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Alicia Byrd

TitleAssistant Professor
InstitutionUniversity of Arkansas for Medical Sciences
DepartmentBiochemistry & Molecular Biology, College of Medicine
DivisionBiochem & Molecular Research
Address433-2 Biomedical Research II
200 South Cedar
Mail Slot # 516
Little Rock AR 72202
Phone501-686-7254
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    Collapse Overview 
    Collapse overview
    DNA damage occurs tens of thousands of times per day in human cells from both endogenous and environmental sources. In order to preserve the genetic material, cells have evolved multiple mechanisms to detect and repair DNA damage. However, inaccurate DNA repair can cause genomic instability such as chromosomal rearrangements and expansion of repetitive sequences which can lead to the development of cancer or diseases such as Fragile X Syndrome. One area my research focuses on is the enzymes that regulate the DNA damage response. In particular, I am interested in a family of enzymes called helicases which remove secondary structures from DNA and RNA. At least 10 different human helicases are involved in DNA repair.

    My research is focused on understanding the fundamental mechanisms of these enzymes using biophysical and biochemical techniques including ensemble and single molecule kinetics, proteomics, and genomics. The molecular mechanisms of these proteins, both individually and as components of multi-protein complexes, are of interest, as are the effects of posttranslational modifications on their activity.


    Collapse Affiliation 
    Collapse member of
    American Chemical Society
    American Association for the Advancement of Science
    American Association of Biochemistry and Molecular Biology

    Collapse Research Funds 
    Collapse research activities
    R35GM122601     (RANEY, KEVIN DOUGLAS)May 1, 2017 - Apr 30, 2022
    NIH/NIGMS
    Functions and Mechanisms of Helicases and G-Quadruplex Nucleic Acids
    Role: Co-Investigator

    R01GM117439     (RANEY, KEVIN D)Sep 21, 2015 - Jun 30, 2019
    NIH/NIGMS
    G-quadruplex DNA as a chemical signaling agent
    Role: Co-Investigator

    1012716     (BYRD, ALICIA)May 24, 2013 - Dec 31, 2014
    Burroughs Wellcome Fund
    Measurement of Helicase Diffusion and Cooperativity at the Single Molecule Level
    Role: Principal Investigator

    R01GM098922     (RANEY, KEVIN D)Sep 1, 2011 - Dec 31, 2019
    NIH/NIGMS
    DNA Helicases: Mechanism and Function
    Role: Co-Investigator

    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. Don't see publications published under other names? Login to add alternative names.
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    1. Butler TJ, Estep KN, Sommers JA, Maul RW, Moore AZ, Bandinelli S, Cucca F, Tuke MA, Wood AR, Bharti SK, Bogenhagen DF, Yakubovskaya E, Garcia-Diaz M, Guilliam TA, Byrd AK, Raney KD, Doherty AJ, Ferrucci L, Schlessinger D, Ding J, Brosh RM. Mitochondrial genetic variation is enriched in G-quadruplex regions that stall DNA synthesis in vitro. Hum Mol Genet. 2020 Mar 19. PMID: 32191790.
      View in: PubMed
    2. Su N, Byrd AK, Bharath SR, Yang O, Jia Y, Tang X, Ha T, Raney KD, Song H. Structural basis for DNA unwinding at forked dsDNA by two coordinating Pif1 helicases. Nat Commun. 2019 11 26; 10(1):5375. PMID: 31772234.
      View in: PubMed
    3. Lu C, Le S, Chen J, Byrd AK, Rhodes D, Raney KD, Yan J. Direct quantification of the translocation activities of Saccharomyces cerevisiae Pif1 helicase. Nucleic Acids Res. 2019 08 22; 47(14):7494-7501. PMID: 31216020.
      View in: PubMed
    4. Gao J, Byrd AK, Zybailov BL, Marecki JC, Guderyon MJ, Edwards AD, Chib S, West KL, Waldrip ZJ, Mackintosh SG, Gao Z, Putnam AA, Jankowsky E, Raney KD. DEAD-box RNA helicases Dbp2, Ded1 and Mss116 bind to G-quadruplex nucleic acids and destabilize G-quadruplex RNA. Chem Commun (Camb). 2019 Apr 11; 55(31):4467-4470. PMID: 30855040.
      View in: PubMed
    5. Marecki JC, Aarattuthodiyil S, Byrd AK, Penthala NR, Crooks PA, Raney KD. N-Naphthoyl-substituted indole thio-barbituric acid analogs inhibit the helicase activity of the hepatitis C virus NS3. Bioorg Med Chem Lett. 2019 02 01; 29(3):430-434. PMID: 30578035.
      View in: PubMed
    6. Byrd AK, Bell MR, Raney KD. Pif1 helicase unfolding of G-quadruplex DNA is highly dependent on sequence and reaction conditions. J Biol Chem. 2018 11 16; 293(46):17792-17802. PMID: 30257865.
      View in: PubMed
    7. Byrd AK, Raney KD. Structure and function of Pif1 helicase. Biochem Soc Trans. 2017 Oct 15; 45(5):1159-1171. PMID: 28900015.
      View in: PubMed
    8. 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 06 09; 292(23):9567-9582. PMID: 28416612.
      View in: PubMed
    9. 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 08 19; 291(34):18041-57. PMID: 27369081.
      View in: PubMed
    10. Zybailov BL, Byrd AK, Glazko GV, Rahmatallah Y, Raney KD. Protein-protein interaction analysis for functional characterization of helicases. Methods. 2016 10 01; 108:56-64. PMID: 27090004.
      View in: PubMed
    11. Yu C, Tan HY, Choi M, Stanenas AJ, Byrd AK, D Raney K, Cohan CS, Bianco PR. SSB binds to the RecG and PriA helicases in vivo in the absence of DNA. Genes Cells. 2016 Feb; 21(2):163-84. PMID: 26766785.
      View in: PubMed
    12. 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.
      View in: PubMed
    13. 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
    14. 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.
      View in: PubMed
    15. 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.
      View in: PubMed
    16. 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.
      View in: PubMed
    17. 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.
      View in: PubMed
    18. 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.
      View in: PubMed
    19. 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.
      View in: PubMed
    20. Mercado CP, Quintero MV, Li Y, Singh P, Byrd AK, Talabnin K, Ishihara M, Azadi P, Rusch NJ, Kuberan B, Maroteaux L, Kilic F. A serotonin-induced N-glycan switch regulates platelet aggregation. Sci Rep. 2013 Sep 30; 3:2795. PMID: 24077408.
      View in: PubMed
    21. 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.
      View in: PubMed
    22. 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
    23. Raney KD, Byrd AK, Aarattuthodiyil S. Structure and Mechanisms of SF1 DNA Helicases. Adv Exp Med Biol. 2013; 767:17-46. PMID: 23161005.
      View in: PubMed
    24. Byrd AK, Raney KD. Superfamily 2 helicases. Front Biosci (Landmark Ed). 2012 Jun 01; 17:2070-88. PMID: 22652765.
      View in: PubMed
    25. 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.
      View in: PubMed
    26. 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.
      View in: PubMed
    27. 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.
      View in: PubMed
    28. 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.
      View in: PubMed
    29. Byrd AK, Raney KD. Displacement of a DNA binding protein by Dda helicase. Nucleic Acids Res. 2006; 34(10):3020-9. PMID: 16738140.
      View in: PubMed
    30. 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
    31. 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
    32. Ziemba A, Reed M, Raney KD, Byrd AB, Ebbinghaus S. A bis-conjugated TFO inhibits target gene expression intracellularly and prevents triplex unwinding due to helicase activity. Biochemistry. 2003; 42(17):5013-5024.
    33. 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.
      View in: PubMed
    34. 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
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