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2012 – to date    History and Philosophy of Biology

1993 – 2012       Quadruplex Nucleic Acids Interacting Proteins;

                           Fragile X Syndrome

1972 – 2012      Eukaryotic DNA Processing Enzymes;

                           DNA Interacting Proteins

1966 – 1972       Metabolism of Bacterial and Phage RNA



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History and Philosophy of Biology

Refereed Papers

Fry, M. Ontologically simple theories do not indicate the true nature of complex biological systems: three test cases. Hist. Phil. Life Sci. 42: (2020) 17., 44 pp.

Fry, M. Crick’s adaptor hypothesis and the discovery of transfer RNA: Experiment surpassing theoretical prediction. (2020) revision submitted

Fry, M. Predictive hypotheses are ineffectual in resolving complex biochemical systems. Hist. Phil. Life Sci.  40: (2018) 25.,  46 pp.

Fry, M. Dissolution of hypotheses in biochemistry: case studies. Hist. Phil. Life Sci.  38: (2016) 17., 40 pp.

Authored Book

Fry, M. Landmark Experiments in Molecular Biology. Elsevier/Academic Press,   Amsterdam, Boston, Heidelberg, ISBN: 9780128020746 (2016) 570 pp.


Eukaryotic DNA Processing Enzymes and DNA Interacting Proteins

Refereed Papers

Kamath-Loeb, A.S., Shen, J.-C., Loeb, L.A., and Fry, M. Werner syndrome protein:  2) Characterization of the integral 3’→5’ DNA exonuclease.  J. Biol. Chem. 273: (1998) 34145-34150

Shen, J.-C., Gray, M.D., Kamath-Loeb, A., Oshima, J., Fry, M., and Loeb, L.A. Werner syndrome protein: 1) DNA helicase and DNA exonuclease reside on the same polypeptide.  J. Biol. Chem. 273: (1998) 34139-34144

Hoffman, J.S., Fry, M., Ji, J., Williams, K., and Loeb, L.A.  Codons 12 and 13 of H-ras proto-oncogene interrupt the progression of DNA synthesis catalyzed by DNA polymerase α.  Cancer Res. 53: (1993) 2895-2900

Fry, M., and Loeb, L.A.  A DNA polymerase α pause site is a hot spot for nucleotide misinsertion.  Proc. Natl. Acad. Sci. USA 89: (1992) 763-767

Williams, K.J., Loeb, L.A., and Fry, M.  Synthesis of DNA by human immunodeficiency virus reverse transcriptase is specifically blocked at template oligo(deoxyadenosine) tracts.  J. Biol. Chem. 265: (1990) 18682-186

Weisman-Shomer, P., Dube, D., Perrino, F.W., Stokes, K., Loeb, L.A., and Fry, M. Sequence-specificity of the pausing of DNA polymerases.  Biochem. Biophys. Res. Commun. 164: (1989) 1149-1156

Asna, N., Weisman-Shomer, P., Waldman, E., and Fry, M.  Factor C from rabbit liver: A new poly(dC) and poly[d(G-C)] template-selective stimulatory protein of DNA polymerases.  J. Biol. Chem. 264: (1989) 5245-5252

Fry, M., Perrino, F.W., Levy, A., and Loeb, L.A.  Factor D is a selective single strand oligothymidine binding protein.  Nucleic Acids Res. 16: (1988) 199-211

Sharf, R., Weisman-Shomer, P., and Fry, M.  Rabbit liver factor D: A poly(thymidine) template stimulatory protein of DNA polymerases:  Purification and characterization.  Biochemistry 27: (1988) 2990-2997

Fry, M., Sharf, R., Weisman-Shomer, P., Evers, P. C., and Loeb, L.A.  The sequence specificity of stimulation of DNA polymerases by factor D.  J. Biol. Chem. 262: (1987) 8868-8874

Fry, M., Weisman-Shomer, P., Lapidot, J., and Sharf, R. Template-selective stimulation of diverse DNA polymerases by the murine DNA binding protein factor D. J. Biol. Chem. 262: (1987) 8861-8867

Fry, M., Lapidot, J., and Weisman-Shomer, P. A DNA template recognition protein: Partial purification from mouse liver and stimulation of DNA polymerase α. Biochemistry 24: (1985) 7549-7556

Silber, J.A., Fry, M., and Loeb, L.A.  Fidelity of DNA polymerases isolated from regenerating liver chromatin of Mus musculus.  J. Biol. Chem. 260: (1985) 1304-1310

Fry, M., Silber, J.A., Loeb, L.A., and Martin, G.M.  Delayed and reduced cell replication and diminished levels of DNA polymerase α in regenerating livers of aging mice.  J. Cell. Physiol. 118: (1984) 225-232

Fry, M., Shearman, C.W., Martin, G.M., and Loeb, L.A.  On the accuracy of DNA synthesis directed by chromatin-associated DNA polymerase β. Biochemistry 19: (1980) 5939-5942

Kaftory, A. and Fry, M.   Highly efficient copying of single-stranded DNA by eukaryotic cell chromatin.  Nucleic Acids Res. 5: (1978) 2679-2693

Fry, M. and Weisman-Shomer, P.  Altered deoxyribonucleic acid a-polymerase in senescent cultured chick embryo fibroblasts.  Biochemistry 15: (1976) 4319-4329

Fry, M. and Weissbach, A.  The utilization of synthetic DNA templates by a new DNA polymerase from culture murine cells.  J. Biol. Chem. 248: (1973) 2678-2683

Fridlender, B., Fry, M., Bolden, A., and Weissbach, A.  A new synthetic RNA-dependent DNA polymerase from human tissue culture cells.  Proc. Natl. Acad. Sci. USA 69: (1972) 452-455

Authored Book

Fry, M. and Loeb, L.A.  Animal Cell DNA Polymerases.  CRC Press, Boca Raton, Fl ISBN: 0-849-36507-4 (1986) 221 pp.

Book Chapters and Review Articles

Kamath-Loeb, A.S., Fry, M., and Loeb, L.A. DNA helicases in human disease.  in: DNA Replication and Human Disease DePamphilis, M.L., ed., (ISBN-0-87969-766-0) Cold Spring Harbor Laboratory Press, New York (2006) pp. 435-460

Fry, M. Biochemical characterization of Werner syndrome exonuclease and helicase. In: Molecular Mechanisms of Werner Syndrome Lebel, M., ed., (ISBN-0-306-4823-9) Landes Bioscience, Georgetown, TX. (2004) pp. 22-43

Fry, M. The Werner syndrome helicase-nuclease – one protein, many mysteries. Science SAGE KE (2002) 10 pp.;2002/13/re2

Fry, M. and Loeb, L.A.  The three faces of the WS helicase. Nature Genet. 19: (1998) 308-309

Loeb, L.A., Liu, P.K. and Fry, M.  DNA polymerase a enzymology, function, fidelity and mutagenesis. Prog. Nucleic Acids Res. Mol. Biol.  33: (1986) 57-110

Fry, M. Eukaryotic DNA polymerases.  in: Enzymes of Nucleic Acids Synthesis and Modification (Jacob, S.T., ed., ISBN 08493-5517-6) CRC Press, Boca Raton, Fl. (1983) pp. 39-92


Quadruplex Nucleic Acids Interacting Proteins; Fragile X Syndrome

Refereed Papers

Kamath-Loeb, A., Loeb, L.A., and Fry, M. The Werner syndrome protein is distinguished from the Bloom syndrome protein by its capacity to tightly bind diverse DNA structures. PLoS ONE  7: (2012) e30189. doi:10.1371/journal.pone.003018

Shklover, J., Weisman-Shomer, P., Yafe, A. and Fry, M. Quadruplex structures of muscle gene promoter sequences enhance in vivo MyoD-dependent gene expression. Nucleic Acids Res. 38: (2010) 2369-2377

Ofer, N., Weisman-Shomer, P., Shklover, J., and Fry, M. The quadruplex  r(CGG)n destabilizing cationic porphyrin TMPyP4 cooperates with hnRNPs to increase the translation efficiency of fragile X premutation mRNA. Nucleic Acids Res. 37: (2009) 2712-2722

Yafe, A., Shklover, J., Weisman-Shomer, P., Bengal, E., and Fry, M. Differential binding of quadruplex structures of muscle-specific genes regulatory sequences by MyoD, MRF4 and Myogenin. Nucleic Acids Res. 36: (2008) 3916-3925

Shkolver, J., Etzioni, S., Weisman-Shomer, P., Yafe, A., Bengal, E., and Fry, M. MyoD uses overapping but distinct elements to bind E-box and tetraplex structures of regulatory sequences of muscle-specific genes. Nucleic Acids Res. 35: (2007) 7087-7095

Khateb, S., Weisman-Shomer, P., Hershco-Shani, I., Ludwig, A.L., and Fry, M. The tetraplex (CGG)n destabilizing proteins hnRNP A2 and CBF-A enhance the in vivo translation of fragile X premutation mRNA. Nucleic Acids Res. 35: (2007) 5775-5788

Etzioni, S., Yafe, A., Khateb, S., Weisman-Shomer, P., Bengal, E., and Fry, M. Homodimeric MyoD binds preferentially tetraplex structures of regulatory sequences of muscle-specific genes.   J. Biol. Chem. 280: (2005) 26805-26812

Yafe, A., Etzioni, S., Weisman-Shomer, P., and Fry, M. Formation and properties of hairpin and tetraplex structures of guanine-rich regulatory sequences of muscle-specific genes.  Nucleic Acids Res. 33: (2005) 2877-2900

Khateb, S., Weisman-Shomer, P., Hershco, I., Loeb, L.A., and Fry, M.  Destabilization of tetraplex structures of the fragile X repeat sequence (CGG)n is mediated by homolog conserved domains in three members of the hnRNP family. Nucleic Acids Res. 32: (2004) 4145-4154

Weisman-Shomer, P., Cohen, E., Hershco, I., Khateb, S., Wolfovitz-Barchad, O., Hurley, L.H., and Fry, M.  The cationic porphyrin TMPyP4 destabilizes tetraplex form of the fragile X syndrome expanded sequence d(CGG)n. Nucleic Acids Res. 31: (2003) 3963-3970

Weisman-Shomer, P., Cohen, E., and Fry, M. Distinct domains in the CArG-box binding factor-A destabilize tetraplex forms of the fragile X expanded sequence d(CGG)nNucleic Acids Res. 30: (2002) 3672-3681

Kamath-Loeb, A.S., Loeb, L.A., Johansson, E., Burgers, P.M.J., and Fry, M. interactions between the Werner syndrome helicase and DNA polymerase d facilitate copying of tetraplex and hairpin structures of the d(CGG)n trinucleotide repeat sequence.  J. Biol. Chem. 276: (2001) 16439-16446

Uliel, L., Weisman-Shomer, P., Oren-Jazan, H., Newcomb, T., Loeb, L.A., and Fry, M. Human Ku antigen tightly binds and stabilizes a tetrahelical form of the fragile X syndrome d(CGG)n expanded sequence. J. Biol. Chem. 275: (2000) 33134-33141

Weisman-Shomer, P., Cohen, E. and Fry, M.  Interruption of the fragile X   syndrome expanded sequence d(CGG)n by interspersed d(AGG) trinucleotides   diminishes the formation and stability of d(CGG)n tetrahelical structures. Nucleic Acids Res. 28: (2000) 1535-1541

Weisman-Shomer, P., Naot, Y. and Fry, M.  Tetrahelical forms of the fragile X syndrome expanded sequence d(CGG)n are destabilized by two hnRNP-related telomeric DNA binding proteins qTBP42 and uqTBP25.  J. Biol. Chem. 275: (2000) 2231-2238

Fry, M. and Loeb, L.A.  Human Werner syndrome DNA helicase unwinds tetrahelical structures of the fragile X syndrome repeat sequence d(CGG)n. J. Biol. Chem. 274: (1999) 12797-12803

Sarig, G., Weisman-Shomer, P. and Fry, M.  Telomeric and tetraplex DNA binding properties of qTBP42: a homolog of the CArG box binding protein CBF-A. Biochem. Biophys. Res. Commun. 237: (1997) 617-623

Erlitzki, R. and Fry, M.  Sequence-specific binding protein of single strand and unimolecular quadruplex telomeric DNA from rat hepatocytes.  J. Biol. Chem. 272: (1997) 15881-15890

Sarig, G., Weisman-Shomer, P., Erlitzki, R. and Fry, M. Purification and characterization of qTBP42, a new single strand and quadruplex telomeric DNA binding protein from rat hepatocytes.  J. Biol. Chem. 272: (1997) 4474-4482

Nadel, Y., Weisman-Shomer, P. and Fry, M.  The Fragile X syndrome single-strand d(CGG)n nucleotide repeats readily fold-back to form unimolecular hairpin structures.  J. Biol. Chem. 270: (1995) 28970-28978

Weisman-Shomer, P. and Fry, M.  Stabilization of tetrahelical DNA by the quadruplex DNA binding protein QUAD.  Biochem. Biophys. Res. Commun. 205: (1994) 305-311

Fry, M. and Loeb, L. A.  The fragile X syndrome d[CGG]n nucleotide repeats form a stable tetrahelical structure.  Proc. Natl. Acad. Sci. USA 91: (1994) 4950-4954

Weisman-Shomer, P. and Fry, M.  QUAD, a protein from hepatocyte chromatin that binds selectively to guanine-rich tetrahelical DNA. J. Biol. Chem. 268: (1993) 3306-3312

Edited Book

Fry, M. and Usdin, K. Human Nucleotide Expansion Disorders. (Vol. 19 in a Nucleic Acids and Molecular Biology Series. Gross, H.G., ed., ISBN: 3-540-33335-5. Springer, Berlin, Heidelberg, New York (2006) 292 pp.

Book Chapters and Review Articles

Fry, M. Regulation of gene transcription by DNA G-quadruplexes. In: Guanine Quartets: Structure and Application L. Spindler and W. Fritzsche, eds., ISBN: 978-1-84973-695-4. Royal Society of Chemistry Publishing (2012) pp. 223-236

Fry, M. Tetraplex DNA and its interacting proteins. Frontiers in Bioscience 12: (2007) 4336-4351

Dexheimer, T.S., Fry, M. and Hurley, L.H. DNA quadruplexes and gene regulation.  In: Quadruplex Nucleic Acids S. Balasubramanian and S. Neidle, eds., ISBN-10: 0-85404-374-8. Royal Society of Chemistry Publishing (2006) pp. 180-202


Metabolism of Bacterial and Phage RNA

Refereed Papers

Fry, M., Israeli-Reches, M., and Artman, M. Messenger RNA of phage infected E. coli: Isolation and size distribution.  Biochim. Biophys. Acta 281: (1972) 365-370

Fry, M., Israeli-Reches, M., and Artman, M. Stabilization and breakdown of E. coli messenger RNA in the presence of chloramphenicol. Biochemistry 11: (1972) 3054-3059

Fry, M. and Artman, M. Studies on newly synthesized ribosomal ribonucleic acid of Escherichia coli.  Biochem. J. 115: (1969) 295-305

Fry. M. and Artman, M. Deoxyribonucleic acid-ribonucleic acid hybridization: Annealing and quantitative recovery of intact ribosomal ribonucleic acid molecules from hybrids.  Biochem. J. 115: (1969) 287-294

Fry, M. and Artman, M. Sedimentation behaviour of rapidly labeled RNA from Escherichia coli.  Nature 217: (1968) 661-664

Artman, M., Fry, M., and Engelberg, H. The preparation and characterization of ribonucleic acid obtained by direct phenol extraction of intact cells of Escherichia coli from low ionic strength environment.  Biochem. Biophys. Res. Commun. 25: (1966) 49-53