Public Health Research Institute Center and
Dept. Microbiology & Molecular Genetics
New Jersey Medical School
University of Medicine and Dentistry of New Jersey
225 Warren Street
Newark, New Jersey 07103

Phone: (973) 854-3373
e-mail: marrassa@umdnj.edu



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.



For more information on the molecular beacon probe technology, please visit www.molecular-beacons.org




Recent Articles


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

Marras SAE. (2006)
Selection of fluorophore and quencher pairs for fluorescent nucleic acid hybridization probes.
In Didenko VV (ed.), Fluorescent Energy Transfer: Nucleic Acid Probes and Protocols. Humana Press, Totowa, NJ, Vol. 335, pp. 3-16.

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

Vargas DY, Raj A, Marras SAE, Kramer FR, and Tyagi S. (2005)
Mechanism of messenger RNA transport in the nucleus.
Proceedings of the National Academy of Science USA, 102, 17008-17013.

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

Waltz TL, Marras SAE, Rochford G, Nolan J, Lee E, Melegari M, and 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.

Vet JAM and Marras SAE. (2004)
Design and optimization of molecular beacon real-time polymerase chain reaction assays.
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, and Tyagi S. (2004)
Real-time measurement of in vitro transcription.
Nucleic Acids Research, 32, e72.

Varma-Basil M, El-Hajj H, Marras SAE, Hazbon MH, Mann JM, Connell ND, Kramer FR, and Alland D. (2004)
Molecular beacons for multiplex detection of four bacterial bioterrorism agents.
Clinical Chemistry, 50, 1060-1062.

Kuckleburg CJ, Chase CC, Nelson EA, Marras SAE, Dammen A, and Christopher-Hennings J. (2003)
Detection of bovine leukemia virus in blood and milk by nested and real-time polymerase chain reaction.
Journal of Veterinary Diagnostic Investigation, 15, 72-76.

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

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

Nascimento AM, Goldman GH, Park S, Marras SAE, Delmas G, Oza U, Lolans K, Dudley MN, Mann PA, and Perlin DS. (2003)
Multiple resistance mechanisms among Aspergillus fumigatus mutants with high-level resistance to Itraconazole.
Antimicrobial Agents and Chemotherapy, 47, 1719-1726.

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

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

Mathema B, Bifani PJ, Driscoll J, Steinlein L, Kurepina N, Moghazeh SL, Shashkina E, Marras SAE, Campbell S, Mangura B, Shilkret K, Crawford JT, Frothingham R, and Kreiswirth BN. (2002)
Identification and evolution of an IS6110 low-copy-number Mycobacterium tuberculosis cluster.
Journal of Infectious Diseases, 185, 641-649.

Dracheva S, Marras SAE, Elhakem SL, Kramer FR, Davis KL, and 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.

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

Gold B, Rodriguez GM, Marras SAE, Pentecost M, and Smith I. (2001)
The Mycobacterium tuberculosis IdeR is a dual functional regulator that controls transcription of genes involved in iron acquisition, iron storage and survival in macrophages.
Molecular Microbiology, 42, 851-865.

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

Van Beuningen R, Marras SAE, Kramer FR, Oosterlaken T, Weusten J, Borst G, and 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.

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

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

Tyagi S, Marras SAE, Vet JAM, and Kramer FR. (2000)
Molecular beacons: hybridization probes for detection of nucleic acids in homogeneous solutions.
In Kessler C (ed.), Nonradioactive Analysis of Biomolecules, second edition. Springer Verlag, Berlin, Germany, pp. 606-616.

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

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






C.V.


Education

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, University of Medicine and Dentistry 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.