Marvin H. Caruthers

Nucleic Acid Chemistry and Biochemistry

Professor Caruthers' interests include nucleic acid chemistry and biochemistry. Approximately 30 years ago, the methodologies that are currently used for chemically synthesizing DNA were developed in this laboratory (Fig. 1). These procedures have been incorporated into so-called "gene machines" for the purpose of synthesizing DNA that is used by biochemists, biologists, molecular biologists and biophysical chemists for various research applications. More recently, in a collaboration with Agilent Laboratories, this procedure has been adapted for use with modified ink jet printers in order to synthesize DNA on glass chips. Using this modified chemistry, Agilent has developed instruments that synthesize the equivalent of the human genome each day (DNA 300 nucleotides in length, 3 billion base pairs, 6 billion coupling reactions). Currently underway in the Caruthers' laboratory are investigations desinged to imporve the chemistry further so that we can chemically generate DNA 600-900 nucleotides in length.

The group's interest also focuses on the synthesis of new DNA/RNA analogs (Fig 2) followed by in depth analyses on the use of these derivatives for biology and nanotechnology applications. For example,  ethynylphosphate DNA reacts with azides to generate triazoylphosphonate analogs. Triazoylphosphonate DNA and peptide/amino acid substituted triazoylphosphonate DNA under go rapid transfection into various cell lines (HeLa, WM-239A, Jurkat, and SK-N-F1) and exhibit biological activity as an antimer in a dual luciferase assay. Similar results were obtained with boranephosphonate DNA. 

In the nanotechnology arena, we have recently shown that boranephosphonate DNA reduces silver, gold, and platinum salts to metals. When two-dimensional DNA arrays are constructed with one DNA segment as boranephosphonate DNA, and the arrays are bathed in silver nitrate, silver is deposited at boranephosphonate DNA sites (Fig. 3). The resulting arrays contain repetitive silver spots that are readily detected by transmission electron mircoscopy.

We continue to develop new analogs with several presented in Figure 2. Many of these are expected to find application in biochemistry, human diagnostics, biology, and nanotechnology.

• M.H. Caruthers.  "Studies on Gene Control Regions.  XI.  Deciphering the Protein-DNA Recognition Code."  Acc. Chem. Res. 13, 155 (1980).
• M.D. Matteucci and M.H. Caruthers.  "Studies on Nucleotide Chemistry IV.  Synthesis of Deoxyoligonucleotides on a Polymer Support."  J. Amer. Chem. Soc. 103, 3185 (1981).
• S.L. Beaucage and M.H. Caruthers.  "Studies on Nucleotide Chemistry V.  Deoxynucleoside Phosphoramidites - A New Class of Key Intermediates for Deoxypolynucleotide Synthesis."  Tetrahedron Lett. 22, 1859 (1981).
• M.H. Caruthers.  "Gene Synthesis Machines:  The DNA Chemistry and Its Uses."  Science 230, 281 (1985).
• J.W. Dubendorff, P.L. deHaseth, M.S. Rosendahl and M.H. Caruthers.  "Studies on Gene Control Regions XXII.  DNA Functional Groups Required for Formation of Open Complexes between Escherichia coli RNA Polymerase and the lPR Promoter:  Identification via Base Analog Substitution."  J. Biol. Chem. 262, 892 (1987).
• D. J. Dellinger, D. M. Sheehan, N. Christensen, J. G. Lindberg and M. H. Caruthers. "Solid Phase Chemical Synthesis of Phosphonoacetate and Thiophosphonoacetate Oligodeoxynucleotides."  J. Am. Chem. Soc. 125, 940-950 (2003).
• E. M. LeProust, B. J. Peck, K. Spirin, H. Brummel McCuen, B. Moore, E. Namsaraev and M. H. Caruthers. “Synthesis of High-Quality Libraries of Long (150 mer) Oligonucleotides by a Novel Depurination Controlled Process.”  Nucleic Acids Res. 38, 2522-2540 (2010)
• Streamlined process for the chemical synthesis of RNA using 2'-O-thionocarbamate-protected nucleoside Dellinger DJ, Timár Z, Myerson J, Sierzchala AB, Turner J, Ferreira F, Kupihár Z, Dellinger G, Hill KW, Powell JA, Sampson JR, Caruthers MH. J Am Chem Soc. 133,11540-56 (2011).
• phosphoramidites in the solid phase.
• Solid-phase synthesis, thermal denaturation studies, nuclease resistance, and cellular uptake of
• (oligodeoxyribonucleoside)methylborane phosphine-DNA chimeras. Krishna H, Caruthers MH. J Am Chem Soc. 133, 9844-54 (2011).
• Alkynyl Phosphonate DNA: A Versatile “Click”able Backbone for DNA-Based Biological Applications. Krishna H., Caruthers MH J Am Chem Soc. 134, 11618-11631 (2012).
• Reduction of Metal Ions by Boranephosphonate DNA. Roy S, Olesiak, M, Pader, P, McCuen, H, Caruthers MH. Organic & Biomolecular Chemistry 10, 9130-9133 (2012).
• The Chemical Synthesis of DNA/RNA: Our Gift to Science. M. H. Caruthers. The Journal of Biological Sciences 288, 1420-1427 (2013).
• Silver nanoassemblies constructed from boranephosphonate DNA. Roy S, Olesiak M, Shang S, Caruthers, MH J Am Chem Soc 135, 6234-6241 (2013).