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Items: 44

1.

Corrigendum: Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability.

Tsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw SJ, Algasaier SI, Kim JC, Finger LD, Jardine E, Gotham VJB, Sarker AH, Her MZ, Rashid F, Hamdan SM, Mirkin SM, Grasby JA, Tainer JA.

Nat Commun. 2017 Aug 7;8:16145. doi: 10.1038/ncomms16145. eCollection 2017.

2.

Proliferating cell nuclear antigen-agarose column: A tag-free and tag-dependent tool for protein purification affinity chromatography.

Tehseen M, Raducanu VS, Rashid F, Shirbini A, Takahashi M, Hamdan SM.

J Chromatogr A. 2019 Jun 8. pii: S0021-9673(19)30607-7. doi: 10.1016/j.chroma.2019.06.008. [Epub ahead of print]

3.

Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation.

Rashid F, Raducanu VS, Zaher MS, Tehseen M, Habuchi S, Hamdan SM.

Nat Commun. 2019 May 8;10(1):2104. doi: 10.1038/s41467-019-10137-9.

4.

Resolution of the Holliday junction recombination intermediate by human GEN1 at the single-molecule level.

Sobhy MA, Bralić A, Raducanu VS, Takahashi M, Tehseen M, Rashid F, Zaher MS, Hamdan SM.

Nucleic Acids Res. 2019 Feb 28;47(4):1935-1949. doi: 10.1093/nar/gky1280.

5.

Microfluidics-based super-resolution microscopy enables nanoscopic characterization of blood stem cell rolling.

AbuZineh K, Joudeh LI, Al Alwan B, Hamdan SM, Merzaban JS, Habuchi S.

Sci Adv. 2018 Jul 18;4(7):eaat5304. doi: 10.1126/sciadv.aat5304. eCollection 2018 Jul.

6.

Positioning the 5'-flap junction in the active site controls the rate of flap endonuclease-1-catalyzed DNA cleavage.

Song B, Hamdan SM, Hingorani MM.

J Biol Chem. 2018 Mar 30;293(13):4792-4804. doi: 10.1074/jbc.RA117.001137. Epub 2018 Feb 9.

7.

Missed cleavage opportunities by FEN1 lead to Okazaki fragment maturation via the long-flap pathway.

Zaher MS, Rashid F, Song B, Joudeh LI, Sobhy MA, Tehseen M, Hingorani MM, Hamdan SM.

Nucleic Acids Res. 2018 Apr 6;46(6):2956-2974. doi: 10.1093/nar/gky082.

8.

Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea.

Takahashi M, Takahashi E, Joudeh LI, Marini M, Das G, Elshenawy MM, Akal A, Sakashita K, Alam I, Tehseen M, Sobhy MA, Stingl U, Merzaban JS, Di Fabrizio E, Hamdan SM.

FASEB J. 2018 Jun;32(6):3346-3360. doi: 10.1096/fj.201700862RR. Epub 2018 Jan 24.

9.

What is all this fuss about Tus? Comparison of recent findings from biophysical and biochemical experiments.

Berghuis BA, Raducanu VS, Elshenawy MM, Jergic S, Depken M, Dixon NE, Hamdan SM, Dekker NH.

Crit Rev Biochem Mol Biol. 2018 Feb;53(1):49-63. doi: 10.1080/10409238.2017.1394264. Epub 2017 Nov 6. Review.

PMID:
29108427
10.

Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability.

Tsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw SJ, Algasaier SI, Kim JC, Finger LD, Jardine E, Gotham VJB, Sarker AH, Her MZ, Rashid F, Hamdan SM, Mirkin SM, Grasby JA, Tainer JA.

Nat Commun. 2017 Jun 27;8:15855. doi: 10.1038/ncomms15855. Erratum in: Nat Commun. 2017 Aug 07;8:16145.

11.

Characterization of Recombinant Thermococcus kodakaraensis (KOD) DNA Polymerases Produced Using Silkworm-Baculovirus Expression Vector System.

Yamashita M, Xu J, Morokuma D, Hirata K, Hino M, Mon H, Takahashi M, Hamdan SM, Sakashita K, Iiyama K, Banno Y, Kusakabe T, Lee JM.

Mol Biotechnol. 2017 Jun;59(6):221-233. doi: 10.1007/s12033-017-0008-9.

PMID:
28484957
12.

Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1.

Rashid F, Harris PD, Zaher MS, Sobhy MA, Joudeh LI, Yan C, Piwonski H, Tsutakawa SE, Ivanov I, Tainer JA, Habuchi S, Hamdan SM.

Elife. 2017 Feb 23;6. pii: e21884. doi: 10.7554/eLife.21884.

13.

Replisome speed determines the efficiency of the Tus-Ter replication termination barrier.

Elshenawy MM, Jergic S, Xu ZQ, Sobhy MA, Takahashi M, Oakley AJ, Dixon NE, Hamdan SM.

Nature. 2015 Sep 17;525(7569):394-8. doi: 10.1038/nature14866. Epub 2015 Aug 31.

PMID:
26322585
14.

Quantitative Characterization of E-selectin Interaction with Native CD44 and P-selectin Glycoprotein Ligand-1 (PSGL-1) Using a Real Time Immunoprecipitation-based Binding Assay.

AbuSamra DB, Al-Kilani A, Hamdan SM, Sakashita K, Gadhoum SZ, Merzaban JS.

J Biol Chem. 2015 Aug 28;290(35):21213-30. doi: 10.1074/jbc.M114.629451. Epub 2015 Jun 29.

15.

Two mechanisms coordinate replication termination by the Escherichia coli Tus-Ter complex.

Pandey M, Elshenawy MM, Jergic S, Takahashi M, Dixon NE, Hamdan SM, Patel SS.

Nucleic Acids Res. 2015 Jul 13;43(12):5924-35. doi: 10.1093/nar/gkv527. Epub 2015 May 24.

16.

Dissecting the interactions of SERRATE with RNA and DICER-LIKE 1 in Arabidopsis microRNA precursor processing.

Iwata Y, Takahashi M, Fedoroff NV, Hamdan SM.

Nucleic Acids Res. 2013 Oct;41(19):9129-40. doi: 10.1093/nar/gkt667. Epub 2013 Aug 5.

17.

Sequential and multistep substrate interrogation provides the scaffold for specificity in human flap endonuclease 1.

Sobhy MA, Joudeh LI, Huang X, Takahashi M, Hamdan SM.

Cell Rep. 2013 Jun 27;3(6):1785-94. doi: 10.1016/j.celrep.2013.05.001. Epub 2013 Jun 6.

18.

Racemization of enantiopure secondary alcohols by Thermoanaerobacter ethanolicus secondary alcohol dehydrogenase.

Musa MM, Phillips RS, Laivenieks M, Vieille C, Takahashi M, Hamdan SM.

Org Biomol Chem. 2013 May 7;11(17):2911-5. doi: 10.1039/c3ob27415b. Epub 2013 Mar 22.

PMID:
23525226
19.

A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode.

Jergic S, Horan NP, Elshenawy MM, Mason CE, Urathamakul T, Ozawa K, Robinson A, Goudsmits JM, Wang Y, Pan X, Beck JL, van Oijen AM, Huber T, Hamdan SM, Dixon NE.

EMBO J. 2013 May 2;32(9):1322-33. doi: 10.1038/emboj.2012.347. Epub 2013 Feb 22.

20.

Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics.

Sobhy MA, Elshenawy MM, Takahashi M, Whitman BH, Walter NG, Hamdan SM.

Rev Sci Instrum. 2011 Nov;82(11):113702. doi: 10.1063/1.3657153.

PMID:
22128979
21.

Timing, coordination, and rhythm: acrobatics at the DNA replication fork.

Hamdan SM, van Oijen AM.

J Biol Chem. 2010 Jun 18;285(25):18979-83. doi: 10.1074/jbc.R109.022939. Epub 2010 Apr 9. Review.

22.

Two modes of interaction of the single-stranded DNA-binding protein of bacteriophage T7 with the DNA polymerase-thioredoxin complex.

Ghosh S, Hamdan SM, Richardson CC.

J Biol Chem. 2010 Jun 4;285(23):18103-12. doi: 10.1074/jbc.M110.107656. Epub 2010 Apr 6.

23.

Mechanism of sequence-specific template binding by the DNA primase of bacteriophage T7.

Lee SJ, Zhu B, Hamdan SM, Richardson CC.

Nucleic Acids Res. 2010 Jul;38(13):4372-83. doi: 10.1093/nar/gkq205. Epub 2010 Mar 28.

24.

Thioredoxin suppresses microscopic hopping of T7 DNA polymerase on duplex DNA.

Etson CM, Hamdan SM, Richardson CC, van Oijen AM.

Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):1900-5. doi: 10.1073/pnas.0912664107. Epub 2010 Jan 11.

25.

A literature based study of stormwater harvesting as a new water resource.

Hamdan SM.

Water Sci Technol. 2009;60(5):1327-39. doi: 10.2166/wst.2009.396. Review.

PMID:
19717921
26.

Motors, switches, and contacts in the replisome.

Hamdan SM, Richardson CC.

Annu Rev Biochem. 2009;78:205-43. doi: 10.1146/annurev.biochem.78.072407.103248. Review.

PMID:
19298182
27.

Real-time single-molecule observation of rolling-circle DNA replication.

Tanner NA, Loparo JJ, Hamdan SM, Jergic S, Dixon NE, van Oijen AM.

Nucleic Acids Res. 2009 Mar;37(4):e27. doi: 10.1093/nar/gkp006. Epub 2009 Jan 20.

28.

Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis.

Hamdan SM, Loparo JJ, Takahashi M, Richardson CC, van Oijen AM.

Nature. 2009 Jan 15;457(7227):336-9. doi: 10.1038/nature07512. Epub 2008 Nov 23.

29.

Single-molecule studies of fork dynamics in Escherichia coli DNA replication.

Tanner NA, Hamdan SM, Jergic S, Loscha KV, Schaeffer PM, Dixon NE, van Oijen AM.

Nat Struct Mol Biol. 2008 Sep;15(9):998. No abstract available.

PMID:
18769472
30.

Interactions of Escherichia coli thioredoxin, the processivity factor, with bacteriophage T7 DNA polymerase and helicase.

Ghosh S, Hamdan SM, Cook TE, Richardson CC.

J Biol Chem. 2008 Nov 14;283(46):32077-84. doi: 10.1074/jbc.M805062200. Epub 2008 Aug 30.

31.

Peptide ligands specific to the oxidized form of Escherichia coli thioredoxin.

Scholle MD, Banach BS, Hamdan SM, Richardson CC, Kay BK.

Biochim Biophys Acta. 2008 Nov;1784(11):1735-41. doi: 10.1016/j.bbapap.2008.06.022. Epub 2008 Jul 11.

32.

Single-molecule studies of fork dynamics in Escherichia coli DNA replication.

Tanner NA, Hamdan SM, Jergic S, Loscha KV, Schaeffer PM, Dixon NE, van Oijen AM.

Nat Struct Mol Biol. 2008 Feb;15(2):170-6. doi: 10.1038/nsmb.1381. Epub 2008 Jan 27. Erratum in: Nat Struct Mol Biol. 2008 Sep;15(9):998. Loscha, Karin V [added].

33.

Inadequate inhibition of host RNA polymerase restricts T7 bacteriophage growth on hosts overexpressing udk.

Qimron U, Kulczyk AW, Hamdan SM, Tabor S, Richardson CC.

Mol Microbiol. 2008 Jan;67(2):448-57. Epub 2007 Dec 5.

34.

Hydrolysis of the 5'-p-nitrophenyl ester of TMP by oligoribonucleases (ORN) from Escherichia coli, Mycobacterium smegmatis, and human.

Young Park A, Elvin CM, Hamdan SM, Wood RJ, Liyou NE, Hamwood TE, Jennings PA, Dixon NE.

Protein Expr Purif. 2008 Feb;57(2):180-7. Epub 2007 Oct 17.

PMID:
18023590
35.

Dynamic DNA helicase-DNA polymerase interactions assure processive replication fork movement.

Hamdan SM, Johnson DE, Tanner NA, Lee JB, Qimron U, Tabor S, van Oijen AM, Richardson CC.

Mol Cell. 2007 Aug 17;27(4):539-49.

36.

Exchange of DNA polymerases at the replication fork of bacteriophage T7.

Johnson DE, Takahashi M, Hamdan SM, Lee SJ, Richardson CC.

Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5312-7. Epub 2007 Mar 16.

37.

The unstructured C-terminus of the tau subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the alpha subunit.

Jergic S, Ozawa K, Williams NK, Su XC, Scott DD, Hamdan SM, Crowther JA, Otting G, Dixon NE.

Nucleic Acids Res. 2007;35(9):2813-24. Epub 2007 Mar 13.

38.

Essential residues in the C terminus of the bacteriophage T7 gene 2.5 single-stranded DNA-binding protein.

Marintcheva B, Hamdan SM, Lee SJ, Richardson CC.

J Biol Chem. 2006 Sep 1;281(35):25831-40. Epub 2006 Jun 28.

39.

The C-terminal residues of bacteriophage T7 gene 4 helicase-primase coordinate helicase and DNA polymerase activities.

Lee SJ, Marintcheva B, Hamdan SM, Richardson CC.

J Biol Chem. 2006 Sep 1;281(35):25841-9. Epub 2006 Jun 28.

40.

Structure of the theta subunit of Escherichia coli DNA polymerase III in complex with the epsilon subunit.

Keniry MA, Park AY, Owen EA, Hamdan SM, Pintacuda G, Otting G, Dixon NE.

J Bacteriol. 2006 Jun;188(12):4464-73.

41.

Primer initiation and extension by T7 DNA primase.

Qimron U, Lee SJ, Hamdan SM, Richardson CC.

EMBO J. 2006 May 17;25(10):2199-208. Epub 2006 Apr 27.

42.

DNA primase acts as a molecular brake in DNA replication.

Lee JB, Hite RK, Hamdan SM, Xie XS, Richardson CC, van Oijen AM.

Nature. 2006 Feb 2;439(7076):621-4.

PMID:
16452983
43.

A unique loop in T7 DNA polymerase mediates the binding of helicase-primase, DNA binding protein, and processivity factor.

Hamdan SM, Marintcheva B, Cook T, Lee SJ, Tabor S, Richardson CC.

Proc Natl Acad Sci U S A. 2005 Apr 5;102(14):5096-101. Epub 2005 Mar 28.

44.

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