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Last Name
Institution

Kevin Raney

TitleDepartment Chairperson
InstitutionUniversity of Arkansas for Medical Sciences
DepartmentBiochemistry & Molecular Biology, College of Medicine
AddressB405B Biomedical Research I
325 S. Elm St.
Mail Slot # 516
Little Rock AR 72205
Phone501-686-5244
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    Other Positions
    TitleProfessor
    InstitutionUniversity of Arkansas for Medical Sciences
    DepartmentGenetics, College of Medicine
    DivisionGenetics Faculty

    Other Roles
    Chair, Department of Biochemistry and Molecular Biology
    Treasurer for the Association of Medical and Graduate Departments of Biochemistry

    Collapse Overview 
    Collapse overview
    My laboratory is interested in the enzymology and chemistry of nucleic acid enzymes. Helicases are enzymes that manipulate DNA and RNA in all aspects of nucleic acid metabolism. We are studying a DNA helicase from Bacteriophage T4 called Dda (for DNA-Dependent-ATPase) in order to develop a detailed chemical and kinetic mechanism for DNA unwinding by this model DNA helicase. A second enzyme we study is called Pif1. This helicase is involved in many aspects of DNA metabolism ranging from telomere maintenance to transcription. Pif1 binds tightly to unusual DNA structures called quadruplexes, for which the biological functions are being intensively explored. A second project involves the Hepatitis C viral helicase NS3 (Non-Structural Protein 3). NS3 is an RNA helicase that is capable of unwinding DNA. We are studying the mechanism of NS3 as well as its interactions with other HCV and cellular proteins. Our goal is to recapitulate RNA replication in vitro using biological relevant substrates and proteins and a biologically relevant sub-genomic replicon of HCV. Our research projects are currently expanding in development of new tools for studying and protein-protein interactions and post-translational modifications at specific sites in the genome using a Crispr-based approach coupled with protein mass spectrometry. In a new project, we have recently discovered a possible signaling mechanism by which cells respond to DNA damage. During oxidative stress, guanine residues are oxidized, leading to excision of the damaged DNA. When the excised DNA consists of specific sequences containing runs of guanine, the resulting DNA fragment can fold into a stable structure called quadruplex DNA. Telomeric DNA is particularly susceptible to oxidative stress and contains sequences that readily fold into quadruplex structures. The excised DNA quadruplexes can bind to proteins such as DHX36 (a helicase), leading to formation of sub-organelles called stress granules. The functional role of stress granules is to modulate translation. Hence, this mechanism provides a stepwise chemical mechanism for the cell to respond to DNA damage leading to changes in translation.


    Collapse Affiliation 
    Collapse member of
    Association of Medical and Graduate Departments of Biochemistry
    American Chemical Society
    Collapse collaborator
    Robert Eoff

    Collapse Research Funds 

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Eoff RL, Raney KD. A catch and release program for single-stranded DNA. J Biol Chem. 2017 Aug 04; 292(31):13085-13086. PMID: 28778884.
      View in: PubMed
    2. Lopez CR, Singh S, Hambarde S, Griffin WC, Gao J, Chib S, Yu Y, Ira G, Raney KD, Kim N. Yeast Sub1 and human PC4 are G-quadruplex binding proteins that suppress genome instability at co-transcriptionally formed G4 DNA. Nucleic Acids Res. 2017 Jun 02; 45(10):5850-5862. PMID: 28369605.
      View in: PubMed
    3. Griffin WC, Gao J, Byrd AK, Chib S, Raney KD. A biochemical and biophysical model of G-quadruplex DNA recognition by positive coactivator of transcription 4. J Biol Chem. 2017 Jun 09; 292(23):9567-9582. PMID: 28416612.
      View in: PubMed
    4. Byrd AK, Zybailov BL, Maddukuri L, Gao J, Marecki JC, Jaiswal M, Bell MR, Griffin WC, Reed MR, Chib S, Mackintosh SG, MacNicol AM, Baldini G, Eoff RL, Raney KD. Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress. J Biol Chem. 2016 Aug 19; 291(34):18041-57. PMID: 27369081; PMCID: PMC5016190 [Available on 08/19/17].
    5. Ramachandran A, Nandakumar D, Deshpande AP, Lucas TP, R-Bhojappa R, Tang GQ, Raney K, Yin YW, Patel SS. The Yeast Mitochondrial RNA Polymerase and Transcription Factor Complex Catalyzes Efficient Priming of DNA Synthesis on Single-stranded DNA. J Biol Chem. 2016 Aug 05; 291(32):16828-39. PMID: 27311715; PMCID: PMC4974394 [Available on 08/05/17].
    6. Zybailov BL, Byrd AK, Glazko GV, Rahmatallah Y, Raney KD. Protein-protein interaction analysis for functional characterization of helicases. Methods. 2016 Oct 01; 108:56-64. PMID: 27090004; PMCID: PMC5035562 [Available on 10/01/17].
    7. Chib S, Byrd AK, Raney KD. Yeast Helicase Pif1 Unwinds RNA:DNA Hybrids with Higher Processivity than DNA:DNA Duplexes. J Biol Chem. 2016 Mar 11; 291(11):5889-901. PMID: 26733194; PMCID: PMC4786723 [Available on 03/11/17].
    8. Zybailov B, Gokulan K, Wiese J, Ramanagoudr-Bhojappa R, Byrd AK, Glazko G, Jaiswal M, Mackintosh S, Varughese KI, Raney KD. Analysis of Protein-protein Interaction Interface between Yeast Mitochondrial Proteins Rim1 and Pif1 Using Chemical Cross-linking Mass Spectrometry. J Proteomics Bioinform. 2015 Nov; 8(11):243-252. PMID: 26807012.
      View in: PubMed
    9. Byrd AK, Raney KD. Fine tuning of a DNA fork by the RecQ helicase. Proc Natl Acad Sci U S A. 2015 Dec 15; 112(50):15263-4. PMID: 26582797; PMCID: PMC4687568.
    10. Reynolds KA, Cameron CE, Raney KD. Melting of Duplex DNA in the Absence of ATP by the NS3 Helicase Domain through Specific Interaction with a Single-Strand/Double-Strand Junction. Biochemistry. 2015 Jul 14; 54(27):4248-58. PMID: 26091150.
      View in: PubMed
    11. Gao J, Zybailov BL, Byrd AK, Griffin WC, Chib S, Mackintosh SG, Tackett AJ, Raney KD. Yeast transcription co-activator Sub1 and its human homolog PC4 preferentially bind to G-quadruplex DNA. Chem Commun (Camb). 2015 Apr 28; 51(33):7242-4. PMID: 25813861; PMCID: PMC4465349.
    12. Byrd AK, Raney KD. A parallel quadruplex DNA is bound tightly but unfolded slowly by pif1 helicase. J Biol Chem. 2015 Mar 06; 290(10):6482-94. PMID: 25589786; PMCID: PMC4358282.
    13. Reynolds KA, Raney VM, Raney KD. Probing RNA translocases with DNA. Methods Mol Biol. 2015; 1259:275-91. PMID: 25579592.
      View in: PubMed
    14. Ramanagoudr-Bhojappa R, Byrd AK, Dahl C, Raney KD. Yeast Pif1 accelerates annealing of complementary DNA strands. Biochemistry. 2014 Dec 09; 53(48):7659-69. PMID: 25393406; PMCID: PMC4263423.
    15. Jaiswal M, Crabtree N, Bauer MA, Hall R, Raney KD, Zybailov BL. XLPM: efficient algorithm for the analysis of protein-protein contacts using chemical cross-linking mass spectrometry. BMC Bioinformatics. 2014; 15 Suppl 11:S16. PMID: 25350700; PMCID: PMC4251045.
    16. Aarattuthodiyil S, Byrd AK, Raney KD. Simultaneous binding to the tracking strand, displaced strand and the duplex of a DNA fork enhances unwinding by Dda helicase. Nucleic Acids Res. 2014 Oct; 42(18):11707-20. PMID: 25249618; PMCID: PMC4191417.
    17. Waldrip ZJ, Byrum SD, Storey AJ, Gao J, Byrd AK, Mackintosh SG, Wahls WP, Taverna SD, Raney KD, Tackett AJ. A CRISPR-based approach for proteomic analysis of a single genomic locus. Epigenetics. 2014 Sep; 9(9):1207-11. PMID: 25147920; PMCID: PMC4169012.
    18. Raney KD. Chemical modifications of DNA for study of helicase mechanisms. Bioorg Med Chem. 2014 Aug 15; 22(16):4399-406. PMID: 24931273; PMCID: PMC4135034.
    19. Ramanagoudr-Bhojappa R, Chib S, Byrd AK, Aarattuthodiyil S, Pandey M, Patel SS, Raney KD. Yeast Pifl helicase exhibits a one-base-pair stepping mechanism for unwinding duplex DNA. J Biol Chem. 2013; 288(22):16185-95 PMID: 23596008.
    20. Ramanagoudr-Bhojappa R, Chib S, Byrd AK, Aarattuthodiyil S, Pandey M, Patel SS, Raney KD. Yeast Pif1 helicase exhibits a one-base-pair stepping mechanism for unwinding duplex DNA. J Biol Chem. 2013 May 31; 288(22):16185-95. PMID: 23596008; PMCID: PMC3668774.
    21. Zybailov BL, Sherpa MD, Glazko GV, Raney KD, Glazko VI. [G4-quadruplexes and genome instability]. Mol Biol (Mosk). 2013 Mar-Apr; 47(2):224-31. PMID: 23808155.
      View in: PubMed
    22. Zybailov BL, Glazko GV, Jaiswal M, Raney KD. Large Scale Chemical Cross-linking Mass Spectrometry Perspectives. J Proteomics Bioinform. 2013 Feb 08; 6(Suppl 2):001. PMID: 25045217.
      View in: PubMed
    23. Ramanagoudr-Bhojappa R, Blair LP, Tackett AJ, Raney KD. Physical and functional interaction between yeast Pifl helicase and Rim1 single-stranded DNA binding protein. Nucleic Acids Res. 2013; 41(2):1029-46 PMID: 23175612.
    24. Raney KD, Byrd AK, Aarattuthodiyil S. Structure and Mechanisms of SF1 DNA Helicases. Adv Exp Med Biol. 2013; 767:17-46. PMID: 23161005; PMCID: PMC3806203.
    25. Raney KD, Byrd AK, Aarattuthodiyil S. Structure and Mechanisms of SF1 DNA Helicases. Adv Exp Med Biol. 2013; 973:E1. PMID: 23269543.
      View in: PubMed
    26. Raney VM, Reynolds KA, Harrison MK, Harrison DK, Cameron CE, Raney KD. Binding by the hepatitis C virus NS3 helicase partially melts duplex DNA. Biochemistry. 2012 Sep 25; 51(38):7596-607. PMID: 22916835; PMCID: PMC3554864.
    27. Byrd AK, Raney KD. Superfamily 2 helicases. Front Biosci (Landmark Ed). 2012 Jun 01; 17:2070-88. PMID: 22652765; PMCID: PMC3775597.
    28. He X, Byrd AK, Yun MK, Pemble CW, Harrison D, Yeruva L, Dahl C, Kreuzer KN, Raney KD, White SW. The T4 phage SF1B helicase Dda is structurally optimized to perform DNA strand separation. Structure. 2012 Jul 03; 20(7):1189-200. PMID: 22658750; PMCID: PMC3392491.
    29. Byrd AK, Matlock DL, Bagchi D, Aarattuthodiyil S, Harrison D, Croquette V, Raney KD. Dda helicase tightly couples translocation on single-stranded DNA to unwinding of duplex DNA: Dda is an optimally active helicase. J Mol Biol. 2012 Jul 13; 420(3):141-54. PMID: 22504228; PMCID: PMC3372602.
    30. Benkovic SJ, Raney KD. Mechanisms: molecular machines. Curr Opin Chem Biol. 2011 Oct; 15(5):577-9. PMID: 21920800.
      View in: PubMed
    31. Liu J, Choi M, Stanenas AG, Byrd AK, Raney KD, Cohan C, Bianco PR. Novel, fluorescent, SSB protein chimeras with broad utility. Protein Sci. 2011 Jun; 20(6):1005-20. PMID: 21462278; PMCID: PMC3104230.
    32. Hwang J, Huang L, Cordek DG, Vaughan R, Reynolds SL, Kihara G, Raney KD, Kao CC, Cameron CE. Hepatitis C virus nonstructural protein 5A: biochemical characterization of a novel structural class of RNA-binding proteins. J Virol. 2010 Dec; 84(24):12480-91. PMID: 20926572; PMCID: PMC3004340.
    33. Eoff RL, Raney KD. Kinetic mechanism for DNA unwinding by multiple molecules of Dda helicase aligned on DNA. Biochemistry. 2010 Jun 01; 49(21):4543-53. PMID: 20408588; PMCID: PMC2876234.
    34. Raney KD, Sharma SD, Moustafa IM, Cameron CE. Hepatitis C virus non-structural protein 3 (HCV NS3): a multifunctional antiviral target. J Biol Chem. 2010 Jul 23; 285(30):22725-31. PMID: 20457607; PMCID: PMC2906261.
    35. Matlock DL, Yeruva L, Byrd AK, Mackintosh SG, Langston C, Brown C, Cameron CE, Fischer CJ, Raney KD. Investigation of translocation, DNA unwinding, and protein displacement by NS3h, the helicase domain from the hepatitis C virus helicase. Biochemistry. 2010 Mar 16; 49(10):2097-109. PMID: 20108974; PMCID: PMC2853022.
    36. Perumal SK, Raney KD, Benkovic SJ. Analysis of the DNA translocation and unwinding activities of T4 phage helicases. Methods. 2010 Jul; 51(3):277-88. PMID: 20170733; PMCID: PMC2919206.
    37. Yeruva L, Raney KD. Protein displacement by helicases. Methods Mol Biol. 2010; 587:85-98. PMID: 20225143.
      View in: PubMed
    38. Wang Q, Arnold JJ, Uchida A, Raney KD, Cameron CE. Phosphate release contributes to the rate-limiting step for unwinding by an RNA helicase. Nucleic Acids Res. 2010 Mar; 38(4):1312-24. PMID: 19969541; PMCID: PMC2831328.
    39. Blair LP, Tackett AJ, Raney KD. Development and evaluation of a structural model for SF1B helicase Dda. Biochemistry. 2009 Mar 24; 48(11):2321-9. PMID: 19256528; PMCID: PMC2664552.
    40. Cameron CE, Gotte M, Raney KD. "Viral Genome Replication". 2009.
    41. Jennings TA, Mackintosh SG, Harrison MK, Sikora D, Sikora B, Dave B, Tackett AJ, Cameron CE, Raney KD. NS3 helicase from the hepatitis C virus can function as a monomer or oligomer depending on enzyme and substrate concentrations. J Biol Chem. 2009 Feb 20; 284(8):4806-14. PMID: 19088075; PMCID: PMC2643493.
    42. Sikora B, Chen Y, Lichti CF, Harrison MK, Jennings TA, Tang Y, Tackett AJ, Jordan JB, Sakon J, Cameron CE, Raney KD. Hepatitis C virus NS3 helicase forms oligomeric structures that exhibit optimal DNA unwinding activity in vitro. J Biol Chem. 2008 Apr 25; 283(17):11516-25. PMID: 18283103; PMCID: PMC2431078.
    43. Jennings TA, Chen Y, Sikora D, Harrison MK, Sikora B, Huang L, Jankowsky E, Fairman ME, Cameron CE, Raney KD. RNA unwinding activity of the hepatitis C virus NS3 helicase is modulated by the NS5B polymerase. Biochemistry. 2008 Jan 29; 47(4):1126-35. PMID: 18179252.
      View in: PubMed
    44. Bandyopadhyay S, Raney KD, Liu Y, Hermonat PL. AAV-2 Rep78 and HPV-16 E1 interact in vitro, modulating their ATPase activity. Biochemistry. 2008 Jan 15; 47(2):845-56. PMID: 18092809.
      View in: PubMed
    45. Blair LP, Warthen CR, Tackett AJ, Raney KD. Using Mass Spectrometry to Elucidate the Structure of Dda Helicase. American Society of Mass Spectrometry. 2007.
    46. Sikora B, Eoff RL, Matson SW, Raney KD. DNA unwinding by Escherichia coli DNA helicase I (TraI) provides evidence for a processive monomeric molecular motor. J Biol Chem. 2006 Nov 24; 281(47):36110-6. PMID: 16984922.
      View in: PubMed
    47. Mackintosh SG, Raney KD. DNA unwinding and protein displacement by superfamily 1 and superfamily 2 helicases. Nucleic Acids Res. 2006; 34(15):4154-9. PMID: 16935880; PMCID: PMC1616963.
    48. Raney KD. A helicase staircase. Nat Struct Mol Biol. 2006 Aug; 13(8):671-2. PMID: 16886007.
      View in: PubMed
    49. Sikora B, Raney KD. Kinetic Analysis of DNA Unwinding by E coli DNA Helicase l (Tral) reveals a highly Processive Monomeric Molecule Motor. Federation of European Biochemical Societies (FEBS). 2006.
    50. Byrd AK, Raney KD. Displacement of a DNA binding protein by Dda helicase. Nucleic Acids Res. 2006; 34(10):3020-9. PMID: 16738140; PMCID: PMC1474059.
    51. Eoff RL, Raney KD. Intermediates revealed in the kinetic mechanism for DNA unwinding by a monomeric helicase. Nat Struct Mol Biol. 2006 Mar; 13(3):242-9. PMID: 16474403.
      View in: PubMed
    52. Spurling TL, Eoff RL, Raney KD. Dda helicase unwinds a DNA-PNA chimeric substrate: evidence for an inchworm mechanism. Bioorg Med Chem Lett. 2006 Apr 01; 16(7):1816-20. PMID: 16439125.
      View in: PubMed
    53. Blari LP, Raney KD. Structural Studies of Bacteriophage T4 Helicase Dda. Arkansas Academy of Science. 2006.
    54. Raney KD. "A helicase staircase" Nature Structure and Molecular Biology. Invited 'News and Views' Article. 2006; 13:671.
    55. Spurling TL, Eoff RL, Raney KD. Dda Helicase Unwinds a DNA-PNA Chimeric Substance: Evidence for an Inchworm Mechanism. Bioorganic and Med.Chem.Letters. 2006; 16:1816-1820; PMID 16439125.
    56. Mackintosh SG, Lu ZL, Jordan JB, Harrison MK, Sikora B, Shrama SD, Cameron CE, Raney KD*, Sakon J*. Structure and Biological Identification of Residue on the surface of NS3 Helicase that are required for optimal replication of the Hepatitis C virus. J Bio Chem. 2006; 3528-3535; PMID 16306038.
    57. Sikora B, Eoff RL, Maston SW, Raney KD. DNA Unwinding by Escherichia coli DNA helicase l (Tral) Provides Evidence for a processive Monomeric Molecular Motor. J.Bio.Chem.,. 2006; 281:36110-36116' PMID 16984922.
    58. Eoff RL, Raney KD. "Helicases-catalysed translocation and strand separation". 2005.
    59. Eoff RL, Raney KD. Helicase-catalysed translocation and strand separation. Biochem Soc Trans. 2005 Dec; 33(Pt 6):1474-8. PMID: 16246149.
      View in: PubMed
    60. Mackintosh SG, Lu JZ, Jordan JB, Harrison MK, Sikora B, Sharma SD, Cameron CE, Raney KD, Sakon J. Structural and biological identification of residues on the surface of NS3 helicase required for optimal replication of the hepatitis C virus. J Biol Chem. 2006 Feb 10; 281(6):3528-35. PMID: 16306038.
      View in: PubMed
    61. Byrd AK, Raney KD. Increasing the length of the single-stranded overhang enhances unwinding of duplex DNA by bacteriophage T4 Dda helicase. Biochemistry. 2005 Oct 04; 44(39):12990-7. PMID: 16185067.
      View in: PubMed
    62. Huang L, Hwang J, Sharma SD, Hargittai MR, Chen Y, Arnold JJ, Raney KD, Cameron CE. Hepatitis C virus nonstructural protein 5A (NS5A) is an RNA-binding protein. J Biol Chem. 2005 Oct 28; 280(43):36417-28. PMID: 16126720.
      View in: PubMed
    63. Tang Y, Chen Y, Lichti CF, Hall RA, Raney KD, Jennings SF. CLPM: a cross-linked peptide mapping algorithm for mass spectrometric analysis. BMC Bioinformatics. 2005 Jul 15; 6 Suppl 2:S9. PMID: 16026606; PMCID: PMC1637035.
    64. Eoff RL, Raney KD. The transition from a monomeric to a multimeric molecular motor. International Meeting on Helicases and NTP driven nucleic acid machines. 2005.
    65. Chen Y, Mackintosh SG, Lichti C, Tackett AJ, Dave B, Tang Y, Sakon J, Jordan B, Cameron CE, Raney KD. Identification of Protein-protein Interactions among Non-Structural Proteins from HCV and Evidence for a Dominant-Negative Effect of an ATPase-deficient mutant of NS3. American Society of Virology National Meeting. 2005.
    66. Jennings TA, Mackintosh SG, Cameron CE, Raney KD. Mutation in the Putative Nuclear Localization Sequence of the Hepatitis C NS3 Protein Reduce Colony Formation After Transfection of HCV Replicon RNA into Huh 7 Cell. American Society of Virology National Meeting. 2005.
    67. Mackintosh SG, Sakon J, Cameron CE, Raney KD. Structure of an Apparent Dimeric Form of the HCV NS3 Helicase Reveals Surface Residues that are required for Optimal HCV replication in Huh 7 Cells. American Society of Virology National Meeting. 2005.
    68. Harrison MK, Chen Y, Lichti C, Tackett AJ, Mackintosh SG, Dave B, Tang Y, Sakon J, Jordan B, Cameron CE, Raney KD. Identification of Protein-Protein Interactions among Non-Structural Protein from HCV and Evidence for Dominant Effect of an ATPase-deficient mutant of NS3. American Society for Biochemistry and Molecular Biology. 2005.
    69. Sikora B, Wang W, Cameron CE, Raney KD. Improved Methods for Expression and Purification of the Hepatitis C Virus Helicase. American Society for Biochemistry and Molecular Biology. 2005.
    70. Eoff RL, Spurling TL, Raney KD. Chemically modified DNA substrates implicate the importance of electrostatic interactions for DNA unwinding by Dda helicase. Biochemistry. 2005 Jan 18; 44(2):666-74. PMID: 15641792.
      View in: PubMed
    71. Tackett AJ, Chen Y, Cameron CE, Raney KD. Multiple full-length NS3 molecules are required for optimal unwinding of oligonucleotide DNA in vitro. J Biol Chem. 2005 Mar 18; 280(11):10797-806. PMID: 15634684.
      View in: PubMed
    72. Mackintosh SG, Sakon J, Cameron CE, Raney KD. Structure of an Apparent Dimeric Form of the HCV NS3 Helicase Reveals Surface Residues that are required for HCV Replication. 11th International Conference on Hepatitis C virus. 2004.
    73. Chen Y, Mackintosh SG, Lichti C, Tackett AJ, Dave B, Tang Y, Sakon J, Jordan B, Cameron CE, Raney KD. Identification of Protein-Protein Interactions among Non-Structural Protein from HCV and Evidence for a Dominant Negative Effect of an ATPase-deficient mutant of NS3. 11th International Conference on Hepatitis C Virus. 2004.
    74. Jennings TA, Mackintosh SG, Cameron CE, Raney KD. Mutations in the Putative Nuclear Localization Sequence of the Hepatitis C NS3 Protein Conoly Formation after Transfection of HCV Replicon RNA into Huh 7 Cells. 11th International Conference on Hepatitis C Virus. 2004.
    75. Huang L, Sineva EV, Hargittai MR, Sharma SD, Suthar M, Raney KD, Cameron CE. Purification and characterization of hepatitis C virus non-structural protein 5A expressed in Escherichia coli. Protein Expr Purif. 2004 Sep; 37(1):144-53. PMID: 15294292.
      View in: PubMed
    76. Byrd AK, Raney KD. Protein displacement by an assembly of helicase molecules aligned along single-stranded DNA. Nat Struct Mol Biol. 2004 Jun; 11(6):531-8. PMID: 15146172.
      View in: PubMed
    77. Raney KD, Sakon J, Mackintosh SG, Cameron CE. Identification of Protein Surfaces of NS3 that are Required for HCV Replication. International Meeting on Positive Strand RNA viruses. 2004.
    78. Shammas MA, Liu X, Gavory G, Raney KD, Balasubramanian S, Shmookler Reis RJ. Targeting the single-strand G-rich overhang of telomeres with PNA inhibits cell growth and induces apoptosis of human immortal cells. Exp Cell Res. 2004 Apr 15; 295(1):204-14. PMID: 15051503.
      View in: PubMed
    79. Raney KD, Sakon J, Mackintosh S, Cameron CE. Identification of Protein Surfaces of NS3 that are required for HCV Replication. International Conference on Hepatitis c Virus. 2003.
    80. Chen Yingfeng, Raney KD. The role of NS3 with NS4a in HCV replication. FASEB Summer Conference. 2003.
    81. Eoff Robert L, Spurling, Travis L, Raney Kevin D. Use of Modified DNA Substrates to Elucidate the Molecular Interactions that are important for Helicase Function. FASEB Summer Conference. 2003.
    82. Bhuvanesh D, Tackett AJ, Raney KD. Effect of PNA on the HCV lociferase Replicon. FASEB Summer Conference. 2003.
    83. Ziemba AJ, Reed MW, Raney KD, Byrd AB, Ebbinghaus SW. A bis-alkylating triplex forming oligonucleotide inhibits intracellular reporter gene expression and prevents triplex unwinding due to helicase activity. Biochemistry. 2003 May 06; 42(17):5013-24. PMID: 12718544.
      View in: PubMed
    84. Lichti CF, Cameron CE, Raney KD. Using Chemical Crosslinking to Examine the Oligomeric state of Hepatitis C Virus NS3 Helicase. Experimental Biology. 2003.
    85. Tackett AJ, Raney KD. "RNA Helicases". In Mechanism of Replication and Transcription of RNA Viruses. Zhang X ed. 2003.
    86. Raney KD, Byrd AK, Nanduri B, Eoff RL. Evidence for functional monomeric and multimeric forms of the Dda helicase. Biophysical Society National Meeting. 2003.
    87. Nanduri B, Byrd AK, Eoff RL, Tackett AJ, Raney KD. Pre-steady-state DNA unwinding by bacteriophage T4 Dda helicase reveals a monomeric molecular motor. Proc Natl Acad Sci U S A. 2002 Nov 12; 99(23):14722-7. PMID: 12411580; PMCID: PMC137486.
    88. Piccininni S, Varaklioti A, Nardelli M, Dave B, Raney KD, McCarthy JE. Modulation of the hepatitis C virus RNA-dependent RNA polymerase activity by the non-structural (NS) 3 helicase and the NS4B membrane protein. J Biol Chem. 2002 Nov 22; 277(47):45670-9. PMID: 12235135.
      View in: PubMed
    89. Sikora B, Matson SW, Raney KD. Investigation of the Kinetic of DNA Unwinding by Helicase 1 Optimization of Oligonucleotide Substance and Reaction Conditions. Experimental Biology. 2002.
    90. Mackintosh S, Cameron CE, Bhuvanesh D, Raney KD. Application of a Streptavidan Displacement assay in the Investigation of the avtive species of hepatitis C virus NS3 helicase. Experimental Biology. 2002.
    91. Morris PD, Byrd AK, Tackett AJ, Cameron CE, Tanega P, Ott R, Fanning E, Raney KD. Hepatitis C virus NS3 and simian virus 40 T antigen helicases displace streptavidin from 5'-biotinylated oligonucleotides but not from 3'-biotinylated oligonucleotides: evidence for directional bias in translocation on single-stranded DNA. Biochemistry. 2002 Feb 19; 41(7):2372-8. PMID: 11841230.
      View in: PubMed
    92. Tackett AJ, Corey DR, Raney KD. Non-Watson-Crick interactions between PNA and DNA inhibit the ATPase activity of bacteriophage T4 Dda helicase. Nucleic Acids Res. 2002 Feb 15; 30(4):950-7. PMID: 11842106; PMCID: PMC100347.
    93. Morris PD, Byrd AK, Tackett AJ, Cameron CE, Tanega P, Ott R, Fanning E, Raney KD. HCV NS3 and SV40 T Antigen Helicases displace streptavidin from 5’-biotinylated oligonucleotides but not from 3’-biotinylated oligonucleotides: Evidence for Unidirectional Translocation on Single-stranded DNA. Biochemistry. 2002; 41:2372-2378; PMID 11841230.
    94. Raney KD, Shammas MA, Lui X, Gavory G, Balasubramanian S, Shmookler Reis RJ. Telomere Length Cell Growth Potential and DNA integrity of human immortal Cells are all compromised by pepcide nucleic acids targeted to the telomere or telomerase. Keystone Conference on DNA Replication. 2002.
    95. Nanduri B, Byrd AK, Eoff RL, Tackett AJ, Raney KD. Pre-steady state DNA unwinding by bacteriophate T4 Dda helicase reveals a monomeric molecular motor. Proc. Natl. Acad. Sci. USA. 2002; 99.
    96. Tackett AJ, Cameron CE, Raney KD. Multiple Full- Length NS3 Molecules are Required for Optimal Unwinding Activity. International Conference on Hepatitis C Virus. 2002.
    97. Byrd AK, Raney KD. Dda Helicase Exhibits Functional Cooperativity. FASEB conference on Helicases Structure Function and Roles in Human Disease. 2001.
    98. Tackett AJ, Raney KD. FASEB Conference on Helicases Structure Function and Roles in Human Disease; Vermont. July 2001. FASEB Conference on Helicases Structure Function and Roles in Human Disease. 2001.
    99. Nanduri B, Eoff RL, Tackett AJ, Raney KD. Measurement of steady-state kinetic parameters for DNA unwinding by the bacteriophage T4 Dda helicase: use of peptide nucleic acids to trap single-stranded DNA products of helicase reactions. Nucleic Acids Res. 2001 Jul 01; 29(13):2829-35. PMID: 11433029; PMCID: PMC55784.
    100. Morris PD, Tackett AJ, Babb K, Nanduri B, Chick C, Scott J, Raney KD. Evidence for a functional monomeric form of the bacteriophage T4 DdA helicase. Dda does not form stable oligomeric structures. J Biol Chem. 2001 Jun 08; 276(23):19691-8. PMID: 11278788.
      View in: PubMed
    101. Morris PD, Tackett AJ, Raney KD. Biotin-streptavidin-labeled oligonucleotides as probes of helicase mechanisms. Methods. 2001 Feb; 23(2):149-59. PMID: 11181034.
      View in: PubMed
    102. Tackett AJ, Morris PD, Dennis R, Goodwin TE, Raney KD. Unwinding of unnatural substrates by a DNA helicase. Biochemistry. 2001 Jan 16; 40(2):543-8. PMID: 11148049.
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    103. Tackett AJ, Wei L, Cameron CE, Raney KD. Unwinding of nucleic acids by HCV NS3 helicase is sensitive to the structure of the duplex. Nucleic Acids Res. 2001 Jan 15; 29(2):565-72. PMID: 11139627; PMCID: PMC29657.
    104. Morris PD, Tackett AJ, Raney KD. "Biotin-Streptavidin Labeled Oligonucleotides as probes of Helicase Mechanism". Methods: A Companion to Methods in Enzymology; PMID 1181034. 2001; 23 (149-159).
    105. Goodwin TE, Boylan CJ, Current WL, Byrd JC, Edwards CB, Fuller DA, Green JL, Larocca CD, Raney KD, Ross AS, Tucker WA. Enhanced pneumocystis carinii activity of new primaquine analogues. Bioorg Med Chem Lett. 2000 Oct 02; 10(19):2205-8. PMID: 11012030.
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    106. Raney KD, Nanduri B, Byrd AK, Tackett AJ. Pre-Steady state Kinetic Analysis Indicates that the Bacteriophage T4 Dda Helicase can Function as a Monomer. FASEB Conference on Helicase Structure Function and Roles in Human Disease. 2000.
    107. Dennis R, Akbar S, Raney KD. Evidence that Singal-Stranded DNA and Double-Stranded DNA can Pass Through the Central Channel of a Hexameric Helicase. American Society of Biochemistry and Molecular Biology National Meeting. 2000.
    108. Tackett AJ, Cameron CE, Raney KD. Peptide Nucleic Acid Inhibits HCV-Ns3 Catalyzed Unwinding of DNA and RNA Substrates. American Society of Biochemistry and Molecular Biology National Meeting. 2000.
    109. Morris PD, Tackett AJ, Raney KD. Displacement of Streptavidin from the 5'-ends of biotin labeled Oligonucleotides by 3'-to-5' Helicases. American Society of Biochemistry and Molecular Biology National Meeting. 2000.
    110. Spruling T, Raney KD. A New Synthetic route to Peptide Nucleic Acid Monomers with Base-labile protecting Groups. American Society of Biochemistry and Molecular Biology. 2000.
    111. Nanduri B, Raney KD. Peptide Nucleic Acid(PNA) as a Trapping Strand in Steady State DNA Unwiding Assays. FASEB Conference on Nucleic Acid Enzymology. 2000.
    112. Byrd AK, Morris PD, Hurlburt BK, Raney KD. Cloning of a Helicase from HHV8. American Society of Biochemistry and Molecular Biology National Meeting. 2000.
    113. Raney KD, Tackett AJ, Morris P. Unwinding of Nucleic Acids by the HCVNS3 Helicase. 6th International Conference on Hepatitis C Virus. 1999.
    114. Harrison JG, Frier C, Laurant R, Dennis R, Raney KD, Balasubramanian S. Inhibition of human telomerase by PNA-cationic peptide conjugates. Bioorg Med Chem Lett. 1999 May 03; 9(9):1273-8. PMID: 10340613.
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    115. Dennis R, Harrison JG, Frier C, Laurent R, Balasubramanian S, Raney KD. Inhibition of Human Telomerase by PNA-Peptide Conjuates. American Society of Biochemistry and Molecular Biology National Meeting. 1999.
    116. Morris PD, Raney KD. DNA helicases displace streptavidin from biotin-labeled oligonucleotides. Biochemistry. 1999 Apr 20; 38(16):5164-71. PMID: 10213622.
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    117. Raney KD. DNA Helicase Displaces Streptavidin from Biotin-Labeled Oligonucleotides with a 5'-to-3' Directional Bias. Keystone Meeting on DNA Replication and Recombination. 1999.
    118. Raney KD, Hamilton SE, Corey DR. "Interactions of Peptide Nucleic Acids with DNA Processing Enzymes" in Peptide Nucleic Acids. In Peptide Nucleic Acids: Protocols and Applicants. 1999.
    119. Goodwin TE, Holland RD, Lay JO, Raney KD. A simple procedure for solid-phase synthesis of peptide nucleic acids with N-terminal cysteine. Bioorg Med Chem Lett. 1998 Aug 18; 8(16):2231-4. PMID: 9873519.
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    120. Morris PD, Babb K, Raney KD. Investigation and Binding Topology of Bacteriophage T4 gp41 Helicase to ssDNA. 17th International Congress of Biochemistry and Molecular Biology. 1997.
    121. Raney KD, Babb K, Morris PD. Identification of the Structural Determinants of DNA Required for Supporting Helicase Activity. 17th International Congress of Biochemistry and Molecular Biology. 1997.
    122. Laurent R, Babb K, Raney KD. Investigation of the Oligomeric Structure of the Bacteriophage T4 Dda Helicase. 17th International Cingress of Biochemistry and Molecular Biology. 1997.
    123. Raney KD, Carver TE, Benkovic SJ. Stoichiometry and DNA unwinding by the bacteriophage T4 41:59 helicase. J Biol Chem. 1996 Jun 14; 271(24):14074-81. PMID: 8662873.
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    124. Raney KD, Carver TC, Benkovic SJ. Stoichiometry and DNA Unwinding by the Bacteriophage 41:59 Helicase Complex. Keystone Symposium on DNA Replication. 1996.
    125. Raney KD, Benkovic SJ. Bacteriophage T4 Dda helicase translocates in a unidirectional fashion on single-stranded DNA. J Biol Chem. 1995 Sep 22; 270(38):22236-42. PMID: 7673202.
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    126. Guengerich FP, Shimada T, Yun CH, Yamazaki H, Raney KD, Thier R, Coles B, Harris TM. Interactions of ingested food, beverage, and tobacco components involving human cytochrome P4501A2, 2A6, 2E1, and 3A4 enzymes. Environ Health Perspect. 1994 Nov; 102 Suppl 9:49-53. PMID: 7698084; PMCID: PMC1566791.
    127. Raney KD, Sowers LC, Millar DP, Benkovic SJ. A fluorescence-based assay for monitoring helicase activity. Proc Natl Acad Sci U S A. 1994 Jul 05; 91(14):6644-8. PMID: 8022830; PMCID: PMC44259.
    128. Iyer, RS, Coles BF, Raney KD, Thier R, Guengerich FP, Harris TM. DNA Adduction by the Potent Carcinogen Aflatoxin B1: Mechanistic Studies. J. Am. Chem. Soc. 1994; 116:1603-1609.
    129. Raney KD, Benkovic SJ. Substance Specificity for T4 dda Helicase. Keystone Symposium on Nucleic Acid-Protein Interactions. 1994.
    130. Meyer DJ, Coles B, Harris J, Gilmore KS, Raney K, Harris TM, Guengerich FP, Kensler TW, Ketterer B. Induction of rat liver GSH transferases by 1,2-dithiole-3-thione illustrates both anticarcinogenic and tumor-promoting properties. Basic Life Sci. 1993; 61:171-9. PMID: 8304929.
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    131. Guengerich FP, Shimada T, Raney KD, Yun CH, Meyer DJ, Ketterer B, Harris TM, Groopman JD, Kadlubar FF. Elucidation of catalytic specificities of human cytochrome P450 and glutathione S-transferase enzymes and relevance to molecular epidemiology. Environ Health Perspect. 1992 Nov; 98:75-80. PMID: 1486866; PMCID: PMC1519604.
    132. Raney KD, Meyer DJ, Ketterer B, Harris TM, Guengerich FP. Glutathione conjugation of aflatoxin B1 exo- and endo-epoxides by rat and human glutathione S-transferases. Chem Res Toxicol. 1992 Jul-Aug; 5(4):470-8. PMID: 1391613.
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    133. Raney KD, Coles B, Guengerich FP, Harris TM. The endo-8,9-epoxide of aflatoxin B1: a new metabolite. Chem Res Toxicol. 1992 May-Jun; 5(3):333-5. PMID: 1504254.
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    134. Raney KD, Shimada T, Kim DH, Groopman JD, Harris TM, Guengerich FP. Oxidation of aflatoxins and sterigmatocystin by human liver microsomes: significance of aflatoxin Q1 as a detoxication product of aflatoxin B1. Chem Res Toxicol. 1992 Mar-Apr; 5(2):202-10. PMID: 1643250.
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    135. Guengerich FP, Raney KD, Kim DH, Shimada T, Meyer DJ, Ketterer B, Harris TM. Oxidation and conjugation of aflatoxins by humans and experimental animals. Prog Clin Biol Res. 1992; 374:157-65. PMID: 1620701.
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    136. Raney KD, Shimada T, Kim D-H, Mayer DJ, Ketterner B, Groopman JD, Harris TM, Guengerich FP. Oxidation of Aflatoxin B1 and Glutathione Conjugation of the 8,9-Oxide by Rat and Human Liver Enzymes. American Association of Cancer Research National Meeting. 1992.
    137. Raney KD, Gopalakrishnan S, Byrd S, Stone MP, Harris TM. Alteration of the aflatoxin cyclopentenone ring to a delta-lactone reduces intercalation with DNA and decreases formation of guanine N7 adducts by aflatoxin epoxides. Chem Res Toxicol. 1990 May-Jun; 3(3):254-61. PMID: 2131838.
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    138. Baertschi SW, Raney KD, Shimada T, Harris TM, Guengerich FP. Comparison of rates of enzymatic oxidation of aflatoxin B1, aflatoxin G1, and sterigmatocystin and activities of the epoxides in forming guanyl-N7 adducts and inducing different genetic responses. Chem Res Toxicol. 1989 Mar-Apr; 2(2):114-2. PMID: 2519710.
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    139. Gannon OK, Bibring P, Raney KD, Ward JA, Wilson DJ, Underwood J, Debelak KA. Soil Clean Up by in-situ Surfactant Flushing. III. Laboratory Results. Separation Science and Tech. 1989; 24:1073-1094.
    140. Baertschi SW, Raney KD, Stone MP, Harris TM. Preparation of the 8,9-Epoxide of the Mycotoxin Aflatoxin B1: The Ultimate Carcinogenic Species. J. Am. Chem. Soc. 1988; 110:7929 - 7931.
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