Our Research

In the laboratory, which I share with Fred Russell Kramer and Sanjay Tyagi, we are exploring and developing self-quenching fluorescent nucleic acid hybridization probes. The introduction of these probes has made it possible to detect RNA and DNA molecules in vitro, in vivo, in situ, and in silico with high sensitivity and specificity. My research focuses on the different properties of fluorescent nucleic acid hybridization probes. For example, my group studies the effect of the probe's backbone chemistry (DNA, 2'-O-methyl-RNA, or LNA) on nucleic acid hybridization. In addition, we study the interactions between fluorophore and quencher pairs, which are being used as labels in these probes.

We also develop novel nucleic acid detection methods and assays, which include highly multiplexed real-time nucleic acid amplification assays for clinical diagnostic detection of infectious agents, extremely sensitive, luminescent based in-situ and in-vivo hybridization methods, and self-reporting DNA micro array platforms.

The work in our group has lead to the developed of the molecular beacon probe, one of the first fluorescent nucleic acid hybridization probe technologies. Molecular beacons have found their application in real-time monitoring of nucleic acid amplification assays, such as the Polymerase Chain Reaction (PCR) and Nucleic Acid Sequence Based Amplification (NASBA) assays, which are being utilized in clinical diagnostics and research & development. Real-time nucleic acid amplification assays provide both qualitative and quantitative information on rare RNA and DNA target sequences. Furthermore, these assays can be carried out in sealed tubes, thereby eliminating carryover contamination. Since molecular beacons remain dark when not hybridized to a nucleic acid target sequence, they also enable detection of DNA and RNA targets in living cells. You can find more information on molecular beacons, what they are, and what they can do, on the following web site www.molecular-beacons.org.

Recent Publications

In collaboration with Arkady Mustaev at PHRI, we published on the synthesis of new fluorescent quinoline and quinilone compounds, which can be used to label a variaty of bio-molecules.

Pillai S, Kozlov M, Marras SAE, Krasnoperov LN, and Mustaev A (2012) New cross-linking quinoline and quinolone derivatives for sensitive fluorescent labeling. Journal of Fluorescence, published online ahead of print on March 27, 2012

In the March 21, 2012 issue of Soft Matter, we published our results on a novel self-reporting microarray platform, in which molecular beacons are immobilized within highly hydrated microhydrogels.

Dai A, Yang W, Firlar E, Marras SAE, and Libera M (2012) Surface-patterned microgel-tethered molecular beacons. Soft Matter 8, 3067-3076.

In the November 23, 2011 issue of Cell, using our unique single-molecule imaging approach, we describe circumstances under which splicing is uncoupled from transcription. An interview conducted by Cell's editorial staff with Sanjay Tyagi about this work can be listened to at www.cell.com/../paperclip.mp3

Vargas DY, Shah K, Batish M, Levandoski M, Sinha S, Marras SAE, Schedl P, Tyagi S (2011) Single-molecule imaging of transcriptionally coupled and uncoupled splicing Cell 147, 1054-1065.