Label-free detection of single nucleotide polymorphism and DNA hybridization by terahertz spectrometry
Abstract
Abstract
Time-domain terahertz (THz) spectrometry has been used to analyze a 21-mer nucleotide polymorphism (SNP) sequence in a single and double stranded DNA in a label-free manner. THz temporal signal (or interferogram) converted to frequency domain constitutes a signature of a given molecular “event” (e.g., a vibrational or a conformational state). The temporal signal provides a means of probing a molecular event in an appropriate time window. This is a unique ability of this technique because different molecular events exhibit different time response based on their physical and chemical nature. Conformational difference of a given molecule results in different signature with an appropriate time response that can be accurately probed by a terahertz temporal signal. In this work using a single stranded and double stranded 21-mer oligonucleotides in pico-molar concentration with or without specific SNP we demonstrated that terahertz spectroscopic technique produces distinctly different spectral signature in each case. For each species, peaks were distinctly different allowing a meaningful comparison. Additionally, temporal transmission spectra of the DNA specimens were collected at normal temperature and atmosphere allowing easy handling of the samples. The results clearly demonstrate the ability of the spectrometer to detect a minute amount of biomolecules in a label-free fashion. Based on the results, it is assumed that the spectral signature can be used to identify SNPs as a diagnostic tool for certain disease states, for designing personalized medicine and also can be useful in plant genetics. This capability can be used as a diagnostic tool, as well as for studying molecular reactions such as mutation.Keywords
Full Text:
Subscribers OnlyReferences
Y.H. Lee, J. D. Ji and G. G. Song. Associations between FCGR3A Polymorphisms and Susceptibility to Rheumatoid Arthritis: A Metaanalysis J. Rheumatology, 35: 2129-35, 2008
Y. H. Lee , Y. H. Rho , S. J. Choi , J. D. Ji , G. G. Song , S. K. Nath and J. B. Harley. The PTPN22 C1858T functional polymorphism and autoimmune diseases—a meta-analysis, Rheumatology Advance Access published online on November 29, 2006
Neil Hanchard, Abier Elzein, Clare Trafford, Kirk Rockett, Margaret Pinder, Muminatou Jallow, Rosalind Harding, Dominic Kwiatkowski, and Colin McKenzie. Classical sickle beta-globin haplotypes exhibit a high degree of long-range haplotype similarity in African and Afro-Caribbean populations. BMC Genet, 8: 52, 2007.
Eden R. Martin, William K. Scott, Martha A. Nance, Ray L. Watts, Jean P. Hubble, William C. Koller, Kelly Lyons, Rajesh Pahwa, Matthew B. Stern, Amy Colcher, Bradley C. Hiner, Joseph Jankovic, William G. Ondo, Fred H. Allen, Christopher G. Goetz, Gary W. Small, Donna Masterman, Frank Mastaglia, Nigel G. Laing, Jeffrey M. Stajich, Rbert C. Ribble, Michael W. Booze, Allison Rogala, Michael A. Hauser, Fengyu Zhang, Rachel A. Gibson, Lefkos T. Middleton, Allen D. Roses, Jonathan L. Haines, Burton L. Scott, Margaret A. Pericak-Vance, Jeffery M. Vance. Association of Single-Nucleotide Polymorphisms of the Tau Gene With Late-Onset Parkinson Disease.. JAMA, 286:2245-2250 (2001)
Yi-Ju Li, Sofia A. Oliveira , Puting Xu, Eden R. Marti, Judith E. Stenger, Clemens R. Scherzer, Michael A. Hauser, William K. Scott, Gary W. Small, Martha A. Nance, Ray L. Watts, Jean P. Hubble, William C. Koller, Rajesh Pahwa, Mathew B. Stern, Bradley C. Hiner, Joseph Jankovic, Christopher G. Goetz, Frank Mastaglia, Lefkos T. Middleton, Allen D. Roses, Ann M. Saunders, Donald E. Schmechel, Steven R. Gullans, Jonathan L. Haines , John R. Gilbert , Jeffery M. Vance and Margaret A. Pericak-Vance. Glutathione S-transferase omega-1 modifies age-at-onset of Alzheimer disease and Parkinson disease.. Human Molecular Genetics, 2003, Vol. 12, 3259-3267, 2003
Henning Gohlke, Uta Ferrari, Kerstin Koczwara , Ezio Bonifacio , Thomas Illig, Anette-G. Ziegler. SLC30A8 (ZnT8) Polymorphism is Associated with Young Age at Type 1 Diabetes Onset. Rev. Diabet. Stud, 2008, 5(1):25-27
Scot J. Matkovich, Derek J. Van Booven, Anna Hindes, Min Young Kang, Todd E. Druley, Francesco L.M. Vallania, Robi D. Mitra, Muredach P. Reilly, Thomas P. Cappola and Gerald W. Dorn, II. Cardiac signaling genes exhibit unexpected sequence diversity in sporadic cardiomyopathy, revealing HSPB7 polymorphisms associated with disease. J Clin. Invest. 2010;120(1):280–289.
Kristin J. Meyers; Thomas H. Mosley; Ervin Fox; Eric Boerwinkle; Donna K. Arnett; Richard B. Devereux; Sharon L.R. Kardia Genetic Variations Associated With Echocardiographic Left Ventricular Traits in Hypertensive Blacks. Hypertension. 2007; 49:992-999
Evdoxia Hatjiharissi, Lian Xu, Daniel Ditzel Santos, Zachary R. Hunter, Bryan T. Ciccarelli, Sigitas Verselis, Michael Modica, Yang Cao, Robert J. Mannin, Xavier Leleu, Elizabeth A. Dimmock, Alexandros Kortsaris, Constantine Mitsiades2, , Kenneth C. Anderson, Edward A. Fox, and Steven P. Treon ; Increased natural killer cell expression of CD16, augmented binding and ADCC activity to rituximab among individuals expressing the Fc RIIIa-158 V/V and V/F polymorphism. Prepublished online as Blood First Edition Paper, May 2, 2007
Cartron G, Dacheux L, Salles G, et al. Therapeutic activity of humanized anti-CD20 monoclonal antibody and polymorphism in IgG Fc receptor Fcgamma RIIIA gene. Blood 2002; 99:754–758
Weng WK and Levy R. Two immunoglobulin G Fc receptor polymorphisms independently predict response to rituximab in patients with follicular lymphoma. J Clin Oncol 2003; 21:3940–3947
Treon SP, Hansen M, Branagan AR, et al. Polymorphisms in Fc RIIIA (CD16) receptor expression are associated with clinical responses to rituximab in Waldenstrom's macroglobulinemia. J. Clin. Oncol. 2005; 23:474–481
Wadelius M et al. Blood. 2008 Jun 23. Epub ahead of print . DOI 10.1182/blood-2008-04-149070.
Gage BF, Lesko LJ. Pharmacogenetics of warfarin: Regulatory, scientific and clinical issues. J Thromb Thrombolysis. 2008: 25:45-51
V S Basile , V Özdemir , M Masellis , M L Walker , H Y Meltzer , J A Lieberman , S G Potkin , G Alva , W Kalow , F M Macciardi and J L Kennedy A functional polymorphism of the cytochrome P450 1A2 (CYP1A2) gene: association with tardive dyskinesia in schizophrenia, , Molecular Psychiatry (2000) 5, 410–417.
Dubcovsky, J. 2004. Marker assisted selection in public breeding programs: The wheat experience. Crop Sci. 44:1895–1898
Dekkers, J.C.M., and F. Hospital. 2002. The use of molecular genetics in the improvement of agricultural populations. Nat. Rev. Genet. 3:22–32
John Manners, Lynne McIntyre, Rosanne Casu, Giovanni Cordeiro, Mark Jackson, Karen Aitken, Phillip Jackson, Graham Bonnett, Slade Lee and Robert Henry. Can genomics revolutionise genetics and breeding in sugarcane? Genet. Mol. Biol. vol.32 no.3 São Paulo 2009 Epub June 19, 2009
Feng Li, Hiroyasu Kitashiba, Kiyofumi Inaba and Takeshi Nishio*A Brassica rapa Linkage Map of EST-based SNP Markers for Identification of Candidate Genes Controlling Flowering Time and Leaf Morphological Traits. DNA Research 2009 16(6):311-323
Drmanac, R., Drmanac, S., Strezoka, Z., Paunesku, T., Labat, I., Zeremski, M., Snoddy, J., Funkhouser, W., K., Koop, B., Hood, L., & Crkvenjakov, R. DNA-sequence determination by hybridization – a strategy for efficient large scale sequencing. Science 260:1649-1653, 1993.
Guo, Z., Guilfoyle, R. A., Thiel, A., J., Wang, R. F. & Smith, L. M., Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. Nucl. Acids Res. 22: 5456-5465, 1994.
Chee, M., Yang, R., Hubbel, E., Berno, A., Huang, X. C., Stern, D., Winkler, J., Lockhart, D. J., Morris, M. S., & Fodor, S., A., Accessing genetic information with high density DNA arrays. Science 274: 610-614, 1996.
Ozaki, H. & Mclaughlin, L.W., The estimation of distances between specific backbonelabeled sites in DNA using fluorescence resonance energy transfer. Nucl. Acids Res. 20: 5205-5214, 1992
Zhu, Z. & Waggoner, A., S., Molecular mechanism controlling the incorporation of fluorescent nucleotides into DNA and PCR. Cytometry 28: 206-211, 1997.
Larramendy, M. L., El-Rifai, W. & Knuutila, S., Comparison of fluorescein sothiocyanateand Texas red-conjugated nucleotides for direct labeling in comparative genomic hybridization. Cytometry 31: 174-179, 1998.
VanZandt, L. L. & Saxena, V. K., Millimeter-microwave spectrum of DNA – six predictions for spectroscopy. Phys. Rev. A39: 2672-2674, 1989.
Zhuang, W., Feng, Y., & Prohofsky, E. W., Self-consistant calculation of localized DNA vibrational properties at a double-helix-single-strand junction with anharmonic potential. Phys. Rev. 1990: A41, 7033.
Bolivar, P. H., Nagel, M., Richter, F., Brucherseifer, M., Kurz, H., Bosserhoff, A., and Buttner, R., Label-free THz sensing of genetic sequences: towards ’THz biochips, Phil. Trans.. R. Soc. Lond.. A (2004) 262, 323-335.
Anis Rahman, Bruce Stanley, Aunik K. Rahman, “Ultrasensitive label-free detection and quantitation of DNA hybridization via terahertz spectrometry,”Paper Number: 7568-8, SPIE conference on Imaging, Manipulation, and Analysis of Biomolecules Cells, and Tissues VIII, January 23-28 2010, SPIE Photonics, San Francisco, CA
Markelz, A. G., Roitberg, A., & Heilweil, E. J., Pulsed terahertz spectroscopy of DNA, bovine serum albumin and collagen between 0.1 and 2.0 THz. Chem. Phys. Lett. 320: 42-48, 2000.
Terahertz Spectral Analysis of FCGR3A Genotypes. Gulshan Ara, Aunik K. Rahman, Bruce A. Stanley, Anis Rahman, ACS , 41st Mid-Atlantic Regional Meeting. April 10-13, 2010
Urbe, H. & Tominaga, Y., Low frequency Raman spectra of DNA. Biopolymers 21: 2477-2481, 1982.
Woolard, D., Koscica, T., Rhodes, D. L., Cui, H. L., Pastore, R. A., Jensen, J. O., Jensen, J. L., Loerop, W. R., Jacobsen, R. H., Mittleman, D., & Nuss, M. C., Millimeter wave induced modes in DNA as a possible alternative test to animal tests to probe for carcinogenic mutations. J. Appl. Toxicol. 17: 243, 1997.
Brucherseifer, M., Nagel, M., Bolivar, P. H., Kurz, H., Bosserhoff, A. and Buttner, R., Label-free probing of the binding state of DNA by time-domain terahertz sensing. Appl. Phys. Lett. 77: 4049-4051, 2000.
(a) Rahman, A. "Stimulated emission of terahertz radiation from electro-optic dendrimer" SPIE Proceedings Vol. 7601 Terahertz Technology and Applications III, Laurence P. Sadwick and Creidhe M. M. O'Sullivan Editors, vol. 7601: 76010C-1 – 76010C-5, (2010). (b) Rahman, A., Rahman, A. K., & Tomalia, D. A., “Dendrimer Dipole Excitation: A New Mechanism for Terahertz Generation,” J. Biosens. Bioelectron. 2016, 7:1. DOI: 10.4172/2155-6210.1000196.
DOI: http://dx.doi.org/10.18103/imr.v0i4.90
Refbacks
- There are currently no refbacks.