Marras Laboratory

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.

Energy Transfer

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.

molecular beacon

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

Recent Publications

Marras SAE, Tyagi S, Antson D, and Kramer FR (2019) Color-coded molecular beacons for multiplex PCR screening assays. PLoS One 14: e0213906

Vargas DY, Marras SAE, Tyagi S, and Kramer FR (2018) Suppression of wild-type amplification by selectivity enhancing agents in PCR assays that utilize SuperSelective primers for the detection of rare somatic mutations. The Journal of Molecular Diagnostics, 20, 415-427

Schlachter S, Chan K, Marras SAE, and Parveen N (2017) Detection and differentiation of lyme spirochetes and other tick-borne pathogens from blood using real-time PCR with molecular beacons. Methods in Molecular Biology 1616: 155-170.

Catrina IE, Bayer LV, Yanez G, McLaughlin JM, Malaczek K, Bagaeva E, Marras SAE, and Bratu DP (2016) The temporally controlled expression of Drongo, the fruit fly homolog of AGFG1, is achieved in female germline cells via P-bodies and its localization requires functional Rab11. RNA Biology 13: 1117-1132.

Vargas DY, Kramer FR, Tyagi S, and Marras SAE (2016) Multiplex real-time PCR assays that measure the abundance of extremely rare mutations associated with cancer. PLoS ONE 11, e0156546.

We describe the use of SuperSelective primers that enable the detection and quantitation of somatic mutations whose presence relates to cancer diagnosis, prognosis, and therapy, in real-time multiplex PCR assays that can potentially analyze rare DNA fragments present in blood samples (liquid biopsies), thereby providing information that can be used to modify therapy for individual patients, prolonging (and improving the quality of) life.

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