Fred Russell Kramer, Ph.D.

Professor of Microbiology, Biochemistry & Molecular Genetics   |  view CV |  Laboratory Website

room W310-A


Our group latest publication shows that SuperSelective primer pairs enhance the sensitivity of multiplex PCR assays that identify and quantitate somatic mutations in liquid biopsies obtained from patients with cancer, thereby enabling the choice of a targeted therapy, the determination of its effectiveness over time, and the substitution of a more appropriate therapy as new mutations arise.  Kramer FR, Vargas DY (2021) SuperSelective primer pairs for sensitive detection of rare somatic mutations. Scientific Reports 11: 22384.  Open Access article at:

Our laboratory is developing sensitive, multiplex polymerase chain reaction assays that utilize the DNA fragments transiently occurring in blood samples to detect and quantitate rare somatic mutations that are indicative of cancer diagnosis, prognosis, and therapy.  These assays employ specialized PCR primers that selectively amplify mutant DNA fragments without amplifying the almost identical DNA fragments that come from normal cells.  Because these assays are non-invasive and inexpensive, a patient can be followed over the course of treatment, enabling individualized adjustments in therapy to be made as new somatic mutations occur, resulting in longer life with fewer symptoms.  Our long-term goal is to design an assay that can be carried out on a blood sample obtained during a routine annual medical examination that identifies actionable somatic mutations indicative of cancer anywhere in a person’s body, even though no symptoms have yet occurred.

View all on PubMed

Kramer FR, Vargas DY (2021) SuperSelective primer pairs for sensitive detection of rare somatic mutations. Scientific Reports 11: 22384

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

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. J Mol Diagn 20: 415-427

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

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

El-Hajj HH, Marras SA, 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. J Clin Microbiol 47: 1190-1198. PMI: 19171684

Vargas DY, Raj A, Marras SA, Kramer FR, Tyagi S (2005) Mechanism of mRNA transport in the nucleus. Proc Natl Acad Sci U S A 102: 17008-17013. PMI: 16284251

Varma-Basil M, El-Hajj H, Marras SA, Hazbon MH, Mann JM, Connell ND, Kramer FR, Alland D (2004) Molecular beacons for multiplex detection of four bacterial bioterrorism agents. Clin Chem 50: 1060-1062. PMI: 15161722

Bratu DP, Cha BJ, Mhlanga MM, Kramer FR, Tyagi S (2003) Visualizing the distribution and transport of mRNAs in living cells. Proc Natl Acad Sci U S A 100: 13308-13313. PMI: 14583593

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

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

Vet JA, Majithia AR, Marras SA, Tyagi S, Dube S, Poiesz BJ, Kramer FR (1999) Multiplex detection of four pathogenic retroviruses using molecular beacons. Proc Natl Acad Sci U S A 96: 6394-6399. PMI: 10339598

Marras SA, Kramer FR, Tyagi S (1999) Multiplex detection of single-nucleotide variations using molecular beacons. Genet Anal 14: 151-156. PMI: 10084107

Bonnet G, Tyagi S, Libchaber A, Kramer FR (1999) Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc Natl Acad Sci U S A 96: 6171-6176. PMI: 10339560

Tyagi S, Bratu DP, Kramer FR (1998) Multicolor molecular beacons for allele discrimination. Nat Biotechnol 16: 49-53. PMI: 9447593

Kostrikis LG, Tyagi S, Mhlanga MM, Ho DD, Kramer FR (1998) Spectral genotyping of human alleles. Science 279: 1228-1229. PMI: 9508692

Tyagi S, Landegren U, Tazi M, Lizardi PM, Kramer FR (1996) Extremely sensitive, background-free gene detection using binary probes and beta replicase. Proc Natl Acad Sci U S A 93: 5395-5400. PMI: 8643586

Tyagi S, Kramer FR (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 14: 303-308. PMI: 9630890

Chetverin AB, Kramer FR (1993) Sequencing of pools of nucleic acids on oligonucleotide arrays. Biosystems 30: 215-231. PMI: 8374077

Lomeli H, Tyagi S, Pritchard CG, Lizardi PM, Kramer FR (1989) Quantitative assays based on the use of replicatable hybridization probes. Clin Chem 35: 1826-1831. PMI: 2673578

Miele EA, Mills DR, Kramer FR (1983) Autocatalytic replication of a recombinant RNA. J Mol Biol 171: 281-295. PMI: 6655695

Kramer FR, Mills DR (1981) Secondary structure formation during RNA synthesis. Nucleic Acids Res 9: 5109-5124. PMI: 6171773

Mills DR, Kramer FR (1979) Structure-independent nucleotide sequence analysis. Proc Natl Acad Sci U S A 76: 2232-2235. PMI: 287063

Mills DR, Dobkin C, Kramer FR (1978) Template-determined, variable rate of RNA chain elongation. Cell 15: 541-550. PMI: 719752

Kramer FR, Mills DR (1978) RNA sequencing with radioactive chain-terminating ribonucleotides. Proc Natl Acad Sci U S A 75: 5334-5338. PMI: 281683

Kramer FR, Mills DR, Cole PE, Nishihara T, Spiegelman S (1974) Evolution in vitro: sequence and phenotype of a mutant RNA resistant to ethidium bromide. J Mol Biol 89: 719-736. PMI: 4449129

Mills DR, Kramer FR, Spiegelman S (1973) Complete nucleotide sequence of a replicating RNA molecule. Science 180: 916-927. PMI: 4706684

Kacian DL, Mills DR, Kramer FR, Spiegelman S (1972) A replicating RNA molecule suitable for a detailed analysis of extracellular evolution and replication. Proc Natl Acad Sci U S A 69: 3038-3042. PMI: 4507621

Davidson EH, Crippa M, Kramer FR, Mirsky AE (1966) Genomic function during the lampbrush chromosome stage of amphibian oogenesis. Proc Natl Acad Sci U S A 56: 856-863. PMI: 16578646