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Natalia Kolmakova (Fed)
Biologist
Natalia Kolmakova joined the Biomarker and Genomic Sciences Group, MML in 2018 as part of the NIST Genome Editing Program led by Dr. Samantha Maragh. Natalia’s major projects are aimed at providing comprehensive measurement assurance for novel CRISPR-Cas off-target nomination assays (e.g., CHANGE-seq, ONE-seq, SITE-seq) developed in leading academic labs in the field of CRISPR Genome Editing which present high interest to the genome editing field including other government/regulatory agencies and industry. In her experiments she extensively combines CRISPR molecular biology approach with the power of multidisciplinary metrology techniques, such as DNA fragment analysis (AATI, Advanced Analytical), MiSeq sequencing (Illumina), microfluidic droplet-based high-throughput single-cell targeted sequencing (Tapestri, MissionBio), automated pulsed-field electrophoresis/separation/extraction platform (BluePippin, Sage Science), as well as direct visualization of using atomic force microscopy (Cypher AFM, Asylum Research), towards deep understanding and standardization of evaluating genome editing molecules and the outcomes of utilizing genome editing systems, supporting their further translation to biotechnology products and biotherapeutics.
Research interests
- CRISPR genome editing systems
- Nucleofection and single cell genome editing
- Measurement assurance for CRISPR-Cas off-target nomination assays and SOP development towards further automation
- Development of combinatorial approach using DNA fragment analysis in conjunction with AFM to measure complex topological transformations of tiny dsDNA structures of heterogeneous size 300-1000 bp between their linear and circularized conformations
- IVT-synthesis of sgRNAs and testing their functionality
- In vitro CRISPR-Cas9 cleavage (IVC)
- Qualification of NIST Genome Editing Consortium gDNA samples
Publications
Cicera R. Lazzarotto, Nikolay L. Malinin, Yichao Li, Ruochi Zhang, Yang Yang, Yanghua He, Xin Lan, Kasey Jividen, Varun Katta, Natalia G. Kolmakova, Christopher T. Petersen, Qian Qi, Evgheni Strelcov, Samantha Maragh, Giedre Krenciute, Jian Ma, Yong Cheng, Shengdar Q. Tsai, “Large-scale CHANGE-seq CRISPR-Cas9 Profiling Reveals Genetic and Epigenetic Determinants of Genome-wide Nuclease Activity,’ Nature Biotechnology, NOV 2020, vol. 38, pp. 1317-1327; https://doi.org/10.1038/s41587-020-0555-7
N. Kolmakova and A. Kolmakov, "Scanning Electron Microscopy for in situ Monitoring of Semiconductor-Liquid Interfacial Processes: Electron Assisted Reduction of Ag Ions from Aqueous Solution on the Surface of TiO2 Rutile Nanowire", Journal of Physical Chemistry C vol. 114(40), pp. 17233-17237, 2010; https://doi.org/10.1021/jp1044546
J. M. Fogg, N. Kolmakova, I. Rees, S. Magonov, H. Hansma, J. J. Perona, and E. L. Zechiedrich, "Exploring writhe in supercoiled minicircle DNA," Journal of Physics: Condensed Matter, vol. 18, pp. S145-S159, 2006; https://doi.org/10.1088/0953-8984/18/14/S01
A. Chandrasekaran, A. M. Ojeda, N. G. Kolmakova, and S. M. Parsons, "Mutational and bioinformatics analysis of proline- and glycine-rich motifs in vesicular acetylcholine transporter," Journal of Neurochemistry, vol. 98, pp. 1551-1559, 2006; https://doi.org/10.1111/j.1471-4159.2006.03975.x
D. T. Bravo, N. G. Kolmakova, and S. M. Parsons, "New transport assay demonstrates vesicular acetylcholine transporter has many alternative substrates," Neurochemistry International, vol. 47, pp. 243-247, 2005; https://doi.org/10.1016/j.neuint.2005.05.002
D. T. Bravo, N. G. Kolmakova, and S. M. Parsons, "Mutational and pH analysis of ionic residues in transmembrane domains of vesicular acetylcholine transporter," Biochemistry, vol. 44, pp. 7955-7966, 2005; https://pubs.acs.org/doi/full/10.1021/bi047442y
L. T. Ferreira, M. S. Santos, N. G. Kolmakova, J. Koenen, J. Barbosa, M. V. Gomez, C. Guatimosim, X. Zhang, S. M. Parsons, V. F. Prado, and M. A. M. Prado, "Structural requirements for steady-state localization of the vesicular acetylcholine transporter," Journal of Neurochemistry, vol. 94, pp. 957-969, 2005; https://onlinelibrary.wiley.com/doi/full/10.1111/j.1471-4159.2005.03244…
D. T. Bravo, N. G. Kolmakova, and S. M. Parsons, "Choline is transported by vesicular acetylcholine transporter," Journal of Neurochemistry, vol. 91, pp. 766-768, 2004; https://onlinelibrary.wiley.com/doi/full/10.1111/j.1471-4159.2004.02746…
D. T. Bravo, N. G. Kolmakova, and S. M. Parsons, "Transmembrane reorientation of the substrate-binding site in vesicular acetylcholine transporter," Biochemistry, vol. 43, pp. 8787-8793, 2004; https://pubs.acs.org/doi/full/10.1021/bi049846w
A. M. Ojeda, N. G. Kolmakova, and S. M. Parsons, "Acetylcholine binding site in the vesicular acetylcholine transporter," Biochemistry, vol. 43, pp. 11163-11174, 2004; https://pubs.acs.org/doi/full/10.1021/bi049562b