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Fournier P, Higgins J, Balci H, Maiser E, Lobb CJ, Greene RL. Anomalous saturation of the phase coherence length in underdoped Pr2-xCexCuO4 thin films. Physical review. B. 2000 November; 62(18):R11993. doi: 10.1103/PhysRevB.62.R11993.
Biswas A, Fournier P, Qazilbash MM, Smolyaninova VN, Balci H, Greene RL. Evidence of a d- to s-wave pairing symmetry transition in the electron-doped cuprate superconductor Pr(2-x)CexCuO4. Phys Rev Lett. 2002 May 20;88(20):207004. doi: 10.1103/PhysRevLett.88.207004. Epub 2002 May 7. PubMed PMID: 12005593.
Balci H, Smolyaninova VN, Fournier P, Biswas A, Greene RL. Magnetic-field dependence of electronic specific heat in Pr_(1.85)Ce_(0.15)CuO_4. Physical review. B. 2002 November; 66(17):174510. doi: 10.1103/PhysRevB.66.174510.
Balci H, Hill CP, Qazilbash M, Greene RL. Nernst effect in electron-doped Pr_(2-x)Ce_xCuO_4. Physical review. B. 2003 August; 68(5):054520. doi: 10.1103/PhysRevB.68.054520.
Zamborszky F, Wu G, Shinagawa J, Yu W, Balci H, Greene RL, Clark WG, Brown SE. Inhomogeneous Electronic Structure Probed by Spin-Echo Experiments in the Electron Doped High-Tc Superconductor Pr1.85Ce0.15CuO4−y. Physical review. B. 2004 January; 92(4):047003. doi: 10.1103/PhysRevLett.92.047003.
Balci H, Greene RL. Anomalous change in the field dependence of the electronic specific heat of an electron-doped cuprate superconductor. Phys Rev Lett. 2004 Aug 6;93(6):067001. doi: 10.1103/PhysRevLett.93.067001. Epub 2004 Aug 3. PubMed PMID: 15323654.
Balci H, Greene RL. Thermodynamic properties of Pr1.85Ce0.15CuO4-d. Physical review. B, Condensed matter. 2004 October; 70(14):140508. doi: 10.1103/PhysRevB.70.140508.
Balci H, Greene RL. Thermodynamic properties of Pr_(1.85)Ce_(0.15)CuO_(4-d). Physical review. B. 2004 October; 70(14):140508. doi: 10.1103/PhysRevB.70.140508.
Balci H, Ha T, Sweeney HL, Selvin PR. Interhead distance measurements in myosin VI via SHRImP support a simplified hand-over-hand model. Biophys J. 2005 Jul;89(1):413-7. doi: 10.1529/biophysj.105.060608. Epub 2005 Apr 29. PubMed PMID: 15863481; PubMed Central PMCID: PMC1366541.
Kural C, Balci H, Selvin PR. Molecular motors one at a time: FIONA to the rescue. J Phys Condens Matter. 2005 Nov 30;17(47):S3979-95. doi: 10.1088/0953-8984/17/47/023. Epub 2005 Nov 4. PubMed PMID: 21690736.
Qazilbash MM, Koitzsch A, Dennis BS, Gozar A, Balci H, Kendziora CA, Greene RL, Blumberg G. Evolution of superconductivity in electron-doped cuprates: Magneto-Raman spectroscopy. Physical review. B. 2005 December; 72(21):214510. doi: 10.1103/PhysRevB.72.214510.
Górska M, Łusakowski A, Jȩdrzejczak A, Gołacki Z, Gałązka RR, Anderson JR, Balci H. Magnetic contribution to the specific heat of Pb1−xEuxTe(x=0.027,0.073). Physical review. B. 2006 March; 73(12):125201. doi: 10.1103/PhysRevB.73.125201.
Toprak E, Balci H, Blehm BH, Selvin PR. Three-dimensional particle tracking via bifocal imaging. Nano Lett. 2007 Jul;7(7):2043-5. doi: 10.1021/nl0709120. Epub 2007 Jun 21. Review. PubMed PMID: 17583964.
Selvin PR, Lougheed T, Tonks Hoffman M, Park H, Balci H, Blehm BH, Toprak E. Data Analysis Methods for Fluorescence Imaging with One-Nanometer Accuracy (FIONA). CSH Protoc. 2007 Oct 1;2007:pdb.ip46. doi: 10.1101/pdb.ip46. PubMed PMID: 21356943.
Selvin PR, Lougheed T, Tonks Hoffman M, Park H, Balci H, Blehm BH, Toprak E. Equipment Setup for Fluorescence Imaging with One-Nanometer Accuracy (FIONA). CSH Protoc. 2007 Oct 1;2007:pdb.ip45. doi: 10.1101/pdb.ip45. PubMed PMID: 21356942.
Selvin PR, Lougheed T, Tonks Hoffman M, Park H, Balci H, Blehm BH, Toprak E. Constructing Sample Chambers for Fluorescence Imaging with One-Nanometer Accuracy (FIONA). CSH Protoc. 2007 Oct 1;2007:pdb.prot4867. doi: 10.1101/pdb.prot4867. PubMed PMID: 21356955.
Selvin PR, Lougheed T, Tonks Hoffman M, Park H, Balci H, Blehm BH, Toprak E. Fluorescence Imaging with One-Nanometer Accuracy (FIONA). CSH Protoc. 2007 Oct 1;2007:pdb.top27. doi: 10.1101/pdb.top27. PubMed PMID: 21356960.
Selvin PR, Lougheed T, Tonks Hoffman M, Park H, Balci H, Blehm BH, Toprak E. Fluorescence Imaging with One-Nanometer Accuracy (FIONA) of Cy3-DNA under Deoxygenation Conditions. CSH Protoc. 2007 Oct 1;2007:pdb.prot4868. doi: 10.1101/pdb.prot4868. PubMed PMID: 21356956.
Joo C, Balci H, Ishitsuka Y, Buranachai C, Ha T. Advances in single-molecule fluorescence methods for molecular biology. Annu Rev Biochem. 2008;77:51-76. doi: 10.1146/annurev.biochem.77.070606.101543. Review. PubMed PMID: 18412538.
Balci H, Arslan S, Myong S, Lohman TM, Ha T. Single-molecule nanopositioning: structural transitions of a helicase-DNA complex during ATP hydrolysis. Biophys J. 2011 Aug 17;101(4):976-84. doi: 10.1016/j.bpj.2011.07.010. PubMed PMID: 21843490; PubMed Central PMCID: PMC3175085.
Qureshi MH, Ray S, Sewell AL, Basu S, Balci H. Replication protein A unfolds G-quadruplex structures with varying degrees of efficiency. J Phys Chem B. 2012 May 17;116(19):5588-94. doi: 10.1021/jp300546u. Epub 2012 May 3. PubMed PMID: 22500657; PubMed Central PMCID: PMC3434287.
Lee KS, Balci H, Jia H, Lohman TM, Ha T. Direct imaging of single UvrD helicase dynamics on long single-stranded DNA. Nat Commun. 2013;4:1878. doi: 10.1038/ncomms2882. PubMed PMID: 23695672; PubMed Central PMCID: PMC3674262.
Ray S, Qureshi MH, Malcolm DW, Budhathoki JB, Celik U, Balci H. RPA-mediated unfolding of systematically varying G-quadruplex structures. Biophys J. 2013 May 21;104(10):2235-45. doi: 10.1016/j.bpj.2013.04.004. PubMed PMID: 23708363; PubMed Central PMCID: PMC3660638.
Ray S, Bandaria JN, Qureshi MH, Yildiz A, Balci H. G-quadruplex formation in telomeres enhances POT1/TPP1 protection against RPA binding. Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):2990-5. doi: 10.1073/pnas.1321436111. Epub 2014 Feb 10. PubMed PMID: 24516170; PubMed Central PMCID: PMC3939921.
Budhathoki JB, Ray S, Urban V, Janscak P, Yodh JG, Balci H. RecQ-core of BLM unfolds telomeric G-quadruplex in the absence of ATP. Nucleic Acids Res. 2014 Oct;42(18):11528-45. doi: 10.1093/nar/gku856. Epub 2014 Sep 22. PubMed PMID: 25245947; PubMed Central PMCID: PMC4191421.
Budhathoki JB, Stafford EJ, Yodh JG, Balci H. ATP-dependent G-quadruplex unfolding by Bloom helicase exhibits low processivity. Nucleic Acids Res. 2015 Jul 13;43(12):5961-70. doi: 10.1093/nar/gkv531. Epub 2015 May 18. PubMed PMID: 25990739; PubMed Central PMCID: PMC4499149.
Farhath MM, Thompson M, Ray S, Sewell A, Balci H, Basu S. G-Quadruplex-Enabling Sequence within the Human Tyrosine Hydroxylase Promoter Differentially Regulates Transcription. Biochemistry. 2015 Sep 15;54(36):5533-45. doi: 10.1021/acs.biochem.5b00209. Epub 2015 Aug 28. PubMed PMID: 26284527.
Budhathoki JB, Maleki P, Roy WA, Janscak P, Yodh JG, Balci H. A Comparative Study of G-Quadruplex Unfolding and DNA Reeling Activities of Human RECQ5 Helicase. Biophys J. 2016 Jun 21;110(12):2585-2596. doi: 10.1016/j.bpj.2016.05.016. PubMed PMID: 27332117; PubMed Central PMCID: PMC4919422.
Maleki P, Ma Y, Iida K, Nagasawa K, Balci H. A single molecule study of a fluorescently labeled telomestatin derivative and G-quadruplex interactions. Nucleic Acids Res. 2017 Jan 9;45(1):288-295. doi: 10.1093/nar/gkw1090. Epub 2016 Nov 29. PubMed PMID: 27899628; PubMed Central PMCID: PMC5224478.
Maleki P, Budhathoki JB, Roy WA, Balci H. A practical guide to studying G-quadruplex structures using single-molecule FRET. Mol Genet Genomics. 2017 Jun;292(3):483-498. doi: 10.1007/s00438-017-1288-2. Epub 2017 Feb 1. Review. PubMed PMID: 28150040; PubMed Central PMCID: PMC5429881.
Mustafa G, Chuang CY, Roy WA, Farhath MM, Pokhrel N, Ma Y, Nagasawa K, Antony E, Comstock MJ, Basu S, Balci H. A force sensor that converts fluorescence signal into force measurement utilizing short looped DNA. Biosens Bioelectron. 2018 Dec 15;121:34-40. doi: 10.1016/j.bios.2018.08.073. Epub 2018 Aug 31. PubMed PMID: 30195120; PubMed Central PMCID: PMC6151280.
Gyawali P, Gc K, Ma Y, Abeysirigunawardena S, Nagasawa K, Balci H. Impact of Small Molecules on Intermolecular G-Quadruplex Formation. Molecules. 2019 Apr 20;24(8). doi: 10.3390/molecules24081570. PubMed PMID: 31010019; PubMed Central PMCID: PMC6514588.
Maleki P, Mustafa G, Gyawali P, Budhathoki JB, Ma Y, Nagasawa K, Balci H. Quantifying the impact of small molecule ligands on G-quadruplex stability against Bloom helicase. Nucleic Acids Res. 2019 Nov 18;47(20):10744-10753. doi: 10.1093/nar/gkz803. PubMed PMID: 31544934; PubMed Central PMCID: PMC6847008.
Gc K, Gyawali P, Balci H, Abeysirigunawardena S. Ribosomal RNA Methyltransferase RsmC Moonlights as an RNA Chaperone. Chembiochem. 2020 Jul 1;21(13):1885-1892. doi: 10.1002/cbic.201900708. Epub 2020 Mar 6. PubMed PMID: 31972066.
Gyawali P, Saha R, Smith GP, Salamonczyk M, Kharel P, Basu S, Li R, Fukuto M, Gleeson JT, Clark NA, Jákli A, Balci H, Sprunt S. Mono- and bilayer smectic liquid crystal ordering in dense solutions of "gapped" DNA duplexes. Proc Natl Acad Sci U S A. 2021 Mar 23;118(12). doi: 10.1073/pnas.2019996118. PubMed PMID: 33731478; PubMed Central PMCID: PMC8000353.
Mustafa G, Shiekh S, Gc K, Abeysirigunawardena S, Balci H. Interrogating accessibility of telomeric sequences with FRET-PAINT: evidence for length-dependent telomere compaction. Nucleic Acids Res. 2021 Apr 6;49(6):3371-3380. doi: 10.1093/nar/gkab067. PubMed PMID: 33693934; PubMed Central PMCID: PMC8034622.
Balci H, Globyte V, Joo C. Targeting G-quadruplex Forming Sequences with Cas9. ACS Chem Biol. 2021 Apr 16;16(4):596-603. doi: 10.1021/acschembio.0c00687. Epub 2021 Mar 26. PubMed PMID: 33769784; PubMed Central PMCID: PMC8056391.
Hoque ME, Mustafa G, Basu S, Balci H. Encounters between Cas9/dCas9 and G-Quadruplexes: Implications for Transcription Regulation and Cas9-Mediated DNA Cleavage. ACS Synth Biol. 2021 May 21;10(5):972-978. doi: 10.1021/acssynbio.1c00067. Epub 2021 May 10. PubMed PMID: 33970608; PubMed Central PMCID: PMC9285135.
Shiekh S, Mustafa G, Kodikara SG, Hoque ME, Yokie E, Portman JJ, Balci H. Emerging accessibility patterns in long telomeric overhangs. Proc Natl Acad Sci U S A. 2022 Jul 26;119(30):e2202317119. doi: 10.1073/pnas.2202317119. Epub 2022 Jul 18. PubMed PMID: 35858438; PubMed Central PMCID: PMC9335230.
Mustafa G. A Single Molecule Investigation of I-Motif Stability, Folding Intermediates, and Potential as In-Situ pH Sensor. Frontiers in Molecular Biosciences. 2022 August; 9. doi: 10.3389/fmolb.2022.977113.
Shiekh S, Jack A, Saurabh A, Mustafa G, Kodikara SG, Gyawali P, Hoque ME, Pressé S, Yildiz A, Balci H. Shelterin reduces the accessibility of telomeric overhangs. Nucleic Acids Res. 2022 Dec 9;50(22):12885-12895. doi: 10.1093/nar/gkac1176. PubMed PMID: 36511858; PubMed Central PMCID: PMC9825182.
Kodikara SG, Merkel KJ, Haas SJ, Shiekh S, Balci H. Detecting secondary structure formation with FRET-PAINT. Analyst. 2023 Sep 25;148(19):4655-4658. doi: 10.1039/d3an01118f. PubMed PMID: 37671909; PubMed Central PMCID: PMC10561560.
Shiekh S, Kodikara SG, Balci H. Structure, Topology, and Stability of Multiple G-quadruplexes in Long Telomeric Overhangs. J Mol Biol. 2024 Jan 1;436(1):168205. doi: 10.1016/j.jmb.2023.168205. Epub 2023 Jul 20. Review. PubMed PMID: 37481156; PubMed Central PMCID: PMC10799177.
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