Sajad Shiekh, Amanda Jack, Golam Mustafa, Sineth G. Kodikara, Prabesh Gyawali, Mohammed Enamul Hoque, Ahmet Yildiz and Hamza Balci, "Impact of Shelterin Complex on Telomere Accessibility", Nucleic Acids Research (2022).
Also available at BioRxiv (2022) bioRxiv 2022.05.24.493289; https://www.biorxiv.org/content/10.1101/2022.05.24.493289v1
Sahiti Kuppa, Jaigeeth Deveryshetty, Rahul Chadda, Jenna Mattice, Nilisha Pokhrel, Vikas Kaushik, Angela Patterson, Nalini Dhingra, Sushil Pangeni, Marisa K. Sadauskas, Sajad Shiekh, Hamza Balci, Taekjip Ha, Xiaolan Zhao, Brian Bothner, Edwin Antony, "Rtt105 configurationally staples RPA and blocks facilitated exchange and interactions with RPA-interacting proteins", Nature Communications (2022)
Also availble at bioRxiv 2022.02.05.479199; doi: https://doi.org/10.1101/2022.02.05.479199
Golam Mustafa, Prabesh Gyawali, Jacob A. Taylor, Parastoo Maleki, Marlon V. Nunez, Michael C. Guntrum, Sajad Shiekh, Hamza Balci, “A Single Molecule Investigation of I-Motif Stability, Folding Intermediates, and Potential as In-Situ pH Sensor” In Press, Frontiers in Molecular Biosciences (2022);
Also available at BioRxiv
Prabesh Gyawali, Rony Saha, Sineth G. Kodikara, Ruipeng Li, Masafumi Fukuto, James T. Gleeson, Gregory P. Smith, Noel A. Clark, Antal Jakli, Hamza Balci, and Samuel Sprunt, "Smectic-B phase and temperature-driven smectic-B to -A transition in concentrated solutions of "gapped" DNA", Physical Review Research (2022)
Sajad Shiekh, Golam Mustafa, Mohammed Enamul Hoque, Eric Yokie, John J. Portman, Hamza Balci, "Emerging Accessibility Patterns in Long Telomeric Overhangs", PNAS (2022)
Also available at bioRxiv 2021.11.24.469879; doi: https://doi.org/10.1101/2021.11.24.469879
Commentary about the PNAS article by Prof. Ahmet Yildiz (UC, Berkeley): https://www.pnas.org/doi/full/10.1073/pnas.2211219119
Mohammed Enamul Hoque, Golam Mustafa, Soumitra Basu, Hamza Balci, "Encounters Between Cas9/dCas9 and G-quadruplexes: Implications for Transcription Regulation and Cas9-Mediated DNA Cleavage", ACS Synthetic Biology (2021)
P. Gyawali, R. Saha, M. Salamonczyk, P. Kharel, S. Basu, R. Li, M. Fukuto, G. P. Smith, J. T. Gleeson, A. Jakli, H.Balci, and S. Sprunt, " Mono and bilayer smectic liquid crystal ordering in dense solutions of “gapped” DNA duplexes", PNAS (2021)
Golam Mustafa, Sajad Shiekh, Keshav GC, Sanjaya Abeysirigunawardena, and Hamza Balci, "Interrogating Accessibility of Telomeric Sequences with FRET-PAINT: Evidence for Length-Dependent Telomere Compaction", Nucleic Acids Research (2021)
Keshav GC, Prabesh Gyawali, Hamza Balci, Sanjaya Abeysirigunawardena, "Ribosomal RNA methyltransferase enzyme RsmC moonlights as an RNA chaperone" ChemBioChem, (2020)
Parastoo Maleki, Golam Mustafa, Prabesh Gyawali, Jagat B. Budhathoki, Yue Ma, Kazuo Nagasawa and Hamza Balci, "Quantifying the impact of small molecule ligands on G-quadruplex stability against Bloom helicase", Nucleic Acids Research, (2019)
Prabesh Gyawali, Keshav GC, Yue Ma, Sanjaya Abeysirigunawardena, Kazuo Nagasawa and Hamza Balci, "Impact of Small Molecules on Intermolecular G-Quadruplex Formation", Molecules, 24 (8), 1570, (2019)
Golam Mustafa, Cho-Ying Chuang, William A. Roy, Mohamed M. Farhath, Nilisha Pokhrel, Yue Ma, Kazuo Nagasawa, Edwin Antony, Matthew J. Comstock, Soumitra Basu, Hamza Balci, "A Force Sensor that Converts Fluorescence Signal into Force Measurement Utilizing Short Looped DNA", Biosensors and Bioelectronics (2018). Manuscript & SI.pdf
Parastoo Maleki, Jagat B. Budhathoki, William A. Roy, Hamza Balci "A Practical Guide to Studying G-quadruplex Structures using Single Molecule FRET", Molecular Genetics and Genomics (2017) Manuscript.pdf
Maleki, Parastoo; Ma, Yue,; Iida, Keisuke; Nagasawa, Kazuo; Balci, Hamza "A Single Molecule Study of a Fluorescently Labeled Telomestatin Derivative and G-Quadruplex Interactions" Nucleic Acids Research (2016) Manuscript & SI.pdf
J. B. Budhathoki, P. Maleki, W. A. Roy, P. Janscak, J. G. Yodh, H. Balci "A Comparative Study of G-quadruplex Unfolding and DNA Reeling Activities of Human RECQ5 Helicase" Biophysical Journal, 110, 2585 (2016) Manuscript & SI.pdf
Mohamed Farhath, Matthew Thompson, Sujay Ray, Abby Sewell, Hamza Balci, Soumitra Basu. "G-Quadruplex-Enabling Sequence within the Human Tyrosine Hydroxylase Promoter Differentially Regulates Transcription" ACS Biochemistry, (2015). Manuscript & SI.pdf
Jagat B. Budhathoki, Edward J. Stafford, Jaya G. Yodh, Hamza Balci. "ATP-dependent G-Quadruplex Unfolding by Bloom Helicase Exhibits Low Processivity" Nucleic Acids Research (2015)
Jagat B. Budhathoki, Sujay Ray, Vaclav Urban, Pavel Janscak, Jaya G. Yodh, Hamza Balci. "RecQ-core of BLM Unfolds Telomeric G-quadruplex in the Absence of ATP" Nucleic Acids Research (2014)
Sujay Ray, Jigar Bandaria, Mohammad H. Qureshi, Ahmet Yildiz, Hamza Balci. "G-quadruplex formation in telomeres enhances POT1/TPP1 protection against RPA binding." , PNAS vol. 111 no. 8, 2990–2995 (2014)
A highlight by Prof. Karl-Peter Hopfner: "Single-Molecule Choreography between Telomere Proteins and G-Quadruplexes"
Hamza Balci, Sinan Arslan, Sua Myong, Timothy L. Lohman, Taekjip Ha. “Single Molecule Nano-Positioning: Structural Transitions of a Helicase-DNA Complex during ATP Hydrolysis” Biophysical Journal 101, 976-984 (2011)
Erdal Toprak*, Hamza Balci*, Benjamin H. Blehm, Paul R. Selvin. “Three-Dimensional Particle Tracking via Bifocal Imaging”. Nano Lett., 7 (7),2043 -2045, (2007). *These authors contributed equally to this work
Condensed Matter Physics Publications
Guoqing Wu, W. G. Clark, S. E. Brown, R. L. Greene, H. Balci, A. P. Reyes, P. L. Kuhns, and W. G. Moulton. “Measurements of the anisotropic irreversibility field in the electrondoped high-Tc superconductor Pr2-xCexCuO4-y” Submitted to Phys. Rev. Lett. (2008)
M. Górska, A. Łusakowski, A. Jedrzejczak, Z. Gołacki, R. R. Gałązka, J. R. Anderson and H. Balci. “Magnetic contribution to the specific heat of Pb1−xEuxTe (x=0.027,0.073)” Phys. Rev. B 73, 125201 (2006).
M. M. Qazilbash, A. Koitzsch, B. S. Dennis, A. Gozar, Hamza Balci, C. A. Kendziora, R. L. Greene, and G. Blumberg. “Evolution of superconductivity in electron-doped cuprates: Magneto-Raman spectroscopy” Phys. Rev. B 72, 214510 (2005).
Hamza Balci, C.P.Hill, M.M.Qazilbash, and R.L.Greene. “Nernst Effect in Electron-Doped Pr2-xCexCuO4” Phys. Rev. B 68, 054520 (2003)
Hamza Balci, C.P.Hill, M.M.Qazilbash, and R.L.Greene. ”Superconducting Fluctuations in Cuprates from the Nernst Effect” Physica C, 408-410, 709 (2004).
Hamza Balci, V.N. Smolyaninova, P. Fournier, Amlan Biswas, and R.L.Greene. “Magnetic-field dependence of electronic specific heat in Pr1.85Ce0.15CuO4” Phys. Rev. B 66, 174510 (2002)
F. Zamborszky, G. Wu, J. Shinagawa, W. Yu, H. Balci, R. L. Greene, W. G. Clark, and S. E. Brown . “Inhomogeneous electronic structure probed by spin-echo experiments in the electron doped high-Tc superconductor Pr1.85Ce0.15CuO4-d”, Phys. Rev. Lett. 92, 047003 (2004)
Amlan Biswas, P. Fournier, M. M. Qazilbash, V. N. Smolyaninova, Hamza Balci, and R. L. Greene. ”Evidence of a d- to s-Wave Pairing Symmetry Transition in the Electron-Doped Cuprate Superconductor Pr2-xCexCuO4” Phys. Rev. Lett. 88, 207004 (2002)
P. Fournier, J. Higgins, H. Balci, E. Maiser, C. J. Lobb, and R. L. Greene. “Anomalous saturation of the phase coherence length in underdoped Pr2-xCexCuO4 thin films” Phys. Rev. B 62, R11993 (2000)