Jason W. Rausch, Ph.D.
Jason W. Rausch, Ph.D.
Staff Scientist

Center for Cancer Research
National Cancer Institute

Building 535, Room 325
Frederick, MD 21702-1201
301-846-5384

The primary focus of my research has been to use various biochemistry, molecular biology and computer modeling tools to study the structures and functions of HIV proteins (reverse transcriptase, integrase, capsid, nucleocapsid, rev), HIV-related host proteins (APOBEC3G, DC-SIGN, L-SIGN) and viral RNA motifs (HIV-1 polypurine tracts, HIV-1 and HIV-2 rev-response elements, HIV-1 5’ UTR). My recent emphasis has been on determining the secondary structures of HIV-related RNAs using the chemical probing methodology known as selective 2’ hydroxyl acylation analyzed by primer extension (SHAPE) and expanding this technology for use with next generation sequencing systems.

Areas of Expertise
1) HIV (human immunodeficiency virus), 2) In vitro assay development, 3) Enzymology, 4) RNA structure, 5) Next generation sequencing 6) Molecular modeling

The principal focus of my research has been to use various tools of biochemistry, molecular biology, and computer modeling to understand the interaction between/among retroviral enzymes (reverse transcriptase, integrase) and structural proteins (nucleocapsid, gag) and their nucleic acid substrates. In particular, I have developed a number of in vitro assays utilizing substrates containing nucleoside analogs (e.g., difluorotoluene, iso-guanosine, 2-amino-adenosine, etc.) and purified recombinant enzymes to study how HIV-1 reverse transcripase specifically recognizes its cognate primer for plus-strand DNA synthesis, the HIV-1 polypurine tract (PPT). I am currently also using related methodologies to explore the mechanism(s) by which the ubiquitous cellular enzyme APOBEC3G, an HIV restriction factor, catalyzes cytidine deamination within select target sequences in single-stranded viral DNA.

Finally, I have recently received a 2007 NCI Director's Career Development Innovation Award for my application entitled 'Evolving Sequence-Specific Integrases and Methyltransferases by In Vitro Compartmentalization.' With these funds, I plan to use novel directed evolution techniques to help improve the target-specificity of retroviral gene therapy vectors, as well as tools useful for epigenetics research pertaining to cytosine methylation.

Selected Publications
  1. Abbondanzieri EA, Bokinsky G, Rausch JW, Zhang JX, Le Grice SF, Zhuang X.
    Nature. 453: 184-9, 2008. [ Journal Article ]
  2. Xu L, Stevens J, Hilton MB, Seaman S, Conrads TP, Veenstra TD, Logsdon D, Morris H, Swing DA, Patel NL, Kalen J, Haines DC, Zudaire E, St Croix B.
    Sci Transl Med. 6: 242ra84, 2014. [ Journal Article ]
  3. Smith S, Tripathi R, Goodings C, Cleveland S, Mathias E, Hardaway JA, Elliott N, Yi Y, Chen X, Downing J, Mullighan C, Swing DA, Tessarollo L, Li L, Love P, Jenkins NA, Copeland NG, Thompson MA, Du Y, Davé UP.
    PLoS ONE. 9: e85883, 2014. [ Journal Article ]
  4. Arnold ES, Ling SC, Huelga SC, Lagier-Tourenne C, Polymenidou M, Ditsworth D, Kordasiewicz HB, McAlonis-Downes M, Platoshyn O, Parone PA, Da Cruz S, Clutario KM, Swing D, Tessarollo L, Marsala M, Shaw CE, Yeo GW, Cleveland DW.
    Proc. Natl. Acad. Sci. U.S.A.. 110: E736-45, 2013. [ Journal Article ]
  5. Lee Y, Karuppagounder SS, Shin JH, Lee YI, Ko HS, Swing D, Jiang H, Kang SU, Lee BD, Kang HC, Kim D, Tessarollo L, Dawson VL, Dawson TM.
    Nat. Neurosci.. 16: 1392-400, 2013. [ Journal Article ]

Education:

  • 1990 B.S. (Biology, minor in Mathematics) Syracuse University, Syracuse, New York
  • 1997 Ph.D. (Biochemistry) Case Western Reserve University, Cleveland, Ohio
  • 2002 B.S. (Computer and Information Science, with certificates in UNIX System Administration and Database Design) University of Maryland, University College, Adelphi, Maryland

Professional:

  • 1994-present      33+ Peer-reviewed publications
  • 1999-present      Staff Scientist, Frederick National Laboratory for Cancer Research
  • 2007                     NCI Director's Career Development Innovation Award 'Evolving Sequence-Specific Integrases and Methyltransferases by In Vitro Compartmentalization.'
  • 2009                     NCI Director's Career Development Innovation Award ‘Incorporating unnatural amino acids into the Pol V mutasome for photocrosslinking and single-molecule FRET’
  • 2009-present      Center for Excellence in HIV and Cancer Virology Website Maintenance Committee
  • 2013-present      Member, CCR RNA Biology Initiative

Summary

The primary focus of my research has been to use various biochemistry, molecular biology and computer modeling tools to study the structures and functions of HIV proteins (reverse transcriptase, integrase, capsid, nucleocapsid, rev), HIV-related host proteins (APOBEC3G, DC-SIGN, L-SIGN) and viral RNA motifs (HIV-1 polypurine tracts, HIV-1 and HIV-2 rev-response elements, HIV-1 5’ UTR). My recent emphasis has been on determining the secondary structures of HIV-related RNAs using the chemical probing methodology known as selective 2’ hydroxyl acylation analyzed by primer extension (SHAPE) and expanding this technology for use with next generation sequencing systems.

Areas of Expertise
1) HIV (human immunodeficiency virus), 2) In vitro assay development, 3) Enzymology, 4) RNA structure, 5) Next generation sequencing 6) Molecular modeling

Research

The principal focus of my research has been to use various tools of biochemistry, molecular biology, and computer modeling to understand the interaction between/among retroviral enzymes (reverse transcriptase, integrase) and structural proteins (nucleocapsid, gag) and their nucleic acid substrates. In particular, I have developed a number of in vitro assays utilizing substrates containing nucleoside analogs (e.g., difluorotoluene, iso-guanosine, 2-amino-adenosine, etc.) and purified recombinant enzymes to study how HIV-1 reverse transcripase specifically recognizes its cognate primer for plus-strand DNA synthesis, the HIV-1 polypurine tract (PPT). I am currently also using related methodologies to explore the mechanism(s) by which the ubiquitous cellular enzyme APOBEC3G, an HIV restriction factor, catalyzes cytidine deamination within select target sequences in single-stranded viral DNA.

Finally, I have recently received a 2007 NCI Director's Career Development Innovation Award for my application entitled 'Evolving Sequence-Specific Integrases and Methyltransferases by In Vitro Compartmentalization.' With these funds, I plan to use novel directed evolution techniques to help improve the target-specificity of retroviral gene therapy vectors, as well as tools useful for epigenetics research pertaining to cytosine methylation.

Publications

Selected Publications
  1. Abbondanzieri EA, Bokinsky G, Rausch JW, Zhang JX, Le Grice SF, Zhuang X.
    Nature. 453: 184-9, 2008. [ Journal Article ]
  2. Xu L, Stevens J, Hilton MB, Seaman S, Conrads TP, Veenstra TD, Logsdon D, Morris H, Swing DA, Patel NL, Kalen J, Haines DC, Zudaire E, St Croix B.
    Sci Transl Med. 6: 242ra84, 2014. [ Journal Article ]
  3. Smith S, Tripathi R, Goodings C, Cleveland S, Mathias E, Hardaway JA, Elliott N, Yi Y, Chen X, Downing J, Mullighan C, Swing DA, Tessarollo L, Li L, Love P, Jenkins NA, Copeland NG, Thompson MA, Du Y, Davé UP.
    PLoS ONE. 9: e85883, 2014. [ Journal Article ]
  4. Arnold ES, Ling SC, Huelga SC, Lagier-Tourenne C, Polymenidou M, Ditsworth D, Kordasiewicz HB, McAlonis-Downes M, Platoshyn O, Parone PA, Da Cruz S, Clutario KM, Swing D, Tessarollo L, Marsala M, Shaw CE, Yeo GW, Cleveland DW.
    Proc. Natl. Acad. Sci. U.S.A.. 110: E736-45, 2013. [ Journal Article ]
  5. Lee Y, Karuppagounder SS, Shin JH, Lee YI, Ko HS, Swing D, Jiang H, Kang SU, Lee BD, Kang HC, Kim D, Tessarollo L, Dawson VL, Dawson TM.
    Nat. Neurosci.. 16: 1392-400, 2013. [ Journal Article ]

Biography

Education:

  • 1990 B.S. (Biology, minor in Mathematics) Syracuse University, Syracuse, New York
  • 1997 Ph.D. (Biochemistry) Case Western Reserve University, Cleveland, Ohio
  • 2002 B.S. (Computer and Information Science, with certificates in UNIX System Administration and Database Design) University of Maryland, University College, Adelphi, Maryland

Professional:

  • 1994-present      33+ Peer-reviewed publications
  • 1999-present      Staff Scientist, Frederick National Laboratory for Cancer Research
  • 2007                     NCI Director's Career Development Innovation Award 'Evolving Sequence-Specific Integrases and Methyltransferases by In Vitro Compartmentalization.'
  • 2009                     NCI Director's Career Development Innovation Award ‘Incorporating unnatural amino acids into the Pol V mutasome for photocrosslinking and single-molecule FRET’
  • 2009-present      Center for Excellence in HIV and Cancer Virology Website Maintenance Committee
  • 2013-present      Member, CCR RNA Biology Initiative