Overview

Dr. Marras research has focused on developing fluorogenic probes for nucleic acid detection in nucleic acid amplification assays, on solid surfaces, and
in live and fixed cells. For the last two decades, he collaborated with Drs. Sanjay Tyagi and Fred Kramer on fluorescent nucleic acid hybridization
probes, specializing in molecular beacon probes. He contributed to the molecular beacon probe technology by establishing the thermodynamic
parameters for their design, studying the mechanism of fluorescence energy transfer between fluorescent labels and fluorescence quenchers, and co-
developing "color-coded," "sloppy," and "wavelength-shifting" molecular beacon probes. Since 2006, he has been an independent faculty member at
PHRI and has shared laboratory space with Drs. Tyagi and Kramer. He collaborated with many different groups in academics and industry on designing,
optimizing, and troubleshooting real-time nucleic acid amplification assays - PCR and isothermal-based assays (NASBA, NEAR, and LAMP). He co-
invented SuperSelective primer technology, which enables the detection and quantification of somatic mutations, whose presence relates to cancer
diagnosis, prognosis, and therapy, in real-time multiplex PCR assays that are able to analyze rare DNA fragments present in liquid biopsies. However,
SuperSelective primer applications are not limited to cancer diagnosis; they can also be used to identify and quantify rare mutant DNA fragments in the
presence of a large background of wild-type DNA fragments. He is a co-inventor on 15 issued US patents and their international counterparts,
describing novel fluorescent nucleic acid hybridization probes, hybridization strategies, and PCR primers for nucleic acid amplification. He established a
DNA Synthesis Core Facility at PHRI. The facility includes a K&A H-4 oligonucleotide synthesizer, which simultaneously synthesizes four multi-labeled
probes and/or primers, two HPLC systems for probe purification, and a real-time thermal cycler for pilot PCR assay validation. The time from design to
validating probes and primers in a PCR assay is less than 36 hours. His expertise in the design and synthesis of oligonucleotides, multi-labeled nucleic
acid hybridization probes, fluorescence chemistry, and quantitative real-time nucleic acid amplification assays is instrumental in establishing multiplex
PCR assays for any genotype and for pathogen identification.

Education

PHD, 2003, Leiden, The Netherlands, Not Available
BS, 1994, Niejmegen, The Netherlands, Not Available

Relevant Publications

Dikdan RJ, Marras SAE, Field AP, Brownlee A, Cironi A, Hill DA, and Tyagi S (2022) Multiplex PCR Assays for Identifying all Major Severe Acute Respiratory Syndrome Coronavirus 2 Variants. Journal of Molecular Diagnostics 24: 309-319. PMID: 35121139

Narang A, Marras SAE, Kurepina N, Chauhan V, Shashkina E, Kreiswirth B, Varma-Basil M, Vinnard C, and Subbian S (2022) Ultrasensitive detection of multidrug-resistant Mycobacterium tuberculosis using SuperSelective primer-based real-time PCR assays. International Journal of Molecular Sciences 23(24): 1575223. PMID: 36555395

Marras SAE, Chen L, Shashkina E, Davidson RM, Strong M, Daley CL, Kreiswirth BN (2021) A Molecular- Beacon-Based Multiplex Real-Time PCR Assay To Distinguish Mycobacterium abscessus Subspecies and Determine Macrolide Susceptibility. Journal of Clinical Microbiology 59: e0045521. PMI: 33980653

Marras SAE, Bushkin Y, Tyagi S (2019) High-fidelity amplified FISH for the detection and allelic discrimination of single mRNA molecules. Proceedings of the National Academy of Sciences USA 128: 13921'13926. PMI: 31221755

Marras SAE, Tyagi S, Antson DO, Kramer FR (2019) Color-coded molecular beacons for multiplex PCR screening assays. PLoS One 14: e0213906. PMI: 30883590

Vargas DY, Marras SAE, Tyagi S, 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. Journal of Molecular Diagnostics 20: 415-427. PMI: 29698835

Vargas DY, Kramer FR, Tyagi S, Marras SAE (2016) Multiplex real-time PCR assays that measure the abundance of extremely rare mutations associated with cancer. PLoS One 11: e0156546. PMI: 27244445

El-Hajj HH, Marras SAE, Tyagi S, Shashkina E, Kamboj M, Kiehn TE, Glickman MS, Kramer FR, Alland D (2009) Use of sloppy molecular beacon probes for identification of mycobacterial species. Journal of Clinical Microbiology 47: 1190-1198. PMI: 19171684

Marras SAE, Kramer FR, Tyagi S (2002) Efficiencies of fluorescence resonance energy transfer and contact- mediated quenching in oligonucleotide probes. Nucleic Acids Research 30: e122. PMI: 12409481

Marras SAE, Kramer FR, Tyagi S (1999) Multiplex detection of single-nucleotide variations using molecular beacons. Genetic Analysis: Biomolecular Engineering 14: 151-156.: PMI: 10084107

Course List

Development of nucleic acid amplification methods

Dr. Marras research has focused on developing fluorogenic probes for nucleic acid detection in nucleic acid amplification assays, on solid surfaces, and in live and fixed cells. For the
last two decades, he collaborated with Drs. Sanjay Tyagi and Fred Kramer on fluorescent nucleic acid hybridization probes, specializing in molecular beacon probes. He contributed
to the molecular beacon probe technology by establishing the thermodynamic parameters for their design, studying the mechanism of fluorescence energy transfer between
fluorescent labels and fluorescence quenchers, and co-developing "color-coded," "sloppy," and "wavelength-shifting" molecular beacon probes. Since 2006, he has been an
independent faculty member at PHRI and has shared laboratory space with Drs. Tyagi and Kramer. He collaborated with many different groups in academics and industry on
designing, optimizing, and troubleshooting real-time nucleic acid amplification assays - PCR and isothermal-based assays (NASBA, NEAR, and LAMP). He co-invented
SuperSelective primer technology, which enables the detection and quantification of somatic mutations, whose presence relates to cancer diagnosis, prognosis, and therapy, in real-
time multiplex PCR assays that are able to analyze rare DNA fragments present in liquid biopsies. However, SuperSelective primer applications are not limited to cancer diagnosis;
they can also be used to identify and quantify rare mutant DNA fragments in the presence of a large background of wild-type DNA fragments. He is a co-inventor on 15 issued US
patents and their international counterparts, describing novel fluorescent nucleic acid hybridization probes, hybridization strategies, and PCR primers for nucleic acid amplification.
He established a DNA Synthesis Core Facility at PHRI. The facility includes a K&A H-4 oligonucleotide synthesizer, which simultaneously synthesizes four multi-labeled probes and/or
primers, two HPLC systems for probe purification, and a real-time thermal cycler for pilot PCR assay validation. The time from design to validating probes and primers in a PCR assay
is less than 36 hours. His expertise in the design and synthesis of oligonucleotides, multi-labeled nucleic acid hybridization probes, fluorescence chemistry, and quantitative real-time
nucleic acid amplification assays is instrumental in establishing multiplex PCR assays for any genotype and for pathogen identification.