Saswata Karmakar

Invaders: Recognition of Double‐Stranded DNA by Using Duplexes Modified with Interstrand Zippers of 2′‐O‐(Pyren‐1‐yl)methyl‐ribonucleotides

The invasion has begun: Invaders are shown to recognize DNA hairpins in cell-free assays and chromosomal DNA during non-denaturing fluorescence in situ hybridization (nd-FISH) experiments. As Invaders are devoid of inherent sequence limitations, many previously inaccessible DNA targets could become accessible to exogenous control with important ramifications for karyotyping, in vivo imaging, and gene regulation.

Sandwich assay for mixed-sequence recognition of double-stranded DNA: Invader-based detection of targets specific to foodborne pathogens

A 96-well plate sandwich assay based on Invader capture/signalling probes is used to recognize 28-mer mixed-sequence dsDNA targets specific to Salmonella enterica, Campylobacter jejuni, Escherichia coli. Targets are detected down to 20-55 pM concentration with excellent binding specificity.

Self-Assembled Monolayers of Thiols Adsorbed on Au/ZnO-Functionalized Silica Nanosprings: Photoelectron Spectroscopy-Analysis and Detection of Vaporized Explosives

Self-assembled monolayers (SAMs) of thiols of L-cysteine, 6-mercaptohexanol, 4-mercaptobenzoic acid, DL-thioctic acid and 11-(1-pyrenyl)-1-undecathiol, which have been selected for their propensity to interact with vaporized explosives, have been attached from solution onto gold decorated ZnO-coated nanosprings. X-ray and ultraviolet photoelectron spectroscopies (XPS and UPS) have been used to investigate the surface electronic structure of the SAMs coated nanosprings. On the basis of XPS analysis, it has been determined that the packing densities of L-cysteine, 6-mercaptohexanol, 4-mercaptobenzoic acid, DL-thioctic acid and 11-(1-pyrenyl)-1-undecathiol on gold (zinc oxide) are 5.42 × 10(14) (2.83 × 10(14)), 3.26 × 10(14) (2.54 × 10(14)), 9.50 × 10(13), 2.55 × 10(14) (1.12 × 10(14)), and 5.23 × 10(13) molecules/cm(2), respectively. A single S 2p core level doublet is observed for 4-mercaptobenzoic acid and 11-(1-pyrenyl)-1-undecathiol, which is assigned to the S-Au bond. The S 2p core level for L-cysteine, 6-mercaptohexanol, and DL-thioctic acid consist of two doublets, where one is S-Au bond and the other is the S-Zn bond. Analysis of the C/S ratios agrees well with the stoichiometry of the respective thiols. UPS analysis shows that the hybridization of S 3p states and Au d-bands produces antibonding and bonding states, above and below the Au d-bands, which is characteristic of molecular chemisorption on Au nanoparticles. Gas sensors were constructed with thiolated nanosprings and their responsiveness to ammonium nitrate at 100-150 °C was tested. Nanosprings sensors functionalized with 4-mercaptobenzoic acid and 6-mercaptohexanol showed the strongest responses by a factor of 4 to 5 relative to the less responsive thiols. The response to ammonium nitrate can be correlated to the packing density and ordering of the SAMs.

Mixed-Sequence Recognition of Double-Stranded DNA Using Enzymatically Stable Phosphorothioate Invader Probes

Development of probes that allow for sequence-unrestricted recognition of double-stranded DNA (dsDNA) continues to attract much attention due to the prospect for molecular tools that enable detection, regulation, and manipulation of genes. We have recently introduced so-called Invader probes as alternatives to more established approaches such as triplex-forming oligonucleotides, peptide nucleic acids and polyamides. These short DNA duplexes are activated for dsDNA recognition by installment of +1 interstrand zippers of intercalator-functionalized nucleotides such as 2′-N-(pyren-1-yl)methyl-2′-N-methyl-2′-aminouridine and 2′-O-(pyren-1-yl)methyluridine, which results in violation of the nearest neighbor exclusion principle and duplex destabilization. The individual probes strands have high affinity toward complementary DNA strands, which generates the driving force for recognition of mixed-sequence dsDNA regions. In the present article, we characterize Invader probes that are based on phosphorothioate backbones (PS-DNA Invaders). The change from the regular phosphodiester backbone furnishes Invader probes that are much more stable to nucleolytic degradation, while displaying acceptable dsDNA-recognition efficiency. PS-DNA Invader probes therefore present themselves as interesting probes for dsDNA-targeting applications in cellular environments and living organisms.