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My lab studies DNA and RNA metabolism. DNA and RNA must be
translocated (moved from place to place), unwound, unzipped, and hybridized in
order to serve their functions of information storage and transfer. The enzymes
that perform these critical tasks are called helicases. We study the biological
and biochemical mechanisms of helicases. For example, DNA replication, repair,
and recombination are processes that require the activity of at least one
helicase. If specific helicases are mutated, DNA metabolism can be disrupted
resulting in diseases such as cancer. The importance of RNA helicases is
increasingly becoming recognized. RNA transport, translation, and RNA
interference are some processes that require the activity of at least one RNA
helicase. Many viruses encode their own DNA or RNA helicase; therefore these
enzymes are potential targets for development of anti-viral drugs. We are
studying a DNA helicase from Bacteriophage T4 called Dda (for DNA-Dependent-ATPase).
Our goal in this project is to develop a detailed chemical and kinetic mechanism
for DNA unwinding by this DNA helicase. A second project involves the Hepatitis
C viral helicase NS3 (Non-Structural Protein 3). NS3 is an RNA helicase that is
also 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. This information is being used for development of chemical and
macromolecular approaches for inhibiting HCV replication in human cells. Our
research projects are currently expanding in two new directions: 1) development
of new tools for studying and disrupting protein-protein interactions using a
combination of chemical and macromolecular approaches coupled with protein mass
spectrometry, and 2) development of single-molecule enzymology using highly
fluorescent nanocrystals for studying individual proteins in solution and in
cells.
Selected Publications
Morris, P. D. and
Raney, K. D. (1999) "DNA Helicases Displace Streptavidin from Biotin-Labeled
Oligonucleotides" Biochemistry, 38, 5164-5171. [Abstract]
Tackett, A. J., Morris,
P. D., Dennis, R., Goodwin, T. E., and Raney, K. D. (2001) "Unwinding of
Unnatural Substrates by a DNA Helicase" Biochemistry, 40, 543-548.
[Abstract]
Tackett, A. J.,Wei, L,
Cameron, C. E., and Raney, K. D. (2001) "Unwinding of Nucleic Acids by HCV NS3 Helicase
is Sensitive to the Structure of the Duplex" Nucleic Acids Research,
29, 565-572. [Abstract]
Morris, P. D., Babb,
K., Tackett, Chick, C., Scott, J., and Raney, K. D. (2001) "Evidence for a
Functional Monomeric Form of the Bacteriophage T4 Dda Helicase" J. Biol.
Chem., 276, 19691-19698. [Abstract]
Nanduri, B., Byrd,
A. K., Eoff, R. L., Tackett, A. J., and Raney, K. D. (2002) "Pre-steady state
DNA unwinding by bacteriophate T4 Dda helicase reveals a monomeric molecular
motor" Proc. Natl. Acad. Sci. USA.
99, 14722-14727.[Abstract]
Piccininni, S., A. Varaklioti, M. Nardelli, Dave, B.,
Raney,
K.D. and McCarthy, J. E. (2002) "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 277,45670-9. [Abstract]
Shammas, M., Liu, X.,
Gavory, G., Raney, K. D.*, Balasubramanian, S.*, and Reis, R.* (2004) "Telomere
Length, Cell Growth Potential, and DNA Integrity of Human Immortal Cells are all
Compromised by Peptide Nucleic Acids Targeted to the Telomere or Telomerase" Exp. Cell. Res, 295, 204-214. [Abstract]
*corresponding authors
Byrd, A. K. and Raney,
K. D. (2004) "Protein displacement by an assembly of helicase molecules
aligned along single-stranded DNA" Nature Struct. Mol. Biol.,11, 531- 538. [Abstract]
Eoff, R. E., Spurling,
T. L., and Raney, K. D. (2005) "Chemically modified DNA substrates implicate the
importance of electrostatic interactions for DNA unwinding by Dda helicase"
Biochemistry 44, 666-674. [Abstract]
Tackett, A. J., Chen,
Y., Cameron, C. E., and Raney, K. D. (2005) "Multiple Full-length NS3 Molecules
are Required for Optimal Unwinding of Oligonucleotide DNA in vitro", J. Biol.
Chem., 280, 10797-10806. [Abstract]
Byrd, A. K., and Raney,
K. D. (2005) "Increasing the length of the single stranded overhang enhances
unwinding of duplex DNA by Bacteriophage T4 Dda Helicase" Biochemistry,
44, 12990-12997. [Abstract]
Huang, L., Hwang, J.,
Sharma, S.D., Hargittai, M.R., Chen, Y., Arnold, J.J., Raney, K.D.,
and Cameron, C.E. (2005) "Hepatitis C virus nonstructural protein 5A (NS5A) is
an RNA-binding protein." J. Biol. Chem., 280, 36417-36428. [Abstract]
Tang, Y., Chen, Y., Lichti, C. F., Hall, R. A., Raney, K. D. and Jennings, S. F. (2005)
"CLPM: A
Cross-Linked Peptide Mapping Algorithm for Mass Spectrometric Analysis" BMC
Bioinformatics, 6 (Suppl 2):S9, 1-14.
[Abstract]
Mackintosh, S. G., Lu, Z. L., Jordan, J. B., Harrison, M. K., Sikora, B.,
Sharma, S. D., Cameron, C. E., and Raney, K. D.* and Sakon, J.* (2006)
"Structural and Biological Identification of residues on the surface of NS3 helicase that are required for optimal replication of the Hepatitis C Virus" J.
Biol. Chem. 281, 3528-3535. [Abstract]
*corresponding authors
Eoff, R. L., and Raney,
K. D. (2006) "Intermediates revealed in the kinetic mechanism for DNA unwinding
by a monomeric helicase" Nature. Structural and Mol. Biol. 13, 242-249. [Abstract]
Byrd, A.
K., and Raney, K. D. (2006) "Displacement of a DNA Binding Protein by Dda
Helicase" Nucleic Acids Research, 34,
3020-3029.
[Abstract]
Sikora, B.,
Eoff, R. L., Matson, S. W., and Raney, K. D. (2006) "DNA Unwinding by
Escherichia Coli DNA helicase I (TraI) Provides Evidence for a Processive
Monomeric Molecular Motor" J. Biol.
Chem., in press.
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E-mail:
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RaneyKevinD@uams.edu |
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Office:
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(501)
686-5244 Biomedical
Research Center 2 Room
441-C2 |
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Labs: |
(501)
686-7254 Biomedical Research
Center 2 Rooms 421-2, 433-2, 419-2 and
417-2 |
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FAX: |
(501) 686-8169 |
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