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Scientific Overview Research Interest Summary Principal Investigators    Yuri Bushkin, Ph.D.
   Theresa Chang, Ph.D.
   Neeraj Chauhan, Ph.D.
   Véronique Dartois, Ph.D.
   Thomas Dick, Ph.D.
   Karl Drlica, Ph.D.
   David Dubnau, Ph.D.
   Eliseo A. Eugenin, Ph.D.
   Marila Gennaro, M.D.
   Fred Kramer, Ph.D.
   Barry Kreiswirth, Ph.D.
   Min Lu, Ph.D.
   Leonard Mindich, Ph.D.
   Arkady Mustaev, Ph.D.
   Jyothi Nagajyothi, Ph.D.
   David Perlin, Ph.D.
   Abraham Pinter, Ph.D.
   Marcela Rodriguez, Ph.D.
   Jeanne Salje, Ph.D.
   Lanbo Shi, Ph.D.
   Selvakumar Subbian, Ph.D.
   Sanjay Tyagi, Ph.D.
   Christopher Vinnard, M.D.
   Chaoyang Xue, Ph.D.
   Xilin Zhao, Ph.D.

   Research Faculty
   Liang Chen, Ph.D.
   Eugenie Dubnau, Ph.D.
   Jeanette Hahn, Ph.D.
   Salvatore Marras, Ph.D.
   Yanan Zhao, Ph.D.

Emeritus Faculty Recent Publications
Salvatore A.E. Marras, Ph.D.

Research Summary  |  Selected Publications  |  C.V.

Public Health Research Institute Center and
Dept. Microbiology, Biochemistry & Molecular Genetics
New Jersey Medical School - Rutgers, The State University of New Jersey
225 Warren Street
Newark, New Jersey 07103

Phone: (973) 854-3373
e-mail: marrassa@njms.rutgers.edu
website: www.molecular-beacons.org/toto/Marras_home.html

Research Summary

The introduction of self-quenching fluorescent nucleic acid hybridization probes has markedly improved the ability to detect RNA and DNA sequences with high sensitivity and specificity. Self-quenching probes are useful in situations where it is not possible or desirable to separate probes that are not hybridized to target sequences from probes that are hybridized to target sequences. These probes are used for the real-time monitoring of nucleic acid amplification assays, such as polymerase chain reactions (PCR) and nucleic acid sequence-based amplification (NASBA) assays. Real-time amplification enables the detection and quantitative measurement of rare DNA and RNA targets in clinical samples. Furthermore, these assays can be carried out in sealed reaction tubes, thereby preventing the contamination of untested samples. Since fluorescent nucleic acid hybridization probes remain dark when not hybridized to a target sequence, they also enable the detection of DNA and RNA targets in living cells.

Together with his colleagues, Fred Russell Kramer and Sanjay Tyagi, Salvatore Marras developed molecular beacons, one of the first fluorescent nucleic acid hybridization probe technologies. His research focuses on the different properties of fluorescent hybridization probes, such as design parameters that affect their specificity, and on the effects of interactions between different fluorophore-quencher pairs. His group also develops novel nucleic acid detection methods, including: self-reporting DNA microarray platforms; highly multiplexed, real-time nucleic acid amplification assays for the detection of infectious agents in clinical samples; and extremely sensitive in situ and in vivo hybridization methods, utilizing organic-based fluorescent reporters and metal-based luminescent compounds.

More recently, he co-developed the SuperSelective primer technology, which enables 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). However, SuperSelective primer applications are not limited to cancer diagnosis as they can be used to identify and quantify any rare mutant DNA fragment in a large background of wild-type DNA fragments.

For more information on the research carried out in his laboratory, please visit his web site

Selected Publications

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. The Journal of Molecular Diagnostics 20: 415-427. PMI: 29698835

Schlachter S, Chan K, Marras SAE, 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. PMI: 28600768

Catrina IE, Bayer LV, Yanez G, McLaughlin JM, Malaczek K, Bagaeva E, Marras SAE, 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. PMI: 27654348

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

Stevaert A, Nurra S, Pala N, Carcelli M, Rogolino D, Shepard C, Domaoal RA, Kim B, Alfonso-Prieto M, Marras SAE, Sechi M, Naesens L (2015) An Integrated Biological Approach to Guide the Development of Metal-Chelating Inhibitors of Influenza Virus PA Endonuclease. Molecular Pharmacology 87: 323-337. PMI: 25477342

Chan K, Marras SAE, Parveen N (2013) Sensitive multiplex PCR assay to differentiate Lyme spirochetes and emerging pathogens Anaplasma phagocytophilum and Babesia microti. BMC Microbiology 13: 295. PMI: 24359556

Pilllai S, Kozlov M, Marras SAE, Krasnoperov LN, Mustaev A (2012) The synthesis and characterization of new cross-linkable quinolone and quinoline-based luminescent lanthanide chelates. Progresses in Nanotechnology and Nanomaterials 1: 18-24.

Wirpsza L, Pillai S, Batish M, Marras SAE, Krasnoperov L, Mustaev A (2012) Highly bright avidin-based affinity probes carrying multiple lanthanide chelates. Journal of Photochemistry and Photobiology B: Biology 116: 22-29. PMI: 23018156

Catrina IE, Marras SAE, Bratu DP (2012) Tiny molecular beacons: LNA/2'-O-methyl RNA chimeric probes for imaging dynamic mRNA processes in living cells. ACS Chemical Biology 7: 1586-1595. PMI: 22738327

Pillai S, Kozlov M, Marras SAE, Krasnoperov LN, Mustaev A (2012) New cross-linking quinoline and quinolone derivatives for sensitive fluorescent labeling. Journal of Fluorescence 22: 1021-1032. PMI: 22450725

Dai A, Yang W, Firlar E, Marras SAE, Libera M (2012) Surface-patterned microgel-tethered molecular beacons. Soft Matter 8: 3067-3076. PMI: 0

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. PMI: 22118462

Bratu DP, Catrina IE, Marras SAE (2011) Tiny molecular beacons for in vivo mRNA detection. Methods in Molecular Biology 714: 141-157. PMI: 21431739

Krasnoperov LN, Marras SAE, Kozlov M, Wirpsza L, Mustaev A (2010) Luminescent probes for ultrasensitive detection of nucleic acids. Bioconjugate Chemistry 21: 319-327. PMI: 20085336

Chakravorty S, Aladegbami B, Burday M, Levi M, Marras SAE, Shah D, El-Hajj HH, Kramer FR, Alland D (2010) Rapid universal diagnosis of bacterial pathogens from clinical cultures using a novel sloppy molecular beacon melting temperature signature technique. Journal of Clinical Microbiology 48: 258-267. PMI: 19923485

Saidac DS, Marras SAE, Parveen N (2009) Detection and quantification of Lyme spirochetes using sensitive and specific molecular beacon probes. BMC Microbiololgy 9: 43. PMI: 19239692

Kramer FR, Marras SAE, Tyagi S (2009) In Bustin SA (ed.), The PCR Revolution. Cambridge University Press, Cambridge, pp. 19 - 47.

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

Sinsimer D, Huet G, Manca C, Tsenova L, Koo MS, Kurepina N, Kana B, Mathema B, Marras SAE, Kreiswirth BN, Guilhot C, Kaplan G (2008) The phenolic glycolipid of Mycobacterium tuberculosis differentially modulates the early host cytokine response but does not in itself confer hypervirulence. Infection and Immunity 76: 3027-3036. PMI: 18443098

Marras SAE (2008) Interactive fluorophore and quencher pairs for labeling fluorescent nucleic acid hybridization probes. Molecular Biotechnology 38: 247-255. PMI: 17985254

Marras SAE, Tyagi S, Kramer FR (2006) Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes. Clinica Chimica Acta 363: 48-60. PMI: 16111667

Marras SAE (2006) Selection of fluorophore and quencher pairs for fluorescent nucleic acid hybridization probes. Methods in Molecular Biology 335: 3-16. PMI: 16785616

Waltz TL, Marras SAE, Rochford G, Nolan J, Lee E, Melegari M, Pollack H (2005) Development of a molecular-beacon assay to detect the G1896A precore mutation in hepatitis B virus-infected individuals. Journal of Clinical Microbiology 43: 254-258. PMI: 15634980

Vargas DY, Raj A, Marras SAE, Kramer FR, Tyagi S (2005) Mechanism of mRNA transport in the nucleus. Proceedings of the National Academy of Sciences USA 102: 17008-17013. PMI: 16284251

Sinsimer D, Leekha S, Park S, Marras SAE, Koreen L, Willey B, Naidich S, Musser KA, Kreiswirth BN (2005) Use of a multiplex molecular beacon platform for rapid detection of methicillin and vancomycin resistance in Staphylococcus aureus. Journal of Clinical Microbiology 43: 4585-4591. PMI: 16145111

Vet JAM, Marras SAE (2004) In Herdewijn P (ed.), Oligonucleotide Synthesis: Methods and Applications. Humana Press, Totowa, NJ, Vol. 288, pp. 273-290.

Marras SAE, Gold B, Kramer FR, Smith I, Tyagi S (2004) Real-time measurement of in vitro transcription. Nucleic Acids Research 32: e72. PMI: 15155820

Marras SAE, Kramer FR, Tyagi S (2003) In Kwok PY (ed.), Single Nucleotide Polymorphisms: Methods and Protocols. Humana Press, Totowa, NJ, Vol. 212, pp. 111-128.

Marras SAE (2003) Development of molecular beacons for nucleic acid detection. Doctoral Dissertation, Leiden University, Leiden, the Netherlands.

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 (2002) In Khudyakov YE and Fields HA (eds.), Artificial DNA: Methods and Applications. CRC Press, Boca Raton, FL, pp. 71-89.

Van Beuningen R, Marras SAE, Kramer FR, Oosterlaken T, Weusten J, Borst G, Van de Wiel P (2001) Development of a high-throughput detection system for HIV-1 using real-time NASBA based on molecular beacons. Proceedings - SPIE the International Society for Optical Engineering 4264: 66-71. PMI: 0

Molenaar C, Marras SAE, Slats JC, Truffert JC, Lemaitre M, Raap AK, Dirks RW, Tanke HJ (2001) Linear 2'-O-methyl RNA probes for the visualization of RNA in living cells. Nucleic Acids Research 29: e89. PMI: 11522845

Jones M, Alland D, Marras SAE, El-Hajj H, Taylor MT, McMillan W (2001) Rapid and sensitive detection of Mycobacterium DNA using cepheid SmartCycler (R) and tube lysis system. Clinical Chemistry 47: 1917-1918. PMI: 0

El-Hajj HH, Marras SAE, Tyagi S, Kramer FR, Alland D (2001) Detection of rifampin resistance in Mycobacterium tuberculosis in a single tube with molecular beacons. Journal of Clinical Microbiology 39: 4131-4137.: PMI: 11682541

Dracheva S, Marras SAE, Elhakem SL, Kramer FR, Davis KL, Haroutunian V (2001) N-methyl-D-aspartic acid receptor expression in the dorsolateral prefrontal cortex of elderly patients with schizophrenia. American Journal of Psychiatry 158: 1400-1410.: PMI: 11532724

Van Schie RC, Marras SAE, Conroy JM, Nowak NJ, Catanese JJ, De Jong PJ (2000) Semiautomated clone verification by real-time PCR using molecular beacons. Biotechniques 29: 1296-1308. PMI: 11126133

Tyagi S, Marras SAE, Vet JAM, Kramer FR (2000) In Kessler C (ed.), Nonradioactive Analysis of Biomolecules, second edition. Springer Verlag, Berlin, Germany, pp. 606-616.

Tyagi S, Marras SAE, Kramer FR (2000) Wavelength-shifting molecular beacons. Nature Biotechnology 18: 1191-1196.: PMI: 11062440

Park S, Wong M, Marras SAE, Cross EW, Kiehn TE, Chaturvedi V, Tyagi S, Perlin DS (2000) Rapid identification of Candida dubliniensis using a species-specific molecular beacon. Journal of Clinical Microbiology 38: 2829-2836.: PMI: 10921935

Vet JAM, Majithia AR, Marras SAE, Tyagi S, Dube S, Poiesz BJ, Kramer FR (1999) Multiplex detection of four pathogenic retroviruses using molecular beacons. Proceedings of the National Academy of Sciences USA 96: 6394-6399.: PMI: 10339598

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



Doctoral Degree, cum laude, Leiden University, Leiden, The Netherlands, 2003.
Bachelor of Science, Higher Professional Laboratory Education, Nijmegen, The Netherlands, 1994.

Professional experience

Assistant Professor of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers - The State University of New Jersey, 2006 – present. Senior Research Associate, Department of Molecular Genetics, Public Health Research Institute, 2000 – present. Research Associate, Department of Molecular Genetics, Public Health Research Institute, 1996 – 2000. Research Technician, Department of Urology, Rheinisch-Westfälischen Technischen Hochschule Aachen, Aachen, Germany, 1994 – 1996.

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