Publications

• Mohammad Lutful Kabir, Sineth G. Kodikara, Mohammed Enamul Hoque, Sajad Shiekh, Janan Alfehai, Soumitra Basu, Hamza Balci, "Combining the CRISPR Activation and Interference Capabilities Using dCas9 and G-Quadruplex Structures. Under Review.

Also available at BioRxiv (2024) 

• Kodikara, Sineth; Gyawali, Prabesh; Gleeson, James; Jakli, Antal; Sprunt, Sam; Balci, Hamza, "Sequence-Dependent Liquid Crystalline Ordering of DNA", Submitted.

Also avaialble at BioRxiv (2024)

• Alfehaid, Janan; Kodikara, Sineth; Alhajri, Tuqa;  Kabir, Mohammad; Balci, Hamza, "Reusable Microfluidic Chambers for Single-Molecule Microscopy", ACS Applied Materials & Interfaces (2024). 

Also available at BioRxiv (2024)

• Sajad Shiekh, Darion Feldt, Amanda Jack, Sineth G. Kodikara, Janan Alfehaid, Sabaha Pasha, Ahmet Yildiz, Hamza Balci, "Protection of the Telomeric Junction by the Shelterin Complex", Journal of the American Chemical Society (2024)

Also available on BioRxiv (2024)

• Mohammed Enamul Hoque, Mohammad Lutful Kabir, Sajad Shiekh, Hamza Balci, Soumitra Basu, "Stalling of Transcription by Putative G-quadruplex Sequences and CRISPR-dCas9", Submitted (2024).

Available on BioRxiv (2024)

• Brintha Croos, Sajad Shiekh, Thulasi Mahendran, Jafar Al-Saffar, Prakash Kharel, Hamza Balci and Soumitra Basu, "Oxidative base modifications within the open reading frame of human NAT8L mRNA is detrimental to its translation", Submitted (2023)  

• Kodikara, Sineth; Gyawali, Prabesh; Gleeson, James; Jakli, Antal; Sprunt, Sam; Balci, Hamza, "Impact of Divalent Cations on In-Layer Positional Order of DNA-Based Liquid Crystals: Implications for DNA Condensation" ACS Biomacromolecules (2024) 

Available on BioRxiv

• Sajad Shiekh, Sineth G. Kodikara, Hamza Balci, "Structure, Topology, and Stability of Multiple G-quadruplexes in Long Telomeric Overhangs" Invited Review, Journal of Molecular Biology (2024)

• Sineth G. Kodikara, Kylie J. Merkel, Simon J. Haas, Sajad Shiekh, Hamza Balci,"Detecting Secondary Structure Formation with FRET-PAINT", Royal Society of Chemistry-Analyst (2023) DOI: 10.1039/d3an01118f

• Sineth G. Kodikara, Prabesh Gyawali, James T. Gleeson, Antal Jakli, Samuel Sprunt, and Hamza Balci, "Stability of End-to-End Base Stacking Interactions in Highly Concentrated DNA Solutions", Langmuir (2023)

Also available at BioRxiv (2023)

• Sajad Shiekh, Amanda Jack, Ayush Saurabh, Golam Mustafa, Sineth G Kodikara, Prabesh Gyawali, Mohammed Enamul Hoque, Steve Pressé, Ahmet Yildiz, Hamza Balci , "Shelterin reduces the accessibility of telomeric overhangs", Nucleic Acids Research (2022).

Also available at BioRxiv (2022) 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” 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)

• Hamza Balci, Viktorija Globyte, Chirlmin Joo, "Targeting G-quadruplex Forming Sequences with Cas9", BioRxiv (2020), ACS Chemical Biology (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"

• Kyung Suk Lee, Hamza Balci, Haifeng Jia, Timothy M. Lohman, Taekjip Ha. "Direct imaging of single UvrD helicase dynamics on long single-stranded DNA" Nature Communications 4, Article number: 1878 doi:10.1038/ncomms2882  (2013) .

• Sujay Ray, Mohammad H. Qureshi, Dominic W. Malcolm, Jagat B. Budhathoki, Ugur Celik, Hamza Balci. "RPA Mediated Unfolding of Systematically Varying G-quadruplex Structures" Biophysical Journal 104, Issue 10, pp 2235–2245 (2013).

• Mohammad H. Qureshi, Sujay Ray, Abby L. Sewell, Soumitra Basu, and Hamza Balci. "Replication Protein A Unfolds G-Quadruplex Structures with Varying Degrees of Efficiency" J. Phys. Chem. B, 2012, 116 (19), pp 5588–5594

• 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)

• Chirlmin Joo, Hamza Balci, Yuji Ishitsuka, Chittanon Buranachai, Taekjip Ha. “Advances in Single-Molecule Fluorescence Methods for Molecular Biology”. Annual Reviews of Biochemistry ANRV345-BI77-18, 3:23 (2008).

• Paul R. Selvin, Tyler Lougheed, Melinda Tonks Hoffman, Hyokeun Park, Hamza Balci, Benjamin H. Blehm, and Erdal Toprak. “Watching Molecular Motors Walk with FIONA”. Cold Spring Harbor On-line Protocols, (2007).

• 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

• Comert Kural, Hamza Balci, and Paul R. Selvin. “Molecular Motors One at a Time: FIONA to the Rescue.” Journal of Physics Condensed Matter: Special issue onMolecular Motors, 17, S3979-S3995 (2005).

• Hamza Balci, Taekjip Ha, H. Lee Sweeney, and Paul R. Selvin. " Interhead distance measurements in myosin VI via SHRImP support a simplified hand-over-hand model." Biophysical Journal, 89(1) 413-7 (2005 ).

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 and Richard L. Greene. “Thermodynamic properties of Pr1.85Ce0.15CuO4-d” Phys. Rev. B 70, 140508(R) (2004).

• Hamza Balci and Richard L. Greene. “Anomalous Change in the Field Dependence of the Electronic Specific Heat of an Electron-Doped Cuprate Superconductor” Phys. Rev. Lett. 93, 067001 (2004).

• 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)