1
|
Yeom T, Lee J, Lee S, Kang S, Kim KR, Han B, Lee HS, Jo K. Mass spectrometric investigation of the role of the linking polypeptide chain in DNA polymerase I. Analyst 2015; 139:2432-9. [PMID: 24695614 DOI: 10.1039/c4an00107a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA polymerase I offers great promise for a wide range of biotechnological applications due to its capability to add labeled nucleotides into double-stranded large DNA molecules by using both polymerase and nuclease domains. Accordingly, it is crucially important to thoroughly characterize this enzyme for further developments. Although the enzyme has been thus far characterized using mainly traditional analytical instruments, here we utilized an advanced and convenient means of mass spectrometry to elucidate enzymatic functions and mechanisms by measuring DNA oligomers generated by polymerase and nuclease reactions. Our analysis revealed several novel enzymatic features, including the observation that polymerase readily dissociates from the DNA molecules containing a wide single-stranded section. From this finding, we reasoned a serious situation of DNA break because polymerase domains cannot efficiently repair the wide single-stranded section, which is susceptible to DNA breaks. Furthermore, we deduced a plausible explanation for a paradoxical question as to why two domains of polymerase and 5'-nuclease are linked by a small and flexible polypeptide in polymerase I. The polypeptide link seems to prevent a 5'-nuclease from causing DNA breaks by locating a polymerase domain closely for immediate repair reaction. Here we present experimental evidence to prove our hypothesis via a set of mass spectrometric analyses as well as single DNA molecule observation and bacterial cell growth assay. Consequently, mass spectrometric analysis for DNA polymerase I provides a meaningful biological insight that a polypeptide link can be a molecular leash to control an aggressive domain in order to prevent unmanageable damages.
Collapse
Affiliation(s)
- Taeho Yeom
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 121-742, Republic of Korea.
| | | | | | | | | | | | | | | |
Collapse
|
2
|
Taskinen B, Zauner D, Lehtonen SI, Koskinen M, Thomson C, Kähkönen N, Kukkurainen S, Määttä JAE, Ihalainen TO, Kulomaa MS, Gruber HJ, Hytönen VP. Switchavidin: Reversible Biotin–Avidin–Biotin Bridges with High Affinity and Specificity. Bioconjug Chem 2014; 25:2233-43. [DOI: 10.1021/bc500462w] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Barbara Taskinen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
| | - Dominik Zauner
- Institute
of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020 Linz, Austria
| | - Soili I. Lehtonen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Tampere University Hospital, PL 2000, FI-33521 Tampere, Finland
| | - Masi Koskinen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
| | - Chloe Thomson
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
| | - Niklas Kähkönen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Tampere University Hospital, PL 2000, FI-33521 Tampere, Finland
| | - Sampo Kukkurainen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
| | - Juha A. E. Määttä
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
| | - Teemu O. Ihalainen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
| | - Markku S. Kulomaa
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Tampere University Hospital, PL 2000, FI-33521 Tampere, Finland
| | - Hermann J. Gruber
- Institute
of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020 Linz, Austria
| | - Vesa P. Hytönen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
| |
Collapse
|
3
|
Zhu J, Qiu C, Palla M, Nguyen T, Russo JJ, Ju J, Lin Q. A Microfluidic Device for Multiplex Single-Nucleotide Polymorphism Genotyping. RSC Adv 2014; 4:4269-4277. [PMID: 26594354 PMCID: PMC4651459 DOI: 10.1039/c3ra44091e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are the most abundant type of genetic variations; they provide the genetic fingerprint of individuals and are essential for genetic biomarker discoveries. Accurate detection of SNPs is of great significance for disease prevention, diagnosis and prognosis, and for prediction of drug response and clinical outcomes in patients. Nevertheless, conventional SNP genotyping methods are still limited by insufficient accuracy or labor-, time-, and resource-intensive procedures. Microfluidics has been increasingly utilized to improve efficiency; however, the currently available microfluidic genotyping systems still have shortcomings in accuracy, sensitivity, throughput and multiplexing capability. To address these challenges, we developed a multi-step SNP genotyping microfluidic device, which performs single-base extension of SNP specific primers and solid-phase purification of the extension products on a temperature-controlled chip. The products are ready for immediate detection by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), providing identification of the alleles at the target loci. The integrated device enables efficient and automated operation, while maintaining the high accuracy and sensitivity provided by MS. The multiplex genotyping capability was validated by performing rapid, accurate and simultaneous detection of 4 loci on a synthetic template. The microfluidic device has the potential to perform automatic, accurate, quantitative and high-throughput assays covering a broad spectrum of applications in biological and clinical research, drug development and forensics.
Collapse
Affiliation(s)
- Jing Zhu
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027
| | - Chunmei Qiu
- Department of Chemical Engineering, Columbia University, New York, NY, 10027
| | - Mirkó Palla
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027
- Department of Chemical Engineering, Columbia University, New York, NY, 10027
| | - ThaiHuu Nguyen
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027
| | - James J. Russo
- Department of Chemical Engineering, Columbia University, New York, NY, 10027
| | - Jingyue Ju
- Department of Chemical Engineering, Columbia University, New York, NY, 10027
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027
| |
Collapse
|
4
|
Radisavljević M, Kamceva T, Vukićević I, Nisavić M, Milovanović M, Petković M. Sensitivity and accuracy of organic matrix-assisted laser desorption and ionisation mass spectrometry of FeCl3 is higher than in in matrix-free approach. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2013; 19:77-89. [PMID: 24261080 DOI: 10.1255/ejms.1217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We compare the quality and reliability of laser desorption and ionisation mass spectra of FeCl3 acquired without the assistance of the matrix with the spectra acquired with different organic matrix molecules. Generally, inorganic salts tend to form clusters upon laser irradiation, the signals of which can be easily distinguished from ions arising from the matrix. In the presence of a matrix, cluster ions are, however, mostly suppressed. We have compared the number of analyte signals, accuracy of determination of isotope composition of the analyte and the sensitivity of FeCl3 detection between different approaches. The results obtained imply that the sensitivity of mass spectrometric analysis of FeCl3 is somewhat higher when matrices are applied than in the matrix-free approach. Among all matrices tested in this work, F20TPP seems to be the most promising for further applications as a matrix for mass spectrometry of inorganic salts.
Collapse
Affiliation(s)
- Maja Radisavljević
- Laboratory of Physical Chemistry, Vinća, Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia.
| | | | | | | | | | | |
Collapse
|