S. mutans and CF group showed only 42.7% of positivity. Serotype C showed a higher proportion followed by E' F, and K in the CA group, whereas in the CF group, higher proportion was observed with K followed by C' E, and F. 70.8% cases showed single serotype in the CA group and 83.3% in CF group. Multiple serotypes were seen in 29.2% in the CA group and 16.7% in the CF group. Conclusions: The study clearly established variation in proportions of S. mutans and its serotypes between CA and CF groups. Positive correlation was observed in the CA group for S. mutans and its serotypes.

Association of F. alocis and D. pneumosintes with Periodontitis Disease Severity and Red Complex Bacteria.

Oral biofilms are considered the principal etiological agent in the development of periodontitis. Novel species that may contribute to periodontitis and dysbiosis have been identified recently. The study aims to evaluate the presence of F. alocis and D. pneumosintes in healthy and diseased patients and their association with clinical parameters and with red complex bacteria. The study included 60 subjects, with 30 patients each in the healthy and periodontitis groups. The clinical parameters were noted, and samples were subjected to DNA extraction followed by a polymerase chain reaction. Statistical analysis was performed using the Graph Pad Prism software. Results: F. alocis and D. pneumosintes were detected at a significantly higher percentage in the periodontitis group compared to the healthy group (p < 0.05). D. pneumosintes was significantly associated with T. forsythia in the periodontitis group (p < 0.05). Both of these organisms were present in sites with higher clinical attachment loss (p < 0.05). This study demonstrated that both F. alocis and D. pneumosintes were detected at a significantly higher percentage in periodontitis subjects and were detected more frequently in sites with a greater clinical attachment loss. It was also evident that both F. alocis and D. pneumosintes can be present independently of other putative periodontal pathogens.

Occurrence of Aggregatibacter actinomycetemcomitans in Indian chronic periodontitis patients and periodontally healthy adults.

BACKGROUND: Aggregatibacter actinomycetemcomitans (Aa), an important primary periodontal pathogen, is known for its strong virulence characteristics that cause periodontal disease. We investigated Aa occurrence in Indian individuals using culture and 16 s rDNA polymerase chain reaction (PCR). MATERIALS AND METHODS: A cross-sectional study with 100 participants each in the healthy and chronic periodontitis (CP) groups was conducted. The subgingival plaque was collected and immediately plated on selective media for Aa. The remaining plaque samples were used for DNA extraction. PCR was performed using specific primers for Aa. STATISTICAL ANALYSIS USED: The detection of bacteria and the clinical parameters between the groups were compared using the Mann-Whitney U-test. For assessing the agreement between the results of anaerobic culture and PCR, Kappa analyses were performed. RESULTS: Aa levels using culture and PCR was 51% and 69% in the CP group and 12% and 30% in the healthy group, respectively. The two groups showed significant differences (P < 0.00001). The detection accuracy of culture and PCR was assessed, and the coefficient of accuracy (k) was highly significant in the healthy (0.3103; P < 0.0001) and CP groups (0.1536; P < 0.0497). CONCLUSIONS: Aa was predominantly found in the CP group compared with the healthy group, which is consistent with previous findings. Our results showed that both techniques can be used for detecting Aa. An ideal technique for detecting subgingival microorganisms should be carefully selected depending on the scope of the intended future work.

Collagen-collagen interactions mediated by plant-derived proanthocyanidins: A spectroscopic and atomic force microscopy study.

UNLABELLED: Collagen cross-linkings are determinant of biological tissue stability and function. Plant-derived proanthocyanidins (PACs) mimic different hierarchical levels of collagen cross-links by non-enzymatic interactions resulting in the enhancement to the biomechanics and biostability of collagen-rich tissues such as dentin. This study investigated the interaction of PACs from Vitis vinifera grape seed extract with type I collagen in solubilized form and in the demineralized dentin matrix (DDM) by fluorescence spectral analysis; collagen-collagen binding forces in presence of cross-linking solutions by atomic force microscopy (AFM); and spectroscopic analysis of the DDM using attenuated total reflectance Fourier transform-infrared spectroscopy (ATR-FTIR). Glutaraldehyde (GA) and carbodiimide hydrochloride (EDC) with known cross-linking mechanisms were selected for comparative analyses. Changes in fluorescence upon interaction of solubilized type I collagen with PACs, EDC and GA reflected pronounced modifications in collagen conformation. PACs also promoted stronger collagen-collagen fibrils interaction than EDC and GA. A new feature was observed using ATR-FTIR spectroscopic analysis in PACs-treated collagen and DDM. The findings suggest covalent interactions between collagen and PACs. The mechanisms of interaction between PACs-collagen hold attractive and promising tissue-tailored biomedical applications and the binding forces that potentially drive such interaction were characterized. STATEMENT OF SIGNIFICANCE: Connective tissues such as skin, bone and dentin are mainly composed of type I collagen, which is cross-linked to promote tissue stability, strength and function. Novel therapies using substances that mimic cross-links have been proposed to promote repair of collagen-based-tissues. In dentistry, naturally occurring proanthocyanidins (PACs) have the potential to enhance dentin mechanical properties and reduce its enzymatic degradation, but their mechanisms of cross-linking are unclear. The present study investigated the specific interactions between PACs-type I collagen in purified and dentin collagen and compared to the well described cross-linking mechanisms promoted by synthetic chemical substances. Findings reveal that covalent-like bonds are induced by plant PACs in type I collagen as well as in complex dental native tissue, promoting strong collagen-collagen interactions.

Seamless metallic coating and surface adhesion of self-assembled bioinspired nanostructures based on di-(3,4-dihydroxy-L-phenylalanine) peptide motif.

The noncoded aromatic 3,4-dihydroxy-L-phenylalanine (DOPA) amino acid has a pivotal role in the remarkable adhesive properties displayed by marine mussels. These properties have inspired the design of adhesive chemical entities through various synthetic approaches. DOPA-containing bioinspired polymers have a broad functional appeal beyond adhesion due to the diverse chemical interactions presented by the catechol moieties. Here, we harnessed the molecular self-assembly abilities of very short peptide motifs to develop analogous DOPA-containing supramolecular polymers. The DOPA-containing DOPA-DOPA and Fmoc-DOPA-DOPA building blocks were designed by substituting the phenylalanines in the well-studied diphenylalanine self-assembling motif and its 9-fluorenylmethoxycarbonyl (Fmoc)-protected derivative. These peptides self-organized into fibrillar nanoassemblies, displaying high density of catechol functional groups. Furthermore, the Fmoc-DOPA-DOPA peptide was found to act as a low molecular weight hydrogelator, forming self-supporting hydrogel which was rheologically characterized. We studied these assemblies using electron microscopy and explored their applicative potential by examining their ability to spontaneously reduce metal cations into elementary metal. By applying ionic silver to the hydrogel, we observed efficient reduction into silver nanoparticles and the remarkable seamless metallic coating of the assemblies. Similar redox abilities were observed with the DOPA-DOPA assemblies. In an effort to impart adhesiveness to the obtained assemblies, we incorporated lysine (Lys) into the Fmoc-DOPA-DOPA building block. The assemblies of Fmoc-DOPA-DOPA-Lys were capable of gluing together glass surfaces, and their adhesion properties were investigated using atomic force microscopy. Taken together, a class of DOPA-containing self-assembling peptides was designed. These nanoassemblies display unique properties and can serve as multifunctional platforms for various biotechnological applications.

Sequence-dependent force response during peeling of single-stranded DNA from graphite.

We have analyzed the statistical thermodynamics of peeling single-stranded DNA (ssDNA) from the surface of graphite. Using recently measured parameters, we represent ssDNA as a polymer chain strongly adsorbed to a frictionless substrate using the freely jointed chain, wormlike chain, and rotational isomeric state models. All three models predict steady peeling force under force control, in agreement with single-molecule experiments. We predict that, for finite-length chains, the force response has measurable spikes under displacement control. These force spikes carry information about the underlying sequence of ssDNA, which might thus be measurable with a sufficiently stiff loading system. For the freely jointed chain model, under force control, we have obtained several exact closed-form results and provide relations between the measured peel force and the underlying adhesion free energy.

Peeling single-stranded DNA from graphite surface to determine oligonucleotide binding energy by force spectroscopy.

We measured the force required to peel single-stranded DNA molecules from single-crystal graphite using chemical force microscopy. Force traces during retraction of a tip chemically modified with oligonucleotides displayed characteristic plateaus with abrupt force jumps, which we interpreted as a steady state peeling process punctuated by complete detachment of one or more molecules. We were able to differentiate between bases in pyrimidine homopolymers; peeling forces were 85.3 - 4.7 pN for polythymine and 60.8 +/- 5.5 pN for polycytosine, substantially independent of salt concentration and the rate of detachment. We developed a model for peeling a freely jointed chain from the graphite surface and estimated the average binding energy per monomer to be 11.5 +/- 0.6 k(B)T and 8.3 +/- 0.7 k(B)T in the cases of thymine and cytosine nucleotides, respectively. The equilibrium free-energy profile simulated using molecular dynamics had a potential well of 18.9 k(B)T for thymidine, showing that nonelectrostatic interactions dominate the binding. The discrepancy between the experiment and theory indicates that not all bases are adsorbed on the surface or that there is a population of conformations in which they adsorb. Force spectroscopy using oligonucleotides covalently linked to AFM tips provides a flexible and unambiguous means to quantify the strength of interactions between DNA and a number of substrates, potentially including nanomaterials such as carbon nanotubes.