Ph.D., University of Arkansas for Medical SciencesAlicia K. Byrd, Ph.D.
B.S., University of Missouri-Rolla (now Missouri University of Science and Technology)

Office:  (501)526-7520 – Biomedical Research Center B421G
Lab:  (501)686-7254 – Biomedical Research Center 2 433-2
Fax:  (501)686-8169


Helicase Enzymology

The major focus of my research in the Raney lab is helicase enzymology.  Helicases are enzymes that remove secondary structures from DNA and RNA.  We study two DNA helicases, Dda, from Bacteriophage T4, and a eukaryotic helicase, Pif1.  In addition to unwinding duplex DNA, both helicases are known to displace proteins from DNA, and Pif1 unfolds an unusual four stranded DNA structures called a G-quadruplex.  We also study a number of RNA helicases which we found bind tightly to G-quadruplex DNA.  We use a number of methods to study helicases including equilibrium binding, ensemble kinetics (both pre-steady state and steady state), and single molecule kinetics (single molecule total internal reflection fluorescence microscopy).


Selected Publications

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. (2016) “Evidence that G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress.” J Biol Chem. 291(34):18041-57 PMID: 27369081 [Abstract]

Chib, S., Byrd, A.K., and Raney, K.D. (2016) “Yeast Helicase Pif1 unwinds RNA:DNA hybrids with higher processivity than DNA:DNA Duplexes” J. Biol. Chem. 291(11):5889-901. PMID: 26733194  [Abstract]

Byrd AK*, Raney KD.* (2015) “Fine tuning of a DNA fork by the RecQ helicase.” Proc Natl Acad Sci U S A. 112(50):15263-4. PMID:26582797. *corresponding authors [Abstract]

Gao, J, Zybailov, BL, Byrd, AK, Griffin, WC, Chib, S, Mackintosh, SG, Tackett, AJ, and Raney, KD, (2015) “Yeast transcription co-activator Sub1 and its human homolog PC4 preferentially bind to G-quadruplex DNA” Chem. Commun (Camb). 51(33):7242-7244. PMID: 25813861. [Abstract]

Byrd, AK and Raney, KD (2015) “A parallel quadruplex DNA is bound tightly but unfolded slowly by Pif1 helicase” J. Biol. Chem. 290(10):6482-94 PMID:25589786. [Abstract]

Ramanagoudr-Bhojappa, R.*, Byrd, A.K*, Dahl, C., and Raney, K.D. (2014) “Yeast Pif1 Accelerates Annealing of Complementary DNA Strands” Biochemistry. 53(48):7659-69. PMID:25393406. *co-first authors [Abstract]

Aarattuthodiyil, S., Byrd, A.K., and Raney, K.D. (2014) “Simultaneous binding to the tracking strand, displaced strand, and the duplex of a DNA fork enhances unwinding by Dda helicase” Nucleic Acids Res. 42(18):11707-20. PMID:25249618 [Abstract]

Waldrip, Z.J., Byrum, S. D., Storey, A. J., Gao, J., Byrd, A. K., Mackintosh, S. G., Wahls, W.P., Taverna, S.D., Raney, K.D., and Tackett, A.J.* (2014) “A CRISPR-based Approach for Proteomic Analysis of a Single Genomic Locus” Epigenetics, 9(9):1207-1211. PMID: 25147920.  [Abstract]

Ramanagoudr-Bhojappa R., Chib, S., Byrd, A.K., Pandey, M., Patel, S.S., and Raney, K.D. (2013) “Yeast Pif1 Helicase Exhibits a One-base-pair Stepping Mechanism for Unwinding Duplex DNA” J. Biol. Chem. 288, 16185-16195. PMID:23596008 [Abstract]

He, X.*, Byrd, A.K.*, Yun, M.-K., Pemble, C.W., Harrison, D., Yeruva, L., Dahl, C., Kreuzer, K.N., Raney, K.D., and White, S.W. (2012) “The T4 Phage SF1B Helicase Dda is Structurally Optimized to Perform DNA Strand Separation” Structure. 20(7):1189-200. *co-first authors [Abstract]

Byrd, A.K., Matlock, D.L., Bagchi, D., Aarattuthodiyil, S., Harrison, D.K., Croquette, V., and Raney, K.D. (2012) “Dda Helicase Tightly Couples Translocation on Single-stranded DNA to Unwinding of Duplex DNA: Dda is an Optimally Active Helicase” J. Mol. Biol. 420(3):141-54. PMID: 22504228 [Abstract]

Matlock, D.L., Yeruva, L., Byrd, A.K., Mackintosh, S.G., Langston, C., Brown, C., Cameron, C.E., Fischer, C.J., and Raney, K.D. (2010) Investigation of translocation, DNA unwinding, and protein displacement by NS3h, the helicase domain from the hepatitis C virus helicase” Biochemistry, 49, 2097-2109. PMID:20108974 [Abstract]

Byrd AK and Raney KD. (2006) “Displacement of a DNA binding protein by Dda helicase. Nucleic Acids Res. 34(10):3020-9. PMID: 16738140 [Abstract]

Byrd AK and Raney KD. (2005) “Increasing the length of the single-stranded overhang enhances unwinding of duplex DNA by bacteriophage T4 Dda helicase.” Biochemistry. 44(39):12990-7. PMID: 16185067 [Abstract]

Byrd AK and Raney KD. (2004) “Protein displacement by an assembly of helicase molecules aligned along single-stranded DNA.” Nat Struct Mol Biol. 11(6):531-8. PMID:15146172 [Abstract]

Nanduri B, Byrd AK, Eoff RL, Tackett AJ, Raney KD. (2002) “Pre-steady-state DNA unwinding by bacteriophage T4 Dda helicase reveals a monomeric molecular motor.” Proc Natl Acad Sci U S A. 99(23):14722-7. PMID: 12411580 [Abstract]

Complete List of Published Work in My Bibliography