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Alicia K. Byrd, Ph.D. - Publications

Affiliations: 
2003 University of Arkansas for Medical Sciences, United States 
Area:
Biochemistry, Molecular Biology
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43 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 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. PMID 37948114 DOI: 10.1021/acs.biochem.3c00441  0.754
2022 Belachew B, Gao J, Byrd AK, Raney KD. Hepatitis C virus non-structural protein NS3 unfolds viral G-quadruplex RNA structures. The Journal of Biological Chemistry. 102486. PMID 36108740 DOI: 10.1016/j.jbc.2022.102486  0.605
2022 Ozaslan D, Byrd AK, Belachew B, Raney KD. Alignment of helicases on single-stranded DNA increases activity. Methods in Enzymology. 672: 29-54. PMID 35934480 DOI: 10.1016/bs.mie.2022.03.066  0.765
2022 Thompson MD, Malone EG, Byrd AK. Monitoring helicase-catalyzed unwinding of multiple duplexes simultaneously. Methods in Enzymology. 672: 1-27. PMID 35934470 DOI: 10.1016/bs.mie.2022.02.018  0.533
2022 Malone EG, Thompson MD, Byrd AK. Role and Regulation of Pif1 Family Helicases at the Replication Fork. International Journal of Molecular Sciences. 23. PMID 35409096 DOI: 10.3390/ijms23073736  0.403
2021 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 Science : a Publication of the Protein Society. PMID 34761452 DOI: 10.1002/pro.4232  0.772
2021 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. Chemical Communications (Cambridge, England). PMID 34232232 DOI: 10.1039/d1cc01479j  0.674
2021 Marecki JC, Byrd AK, Raney KD. Identifying RNA Helicase Inhibitors Using Duplex Unwinding Assays. Methods in Molecular Biology (Clifton, N.J.). 2209: 53-72. PMID 33201462 DOI: 10.1007/978-1-0716-0935-4_4  0.564
2020 Edwards AD, Marecki JC, Byrd AK, Gao J, Raney KD. G-Quadruplex loops regulate PARP-1 enzymatic activation. Nucleic Acids Research. PMID 33313902 DOI: 10.1093/nar/gkaa1172  0.7
2020 Zafar M, Hazeslip L, Chauhan M, Byrd AK. Expression of human DNA helicase B is affected by G-quadruplexes in the promoter. Biochemistry. PMID 32478505 DOI: 10.1021/Acs.Biochem.0C00218  0.514
2020 Hazeslip L, Zafar MK, Chauhan MZ, Byrd AK. Genome Maintenance by DNA Helicase B. Genes. 11. PMID 32455610 DOI: 10.3390/Genes11050578  0.583
2020 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, et al. Mitochondrial genetic variation is enriched in G-quadruplex regions that stall DNA synthesis in vitro. Human Molecular Genetics. PMID 32191790 DOI: 10.1093/Hmg/Ddaa043  0.727
2019 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. Nature Communications. 10: 5375. PMID 31772234 DOI: 10.2210/Pdb6L3G/Pdb  0.719
2019 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 Research. PMID 31216020 DOI: 10.1093/Nar/Gkz541  0.752
2019 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. Chemical Communications (Cambridge, England). PMID 30855040 DOI: 10.1039/C8Cc10091H  0.639
2018 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. Bioorganic & Medicinal Chemistry Letters. PMID 30578035 DOI: 10.1016/J.Bmcl.2018.12.026  0.779
2018 Byrd AK, Bell MR, Raney KD. Pif1 helicase unfolding of G-quadruplex DNA is highly dependent on sequence and reaction conditions. The Journal of Biological Chemistry. PMID 30257865 DOI: 10.1074/Jbc.Ra118.004499  0.773
2017 Byrd AK, Raney KD. Structure and function of Pif1 helicase. Biochemical Society Transactions. PMID 28900015 DOI: 10.1042/Bst20170096  0.727
2017 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. The Journal of Biological Chemistry. PMID 28416612 DOI: 10.1074/Jbc.M117.776211  0.832
2016 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. The Journal of Biological Chemistry. PMID 27369081 DOI: 10.1074/Jbc.M116.718478  0.776
2016 Zybailov BL, Byrd AK, Glazko GV, Rahmatallah Y, Raney KD. Protein-Protein Interaction Analysis for Functional Characterization of Helicases. Methods (San Diego, Calif.). PMID 27090004 DOI: 10.1016/J.Ymeth.2016.04.014  0.621
2016 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 to Cells : Devoted to Molecular & Cellular Mechanisms. PMID 26766785 DOI: 10.1111/Gtc.12334  0.616
2016 Chib S, Byrd AK, Raney KD. Yeast Helicase Pif1 Unwinds RNA:DNA Hybrids with Higher Processivity than DNA:DNA Duplexes. The Journal of Biological Chemistry. PMID 26733194 DOI: 10.1074/Jbc.M115.688648  0.76
2015 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. Journal of Proteomics & Bioinformatics. 8: 243-252. PMID 26807012 DOI: 10.4172/Jpb.1000376  0.628
2015 Byrd AK, Raney KD. Fine tuning of a DNA fork by the RecQ helicase. Proceedings of the National Academy of Sciences of the United States of America. 112: 15263-4. PMID 26582797 DOI: 10.1073/Pnas.1520119112  0.773
2015 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. Chemical Communications (Cambridge, England). 51: 7242-4. PMID 25813861 DOI: 10.1039/C5Cc00742A  0.767
2015 Byrd AK, Raney KD. A parallel quadruplex DNA is bound tightly but unfolded slowly by pif1 helicase. The Journal of Biological Chemistry. 290: 6482-94. PMID 25589786 DOI: 10.1074/Jbc.M114.630749  0.779
2014 Ramanagoudr-Bhojappa R, Byrd AK, Dahl C, Raney KD. Yeast Pif1 accelerates annealing of complementary DNA strands. Biochemistry. 53: 7659-69. PMID 25393406 DOI: 10.1021/Bi500746V  0.774
2014 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 Research. 42: 11707-20. PMID 25249618 DOI: 10.1093/Nar/Gku845  0.84
2014 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. 9: 1207-11. PMID 25147920 DOI: 10.4161/Epi.29919  0.688
2013 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. The Journal of Biological Chemistry. 288: 16185-95. PMID 23596008 DOI: 10.1074/Jbc.M113.470013  0.831
2013 Raney KD, Byrd AK, Aarattuthodiyil S. Structure and Mechanisms of SF1 DNA Helicases. Advances in Experimental Medicine and Biology. 973: E1. PMID 23269543 DOI: 10.1007/978-1-4614-5037-5_14  0.824
2013 Raney KD, Byrd AK, Aarattuthodiyil S. Structure and Mechanisms of SF1 DNA Helicases. Advances in Experimental Medicine and Biology. 767: 17-46. PMID 23161005 DOI: 10.1007/978-1-4614-5037-5_2  0.82
2012 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 (London, England : 1993). 20: 1189-200. PMID 22658750 DOI: 10.1016/J.Str.2012.04.013  0.745
2012 Byrd AK, Raney KD. Superfamily 2 helicases. Frontiers in Bioscience (Landmark Edition). 17: 2070-88. PMID 22652765 DOI: 10.2741/4038  0.67
2012 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. Journal of Molecular Biology. 420: 141-54. PMID 22504228 DOI: 10.1016/J.Jmb.2012.04.007  0.836
2011 Liu J, Choi M, Stanenas AG, Byrd AK, Raney KD, Cohan C, Bianco PR. Novel, fluorescent, SSB protein chimeras with broad utility. Protein Science : a Publication of the Protein Society. 20: 1005-20. PMID 21462278 DOI: 10.1002/Pro.633  0.745
2010 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. 49: 2097-109. PMID 20108974 DOI: 10.1021/Bi901977K  0.795
2006 Byrd AK, Raney KD. Displacement of a DNA binding protein by Dda helicase. Nucleic Acids Research. 34: 3020-9. PMID 16738140 DOI: 10.1093/Nar/Gkl369  0.772
2005 Byrd AK, Raney KD. Increasing the length of the single-stranded overhang enhances unwinding of duplex DNA by bacteriophage T4 Dda helicase. Biochemistry. 44: 12990-7. PMID 16185067 DOI: 10.1021/Bi050703Z  0.78
2004 Byrd AK, Raney KD. Protein displacement by an assembly of helicase molecules aligned along single-stranded DNA. Nature Structural & Molecular Biology. 11: 531-8. PMID 15146172 DOI: 10.1038/Nsmb774  0.762
2002 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. Proceedings of the National Academy of Sciences of the United States of America. 99: 14722-7. PMID 12411580 DOI: 10.1073/Pnas.232401899  0.81
2002 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. 41: 2372-8. PMID 11841230 DOI: 10.1021/Bi012058B  0.832
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