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Alicia Byrd

TitleAssistant Professor
InstitutionUniversity of Arkansas for Medical Sciences
DepartmentBiochemistry & Molecular Biology, College of Medicine
Address433-2 Biomedical Research II
325 S. Elm St.
Mail Slot # 516
Little Rock AR 72205
Phone501-526-6488
ORCID ORCID Icon0000-0001-5484-0759 Additional info
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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 
    Collapse research activities and funding
    P20GM121293 Sub-Project 6782     (BYRD, ALICIA K)Jul 20, 2022 - Jun 30, 2027
    NIH/NIGMS
    Role of HELB in the Replication Stress Response
    Role: Principal Investigator

    P20GM121293     (BYRD, ALICIA K)Jul 1, 2022 - Jun 30, 2024
    NIH/Nat. Inst. of General Medical Sciences - Pass Through: Arkansas Children's Research Institute
    Role of HELB in the Replication Stress Response Dr. Tacketts COBRA through ACRI
    Role: Principal Investigator

    Hornick Endowment     (BYRD, ALICIA K)Jan 1, 2021 - Dec 31, 2022
    UAMS Internal Research Awards
    The effect of rs75770066, a stroke associated single nucleotide polymorphism, on enzyme activity
    Role: Principal Investigator

    ABCRP Pilot Award     (BYRD, ALICIA K)Sep 1, 2020 - Aug 31, 2022
    Arkansas Breast Cancer Research Program
    Identification of synthetic lethal targets for treating breast cancer
    Role: Principal Investigator

    Medical Research Endowment Fund     (BYRD, ALICIA K)Sep 1, 2020 - Aug 31, 2021
    UAMS Internal Research Awards
    The Role of DNA Helicase B in Response to DNA Replication Stress
    Role: Principal Investigator

    GR034993     (BYRD, ALICIA K)Jul 1, 2019 - Jun 30, 2022
    UAMS ACHRI Flow Through
    No FP attached
    Role: Principal Investigator

    Seeds of Science FY19     (BYRD, ALICIA K)Feb 1, 2019 - Jan 31, 2020
    UAMS Internal Research Awards
    Seeds of Science Pilot award
    Role: Principal Investigator

    SeedsofScienceFY19     (BYRD, ALICIA K)Feb 1, 2019 - Jan 31, 2020
    UAMS Internal Research Awards
    Seeds of Science Pilot award
    Role: Principal Investigator

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

    ACRI # TBD     (CHEN, JIN-RAN)May 15, 2016 - Apr 30, 2021
    UAMS ACHRI Flow Through
    No FP attached
    Role: Principal Investigator

    1012716     (BYRD, ALICIA K)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 DOUGLAS)Sep 1, 2011 - Dec 31, 2019
    NIH
    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.
    List All   |   Timeline
    1. He X, Yun MK, Li Z, Waddell MB, Nourse A, Churion KA, Kreuzer KN, Byrd AK, White SW. Structural and functional insights into the interaction between the bacteriophage T4 DNA processing proteins gp32 and Dda. Nucleic Acids Res. 2024 Nov 11; 52(20):12748-12762. PMID: 39417586.
      View in: PubMed
    2. Thompson M, Byrd A. Untargeted CUT&Tag and BG4 CUT&Tag are both enriched at G-quadruplexes and accessible chromatin. bioRxiv. 2024 Sep 29. PMID: 39386625.
      View in: PubMed
    3. Hong Z, Byrd AK, Gao J, Das P, Tan VQ, Malone EG, Osei B, Marecki JC, Protacio RU, Wahls WP, Raney KD, Song H. Eukaryotic Pif1 helicase unwinds G-quadruplex and dsDNA using a conserved wedge. Nat Commun. 2024 Jul 19; 15(1):6104. PMID: 39030241.
      View in: PubMed
    4. Gao J, Proffitt DR, Marecki JC, Protacio RU, Wahls WP, Byrd AK, Raney KD. Two residues in the DNA binding site of Pif1 helicase are essential for nuclear functions but dispensable for mitochondrial respiratory growth. Nucleic Acids Res. 2024 Jun 24; 52(11):6543-6557. PMID: 38752483.
      View in: PubMed
    5. Osei B, May BH, Stiefel CM, West KL, Zafar MK, Thompson MD, Bergstrom E, Leung JW, Enemark EJ, Byrd AK. Rare SNP in the HELB gene interferes with RPA interaction and cellular function of HELB. bioRxiv. 2024 Mar 02. PMID: 38464108.
      View in: PubMed
    6. Chib S, Griffin WC, Gao J, Proffitt DR, Byrd AK, Raney KD. Pif1 Helicase Mediates Remodeling of Protein-Nucleic Acid Complexes by Promoting Dissociation of Sub1 from G-Quadruplex DNA and Cdc13 from G-Rich Single-Stranded DNA. Biochemistry. 2023 12 05; 62(23):3360-3372. PMID: 37948114.
      View in: PubMed
    7. Belachew B, Gao J, Byrd AK, Raney KD. Hepatitis C virus nonstructural protein NS3 unfolds viral G-quadruplex RNA structures. J Biol Chem. 2022 11; 298(11):102486. PMID: 36108740.
      View in: PubMed
    8. Ozaslan D, Byrd AK, Belachew B, Raney KD. Alignment of helicases on single-stranded DNA increases activity. Methods Enzymol. 2022; 672:29-54. PMID: 35934480.
      View in: PubMed
    9. Malone EG, Thompson MD, Byrd AK. Role and Regulation of Pif1 Family Helicases at the Replication Fork. Int J Mol Sci. 2022 Mar 29; 23(7). PMID: 35409096.
      View in: PubMed
    10. Thompson MD, Malone EG, Byrd AK. Monitoring helicase-catalyzed unwinding of multiple duplexes simultaneously. Methods Enzymol. 2022; 672:1-27. PMID: 35934470.
      View in: PubMed
    11. Byrd AK, Malone EG, Hazeslip L, Zafar MK, Harrison DK, Thompson MD, Gao J, Perumal SK, Marecki JC, Raney KD. A structural feature of Dda helicase which enhances displacement of streptavidin and trp repressor from DNA. Protein Sci. 2022 02; 31(2):407-421. PMID: 34761452.
      View in: PubMed
    12. Chappell K, Manna K, Washam CL, Graw S, Alkam D, Thompson MD, Zafar MK, Hazeslip L, Randolph C, Gies A, Bird JT, Byrd AK, Miah S, Byrum SD. Multi-omics data integration reveals correlated regulatory features of triple negative breast cancer. Mol Omics. 2021 10 11; 17(5):677-691. PMID: 34142686.
      View in: PubMed
    13. Gao J, Gao Z, Putnam AA, Byrd AK, Venus SL, Marecki JC, Edwards AD, Lowe HM, Jankowsky E, Raney KD. G-quadruplex DNA inhibits unwinding activity but promotes liquid-liquid phase separation by the DEAD-box helicase Ded1p. Chem Commun (Camb). 2021 Jul 27; 57(60):7445-7448. PMID: 34232232.
      View in: PubMed
    14. Edwards AD, Marecki JC, Byrd AK, Gao J, Raney KD. G-Quadruplex loops regulate PARP-1 enzymatic activation. Nucleic Acids Res. 2021 01 11; 49(1):416-431. PMID: 33313902.
      View in: PubMed
    15. Marecki JC, Byrd AK, Raney KD. Identifying RNA Helicase Inhibitors Using Duplex Unwinding Assays. Methods Mol Biol. 2021; 2209:53-72. PMID: 33201462.
      View in: PubMed
    16. Graw S, Tang J, Zafar MK, Byrd AK, Bolden C, Peterson EC, Byrum SD. proteiNorm - A User-Friendly Tool for Normalization and Analysis of TMT and Label-Free Protein Quantification. ACS Omega. 2020 Oct 13; 5(40):25625-25633. PMID: 33073088.
      View in: PubMed
    17. Zafar MK, Hazeslip L, Chauhan MZ, Byrd AK. The Expression of Human DNA Helicase B Is Affected by G-Quadruplexes in the Promoter. Biochemistry. 2020 07 07; 59(26):2401-2409. PMID: 32478505.
      View in: PubMed
    18. 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 05 28; 29(8):1292-1309. PMID: 32191790.
      View in: PubMed
    19. Hazeslip L, Zafar MK, Chauhan MZ, Byrd AK. Genome Maintenance by DNA Helicase B. Genes (Basel). 2020 05 21; 11(5). PMID: 32455610.
      View in: PubMed
    20. 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
    21. 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
    22. 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
    23. 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
    24. 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
    25. 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
    26. 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
    27. 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
    28. 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
    29. 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
    30. 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):5889-5901. PMID: 26733194.
      View in: PubMed
    31. 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
    32. 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
    33. 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
    34. 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
    35. 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
    36. 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
    37. 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
    38. 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
    39. 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
    40. 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
    41. 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
    42. Byrd AK, Raney KD. Superfamily 2 helicases. Front Biosci (Landmark Ed). 2012 06 01; 17(6):2070-88. PMID: 22652765.
      View in: PubMed
    43. 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
    44. 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
    45. 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
    46. 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
    47. 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
    48. 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
    49. 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
    50. 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.
    51. 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
    52. 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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