Yigit Bionanotechnology Lab

Department of Chemistry and The RNA Institute

State University of New York, Albany

Publications at SUNY Albany

66. Emmett Hanson, Nabeel Kalla, Ram Jeevan Tharu, Mikail M. Demir, Betul H. Tok, M. Abdullah Canbaz, and Mehmet V. Yigit* " CRISPR-Responsive Reprogrammable Label-Free Fluorescent Nanoclusters for ML-Assisted Pathogenic Genome Detection on Solid Substrates". Small, 2025, 21 (15), 2500784. (PDF)

Graphical Abstract for 2024 Advanced Healthcare Materials

Paper Sensor

In article 2400508, Mehmet V. Yigit and co-workers develop a paper-based sensor for the visual detection of Salmonella genome. By incorporating a cell-free protein synthesis reaction with CRISPR-Cas12a, as little as 100 copies of Salmonella genome is detected on a paper disc, indicated by a color change from yellow to red.

65. Mahera J. Kachwala, Farishta Hamdard, Damla Cicek, Hilal Dagci, Christopher W. Smith, Nabeel Kalla and Mehmet V. Yigit* "Universal CRISPR-Cas12a and Toehold RNA Cascade Reaction on Paper Substrate for Visual Salmonella Genome Detection". Advanced Healthcare Materials, 2024, 13 (22), 2400508

64. Md. Nahid Pervez, Tao Jiang, Jaydev Kumar Mahato, Aswin Kumar Ilango, Yamini Kumaran, Yuwei Zuo, Weilan Zhang, Haralabos Efstathiadis, Jeremy I. Feldblyum, Mehmet V. Yigit and Yanna Liang* "Surface Modification of Graphene Oxide for Fast Removal of Per- and Polyfluoroalkyl Substances (PFAS) Mixtures from River Water". ACS EST Water, 2024, 4 (7), 2968–2980

63. Mahera J. Kachwala, Christopher W. Smith, Nidhi Nandu, and Mehmet V. Yigit*. "Recombinase Amplified CRISPR Enhanced Chain Reaction (RACECAR) for Viral Genome Detection". Nanoscale, 2022, 14, 13500 - 13504

62. Christopher W. Smith, Mahera J. Kachwala, Rachel L. Cole, and Mehmet V. Yigit*. "Machine Learning Enabled Nanosensor Array for "Monitoring" Citrus Juice Adulteration". ACS Food Science and Technology, 2022, 2, 8, 1217-1223.

61. Tao Jiang, Md. Nahid Pervez, Aswin Kumar Ilango, Yukesh Kannah Ravi, Weilan Zhang, Jeremy I. Feldblyum, Mehmet V. Yigit, Haralabos Efstathiadis, Yanna Liang "Magnetic surfactant-modified clay for enhanced adsorption of mixtures of per- and polyfluoroalkyl substances (PFAS) in snowmelt: Improving practical applicability and efficiency". Journal of Hazardous Materials, 471, 2024, 134390

60. Tao, Jiang; Weilan, Zhang; Aswin Kumar, Ilango; Jeremy, Feldblyum; Zheng, Wei; Haralabos, Efstathiadis; Mehmet V. Yigit; Yanna, Liang. "Surfactant-Modified Clay for Adsorption of Mixtures of Per- and Polyfluoroalkyl Substances (PFAS) in Aqueous Solutions". ACS Appl. Eng. Mater. 2023, 1(1), 394–407

59. Christopher W. Smith, Mustafa S. Hizir, Nidhi Nandu, and Mehmet V. Yigit*. "Algorithmically Guided Optical Nanosensor Selector (AGONS): Guiding Data Acquisition, Processing, and Discrimination for Biological Sampling". Analytical Chemistry, 2022, 94, 2, 1195-1202.

58. Christopher W. Smith, Mahera J. Kachwala, Nidhi Nandu, and Mehmet V. Yigit*. "Recognition of DNA target formulations by CRISPR-Cas12a using a dsDNA reporter". ACS Synth. Biol. 2021, 10, 7, 1785–1791.

57. Mahera J. Kachwala, Christopher W. Smith, Nidhi Nandu, and Mehmet V. Yigit*. "Reprogrammable Gel Electrophoresis Detection Assay Using CRISPR-Cas12a and Hybridization Chain Reaction". Analytical Chemistry, 2021, 93, 4, 1934–1938.

56. Nidhi Nandu, Christopher W. Smith, Taha Bilal Uyar, Yu-Sheng Chen, Mahera J. Kachwala, Muhan He and Mehmet V. Yigit*. "Machine-Learning Single-Stranded DNA Nanoparticles for Bacterial Analysis". ACS Appl. Nano Mater. 2020, 3, 12, 11709–11714.

55. Nidhi Nandu, Christopher W. Smith,, Mahera J. Kachwala and Mehmet V. Yigit*. "Regulation of the peroxidase‐like activity of nGO, MoS2 and WS2 nanozymes using metal cations". ChemBioChem, 2021, 22, 4, 662-665.

54. Muhan He, Nidhi Nandu, Taha Bilal Uyar, Maksim Royzen and Mehmet V. Yigit*. "Small molecule-induced DNA hydrogel with encapsulation and release properties". Chemical Communications, 2020,56, 7313-7316 .

53. Christopher W. Smith, Nidhi Nandu, Mahera J. Kachwala, Yu-Sheng Chen, Taha Bilal Uyar and Mehmet V. Yigit*. "Probing CRISPR-Cas12a nuclease activity using dsDNA-templated fluorescent substrates". Biochemistry, 2020, 59, 15, 1474–1481.

52. Taha Bilal Uyar, Kui Wu, Muhan He, Irfan Khan, Maksim Royzen and Mehmet V. Yigit*. "Switchable fluorescence of doxorubicin for label-free imaging of bioorthogonal drug release". ChemMedChem, 2020, 15, 11, 988-994. (very important paper - VIP)

51. Christopher W. Smith, Yu-Sheng Chen, Nidhi Nandu, Mahera Kachwala and Mehmet V. Yigit*. "The Analysis of Zirconium (IV) Oxide (ZrO2) Nanoparticles for Peroxidase Activity". J. Anal. Test., 2019, 3(3), 246-252.

50. Nidhi Nandu, Mustafa S. Hizir, Neil Robertson, Birol Ozturk and Mehmet V. Yigit*. "Masking the peroxidase‐like activity of MoS2 nanozyme enables label‐free lipase detection". ChemBioChem, 2019, 20, 1861.

49. Alperen Guver, Nafetalai Fifita, Peker Milas, Michael Straker, Michael Guy, Kara Green, Taha Yildirim, Ilyas Unlu, Mehmet V. Yigit and Birol Ozturk*. "A low-cost and high-precision scanning electrochemical microscope built with open source tools". HardwareX, 6, e00082.

48. Alperen Guver, Peker Milas, Michael Guy, Mustafa T. Sigindere, Mehmet V. Yigit, and Birol Ozturk*. "A Novel Nanoscale Electrode for Biosensing ". IEEE Healthcare Innovation Point-Of-Care Technologies. IEEE, 2019.

47. Erik Augspurger, Muhit Rana and Mehmet V. Yigit*. "Chemical and Biological Sensing using Hybridization Chain Reaction". ACS Sensors, 2018, 3 (5), pp 878–902.

46. Mustafa Salih Hizir, Nidhi Nandu and Mehmet V. Yigit*. "Homologous miRNA analyses using a combinatorial nanosensor array with two-dimensional nanoparticles". Analytical Chemistry, 2018, 90 (10), pp 6300–6306.

45. Nidhi Nandu, Mustafa Salih Hizir and Mehmet V. Yigit *. "Systematic investigation of two-dimensional DNA nanoassemblies for construction of a nonspecific sensor array". Langmuir, 2018, 34, 14983-14992. Special Issue "Nucleic Acids Nanoscience at Interfaces".

44. Muhit Rana, Erik E. Augspurger, Mustafa Salih Hizir, Esma Alp and Mehmet V. Yigit *. "Molecular logic gate operations using one-dimensional DNA nanotechnology". J. Mater. Chem. C, 2018, 6, 452 - 455.

43. Neil M. Robertson, Yang Yang, Irfan Khan, Vincent E. LaMantia, Maksim Royzen*, and Mehmet V. Yigit *."Single-trigger dual-responsive nanoparticles for controllable and sequential prodrug activation". Nanoscale, 2017,9, 10020-10030

42. Mustafa Salih Hizir, Neil M. Robertson, Mustafa Balcioglu, Esma Alp, Muhit Rana and Mehmet V. Yigit*. "Universal sensor array for highly selective system identification using two-dimensional nanoparticles". Chemical Science, 2017, 8, 5735 - 5745.

41. Irfan Khan, Leah M. Seebald, Neil M. Robertson, Mehmet V. Yigit* and Maksim Royzen*. "Controlled in-cell activation of RNA therapeutics using bond-cleaving bio-orthogonal chemistry". Chemical Science, 2017, 8, 5705 - 5712. (*corresponding authors)

40. Mustafa Balcioglu, Muhit Rana, Neil Robertson, Mustafa Salih Hizir, Kashfia Haque and Mehmet V. Yigit*. "Rapid Visual Screening and Programmable Subtype Classification of Ebola Virus Biomarkers". Advanced Healthcare Materials, 2017, 6, 2, 1600739 (inside front cover)

39. Muhit Rana, Mustafa Balcioglu, Neil M. Robertson, Mustafa Salih Hizir, Sumeyra Yumak and Mehmet V. Yigit*."Low picomolar, instrument-free visual detection of mercury and silver ions using low-cost programmable nanoprobes", Chemical Science, 2017, 8, 1200-1208 .

38. Donald A McCarthy, Ahmad A Nazem, James McNeilan, Nicole L Shakerley, Ryan R Clark, María D Idelchik, Mehmet V Yigit, and J Andrés Melendez. "Nanoenhanced matrix metalloproteinase-responsive delivery vehicles for disease resolution and imaging", Experimental Biology and Medicine, 241, 18, 2023-2032.

37. Srivathsan Ranganathan, Ken Halvorsen, Christopher Myers, Neil M. Robertson, Mehmet Yigit*and Alan Chen*. "Complex Thermodynamic Behavior of Single-Stranded Nucleic Acid Adsorption to Graphene Surfaces", Langmuir, 2016, 32 (24), pp 6028–6034. (*corresponding authors)

36. Irfan Khan, Paul Agris, Mehmet Yigit* and Maksim Royzen*. "In situ activation of a doxorubicin prodrug using imaging-capable nanoparticles", Chemical Communications, 2016,52, 6174-6177. (*corresponding authors)

35. Neil M. Robertson, Amy E. Toscano, Vincent E. LaMantia, Mustafa Salih Hizir, Muhit Rana, Mustafa Balcioglu, Jia Sheng and Mehmet V. Yigit*. “Unlocked Nucleic Acids for miRNA Detection Using Two Dimensional Nano-Graphene Oxide”, Biosensors and Bioelectronics, (2017) pp. 551-557, (invited artice for 2D Materials themed Issue).

34. Muhit Rana, Mustafa Balcioglu, Maya Kovach, Mustafa Salih Hizir, Neil M. Robertson, Irfan Khan and Mehmet V. Yigit*. “Reprogrammable Multiplexed Detection of Circulating OncomiRs Using Hybridization Chain Reaction”, Chemical Communications, 2016, 52, 3524-3527.

33. Mustafa Salih Hizir, Meryem Top, Mustafa Balcioglu, Muhit Rana, Neil M. Robertson, Fusheng Shen, Jia Sheng and Mehmet V. Yigit*. “Multiplexed activity of perAuxidase: DNA-capped AuNPs act as adjustable peroxidase”, Analytical Chemistry, 2016, 88 (1), pp 600–605.

32. Zdravka Medarova, Mustafa Balcioglu and Mehmet V. Yigit*. “Controlling RNA expression in cancer using iron oxide nanoparticles detectable by MRI and in vivo optical imaging”, Methods Mol. Biol., 2016;1372:163-79.

31. Neil M. Robertson, Mustafa Salih Hizir, Mustafa Balcioglu, Rui Wang, Mustafa S. Yavuz, Hasan Yumak, Birol Ozturk, Jia Sheng and Mehmet V. Yigit*. "Discriminating a single nucleotide difference for enhanced miRNA detection using tunable graphene and oligonucleotide nanodevices", Langmuir, 2015, 31 (36), pp 9943–9952.

30. Neil M. Robertson, Mustafa Salih Hizir, Mustafa Balcioglu, Muhit Rana, Hasan Yumak, Ozgur Ecevit and Mehmet V. Yigit*. “Monitoring the multitask mechanism of DNase I activity using graphene nano assemblies”, Bioconjugate Chemistry, 2015, 26 (4), pp 735–745.

29. Abstract: Mustafa Balcioglu, Burak Buyukbekar, Mustafa S. Yavuz and Mehmet V. Yigit*. "Smart polymer functionalized graphene nano-devices for thermo-switch controlled biodetection" Journal of Biomolecular Structure and Dynamics, 2015, V. 33, Supplement 1, pp 47-48.

28. Abstract: Muhit Rana, Mustafa Hizir, Mustafa Balcioglu, Neil Robertson & Mehmet V. Yigit*. "Two dimensional nanomaterials for microRNA analysis" Journal of Biomolecular Structure and Dynamics, 2015, V. 33, Supplement 1, pp 51.

27. Mustafa Balcioglu, Burak Buyukbekar, Mustafa S. Yavuz and Mehmet V. Yigit* “Smart polymer functionalized graphene nano-devices for thermo-switch controlled biodetection”, ACS Biomaterials Science & Engineering, 2015, 1 (1), pp 27–36.

26. Mustafa Salih Hizir, Mustafa Balcioglu, Muhit Rana, Neil Robertson and Mehmet V. Yigit*. “Simultaneous detection of circulating oncomiRs from body fluids for prostate cancer staging using nano-graphene oxide”, ACS Applied Materials & Interfaces, 2014, 6 (17), pp 14772–14778.

25. Mustafa Balcioglu, Muhit Rana, Neil Robertson and Mehmet V. Yigit*.“DNA-Length-Dependent Quenching of Fluorescently Labeled Iron Oxide Nanoparticles with Gold, Graphene Oxide and MoS2 Nanostructures”, ACS Applied Materials & Interfaces, 6 (15), 2014, 12100–12110.

24. Neil Robertson and Mehmet V. Yigit* “The Role of miRNAs in Resistance to Breast Cancer Therapy”, Wiley Interdisciplinary Reviews (WIREs) RNA, 5(6), 2014.

23. Muhit Rana, Mustafa Balcioglu, and Mehmet V. Yigit* “Locked nucleic acid-modified antisense miR-10b oligonucleotides form stable duplexes on gold nanoparticles", BioNanoScience, 4(2), 2014, 195-200.

22. Byunghee Yoo, Subrata K. Ghosh, Mohanraja Kumar, Anna Moore, Mehmet V. Yigit and Zdravka Medarova. “Design of Nanodrugs for miRNA Targeting in Tumor Cells", Journal of Biomedical Nanotechnology 10(6), 2014, 1114-1122.

21. Byunghee Yoo, Amol Kavishwar, Subrata K. Ghosh, Mehmet V. Yigit, Anna Moore, and Zdravka Medarova. “Detection of miRNA Expression in Intact Cells Using Activatable Sensor Oligonucleotides”, Chemistry & Biology, 21(2), 2014, 199-204.

20. Muhit Rana, Mustafa Balcioglu, Neil Robertson and Mehmet V. Yigit*.“Nano-graphene oxide as a novel platform for monitoring the effect of LNA modification in nucleic acid interactions”, Analyst, 2014, 139 (4), 714 - 720.

19. Subrata K. Ghosh,Mehmet V. Yigit, Masashi Uchida, Alana W. Ross, Natalie Barteneva, Anna Moore and Zdravka Medarova. “Sequence-dependent combination therapy with doxorubicin and a survivin-specific small interfering RNA nanodrug demonstrates efficacy in models of adenocarcinoma”, International Journal of Cancer, 2014, 134 (7), 1758–1766.

18. Mustafa Balcioglu, Muhit Rana and Mehmet V. Yigit*. “Doxorubicin loading on graphene oxide, iron oxide and gold nanoparticle hybrid”, Journal of Materials Chemistry B, 2013, 1 (45), 6187 - 6193

17. Mehmet V. Yigit, Subrata K. Ghosh, Mohanraja Kumar, Victoria Petkova, Anna Moore and Zdravka Medarova. “Context-dependent differences in miR-10b breast oncogenesis can be targeted for the prevention and arrest of lymph node metastasis” Oncogene, 2013, 32(12), 1530-1538.

16. Ping Wang, Mehmet V. Yigit, Chongzhao Ran, Alana Ross, Lingling Wei, Guangping Dai, Zdravka Medarova and Anna Moore. “A Theranostic Small Interfering RNA Nanoprobe Protects Pancreatic Islet Grafts From Adoptively Transferred Immune Rejection” Diabetes, 2012, 61(12), 3247-3254.

15. Mehmet V. Yigit, and Zdravka Medarova. "Iron Oxide Nanoparticles and Derivatives for Biomedical Imaging and Application in Cancer Diagnosis and siRNA Therapy” Nano and Micro Flow Systems for Bioanalysis, Editors: M.W.Collins & C.S.König, Chapter 1, Springer, 2013.

14. Mehmet V. Yigit, Anna Moore and Zdravka Medarova. “Magnetic nanoparticles for cancer diagnosis and therapy” Pharmaceutical Research, 2012, 29(5), 1180-1188.

13. Mehmet V. Yigit, Anna Moore and Zdravka Medarova. “In vivo application of gold nanoparticles for biomedical SERS imaging”, Am. J. Nucl. Med. Mol. Imaging, 2012, 2(2), 232-241.

12. Mehmet V. Yigit, Leyun Zhu, Marytheresa A. Ifediba, Yong Zhang, Kevin Carr, Anna Moore, and Zdravka Medarova. “Noninvasive MRI-SERS imaging in living mice using an innately bimodal nanomaterial” ACS Nano, 2011, 5(2), 1056–1066.

11. Ping Wang, Mehmet V. Yigit, Liangli Wei, Guangping Dai, Zdravka Medarova, and Anna Moore. “Combined small interfering RNA therapy and in vivo magnetic resonance imaging in islet transplantation” Diabetes, 2011, 60(2), 565-571.

10. Mohanraja Kumar, Mehmet V. Yigit, Guangping Dai, Anna Moore and Zdravka Medarova. “Image-guided breast tumor therapy using a siRNA nanodrug” Cancer Research, 2010, 70(19),7553-7561.

9. Jung Heon Lee, Mehmet V. Yigit, Debapriya Mazumdar and Yi Lu. “Molecular diagnostic and drug delivery agents based on aptamer-nanomaterial conjugates” Adv. Drug Deliv. Rev. 2010, 62(6),592-605.

8. Mehmet V. Yigit, Abhijit Mishra, Rong Tong, Jianjung Chen, Gerard C. L. Wong and Yi Lu. “Inorganic mercury detection and controlled release of chelating agents from ion-responsive liposomes” Chem Biol. 2009, 16(9), 937-942.

7. Mehmet V. Yigit, Debapriya Mazumdar and Yi Lu. “MRI Detection of thrombin with aptamer functionalized superparamagnetic iron oxide nanoparticles” Bioconjugate Chem., 2008, 19(2),412-417.

6. Mehmet V. Yigit, Debapriya Mazumdar, Hee-Kyung Kim, Jung Heon Lee, Boris Odintsov and Yi Lu. “Smart "turn-on" magnetic resonance contrast agents based on aptamer-functionalized superparamagnetic iron oxide nanoparticles” ChemBioChem 2007,8(14), 1675-1678.

5. Jung Heon Lee, Daryl P. Wernette, Mehmet V. Yigit, Juewen Liu, Zidong Wang and Yi Lu. “Site-specific control of distances between gold nanoparticles using phosphorothioate anchors on DNA and a short bifunctional molecular fastener” Angew. Chem. Int. Ed., 2007, 46(47),9006-9010.

4. Mehmet V. Yigit, Christopher G. F. Cooper, Yu Wang, Brian Moulton and John C. MacDonald. “Reaction of 1,2-bis(2,6-dicarboxypyridin-4-yl)ethyne with Co(II) generates coordination monomers not polymers: Crystal structure of 4-(2,6-dicarboxypyridin-4-yl)ethynylpyridine-2,6- dicarboxylatotriaqua cobalt(II) monohydrate” Journal of Chemical Crystallography 2006, 36(6), 371-379.

3. Mehmet V. Yigit, Yu Wang, Brian Moulton and John C. MacDonald. “Generation of linear coordination polymers of catena-[diaqua-(m-pyrazine-2,6-dicarboxylato-N,O,O'-m-N')copper(II)] via in situ hydro(solvo)thermal decarboxylation of pyrazine-2,3,5,6-tetracarboxylic acid” Crystal Growth & Design2006, 6(4), 829-832.

2. Mehmet V. Yigit, Kasim Biyikli, Brian Moulton and John C. MacDonald. “Bis(imidazolium 2,4,6-tricarboxypyridine) metal(II) complexes: Molecular building blocks that generate isomorphous hydrogen-bonded frameworks” Crystal Growth & Design 2006, 6(1), 63-69.

1. John C. MacDonald,Mehmet V. Yigit and Kyle Mychajlonka. “Two concomitant polymorphs of a supramolecular model of the Asp---His---Ser catalytic triad” Crystal Growth & Design 2005, 5(6),2248-2255.

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