Optical Density in Biochemistry: Principles and Applications in Analytical Methods: A Review

Abstract

Optical density is one of the great principles of optics, expressed as the attenuation of light by a medium through which it passes. In most applications, it provides a critical link between the phenomena of light-matter interactions observed in such diverse fields as photonics, materials science, and nanotechnology. It therefore becomes a key parameter in biochemical analysis that links sample absorbance characteristics at given wavelengths quantitatively to desirable determinations for an array of laboratory applications. The measurement of optical density has recently been reported to become central to enzymatic assays with avenues opened into enzyme kinetics, reaction dynamics, and even biomarker detection. The fact that this method is non-invasive places it among methods whose assays have enhanced sensitivity and specificity possible both in clinical diagnostics and biochemical research. This paper presents a review toward synthesis based on recent investigations related explicitly to principles development with implications and applications thereof. It also brings together recent discoveries about how to use optical density in biochemical tests, mainly looking at its part in improving the sharpness and success of many checks and sensor tools. It also pulls together recent clues about using optical density in enzyme tests, points out missing pieces of what we know, and offers where future studies should go. Even with the progress made in this area there are still gaps in our understanding especially about how to link optical density with new technologies and materials.

Keywords:

Optical density, enzymatic assays, nanotechnology, kinetics

References

Autschbach, J.. (2010). Computing chiroptical properties with first-principles theoretical methods: background and illustrative examples.. Chirality , 21 Suppl 1 , E116-52 . http://doi.org/10.1002/chir.20789

Aziz, S. B., Brza, M. A., Nofal, M. M., Abdulwahid, R. T., Hussen, S. A., Hussein, A. M., & Karim, W. O. (2020). A comprehensive review on optical properties of polymer electrolytes and composites. Materials, 13(17), 3675. https://doi.org/10.3390/ma13173675

Baiz, Carlos R.., Błasiak, B.., Bredenbeck, J.., Cho, M.., Choi, J.., Corcelli, S.., Dijkstra, A.., Feng, Chi-Jui., Garrett-Roe, S.., Ge, N.., Hanson-Heine, M. W.., Hirst, J.., Jansen, T. I.., Kwac, Kijeong., Kubarych, K.., Londergan, C.., Maekawa, Hiroaki., Reppert, M.., Saito, S.., Roy, Santanu., Skinner, J. L.., Stock, G.., Straub, J.., Thielges, M.., Tominaga, K.., Tokmakoff, A.., Torii, H.., Wang, Lu., Webb, Lauren J.., & Zanni, M.. (2020). Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.. Chemical reviews . http://doi.org/10.1021/acs.chemrev.9b00813

Bauch, M.., Toma, Koji., Toma, M.., Zhang, Qingwen., & Dostálek, J.. (2013). Plasmon-Enhanced Fluorescence Biosensors: a Review. Plasmonics (Norwell, Mass.) , 9 , 781 - 799 . http://doi.org/10.1007/s11468-013-9660-5

Berg, B.., Cortazar, Bingen., Tseng, Derek K.., Ozkan, Haydar., Feng, S.., Wei, Qingshan., Chan, R. Y.., Burbano, J.., Farooqui, Qamar., Lewinski, M.., Carlo, D. Di., Garner, O.., & Ozcan, A.. (2015). Cellphone-Based Hand-Held Microplate Reader for Point-of-Care Testing of Enzyme-Linked Immunosorbent Assays.. ACS nano , 9 8 , 7857-66 . http://doi.org/10.1021/acsnano.5b03203

Bhattacharyya, R.., Key, B.., Chen, Hailong., Best, A.., Hollenkamp, A.., & Grey, C.. (2010). In situ NMR observation of the formation of metallic lithium microstructures in lithium batteries.. Nature materials , 9 6 , 504-10 . http://doi.org/10.1038/nmat2764

Biagioni, P.., Huang, Jer‐Shing., & Hecht, B.. (2011). Nanoantennas for visible and infrared radiation. Reports on Progress in Physics , 75 , 024402 . http://doi.org/10.1088/0034-4885/75/2/024402

Chen, Zhebo., Dinh, H.., & Miller, Eric L.. (2013). Photoelectrochemical Water Splitting: Standards, Experimental Methods, and Protocols. . http://doi.org/10.1007/978-1-4614-8298-7

Christensen, Anders S.., Kubař, T.., Cui, Q.., & Elstner, M.. (2016). Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications. Chemical Reviews , 116 , 5301 - 5337 . http://doi.org/10.1021/acs.chemrev.5b00584

Cortes, C.., Newman, W.., Molesky, S.., & Jacob, Z.. (2012). Quantum nanophotonics using hyperbolic metamaterials. Journal of Optics , 14 . http://doi.org/10.1088/2040-8978/14/6/063001

Dai, Wenyang., Shao, F.., Szczerbiński, J.., McCaffrey, Ryan., Zenobi, R.., Jin, Yinghua., Schlüter, A.., & Zhang, Wei. (2016). Synthesis of a Two-Dimensional Covalent Organic Monolayer through Dynamic Imine Chemistry at the Air/Water Interface.. Angewandte Chemie , 55 1 , 213-7 . http://doi.org/10.1002/anie.201508473

Desjardins, L.., Liabeuf, S.., Renard, C.., Lenglet, A.., Lemke, H.., Choukroun, G.., Drueke, T.., Massy, Z.., & Group, O. B. O. A.. (2012). FGF23 is independently associated with vascular calcification but not bone mineral density in patients at various CKD stages. Osteoporosis International , 23 , 2017-2025 . http://doi.org/10.1007/s00198-011-1838-0

D'innocenzo, V.., Grancini, G.., Alcocer, M.., Kandada, A. R. S.., Stranks, S.., Lee, Michael M.., Lanzani, G.., Snaith, H.., & Petrozza, A.. (2014). Excitons versus free charges in organo-lead tri-halide perovskites. Nature Communications, 5. http://doi.org/10.1038/ncomms4586

Drake, G.. (2023). Springer Handbook of Atomic, Molecular, and Optical Physics. Springer Handbook of Atomic, Molecular, and Optical Physics . http://doi.org/10.1007/978-3-030-73893-8

Doughty, M. J., & Jonuscheit, S. (2019). Corneal structure, transparency, thickness and optical density (densitometry), especially as relevant to contact lens wear – a review. Contact Lens and Anterior Eye, 42(3), 238–245. https://doi.org/10.1016/j.clae.2018.11.014

Giri, A.., Jena, B.., Biswal, B.., Pradhan, A.., Arakha, Manoranjan., Acharya, S.., & Acharya, L.. (2022). Green synthesis and characterization of silver nanoparticles using Eugenia roxburghii DC. extract and activity against biofilm-producing bacteria. Scientific Reports , 12 . http://doi.org/10.1038/s41598-022-12484-y

Giustino, F.. (2016). Electron-phonon interactions from first principles. Reviews of Modern Physics , 89 , 015003 . http://doi.org/10.1103/RevModPhys.89.015003

Guo, Dong‐sheng., Uzunova, Vanya D.., Su, Xin., Liu, Yu., & Nau, W.. (2011). Operational calixarene-based fluorescent sensing systems for choline and acetylcholine and their application to enzymatic reactions. Chemical Science , 2 , 1722-1734 . http://doi.org/10.1039/C1SC00231G

Gurav, J.., Jung, In-Keun., Park, Hyung‐Ho., Kang, E.., & Nadargi, D.. (2010). Silica aerogel: synthesis and applications. Journal of Nanomaterials , 2010 , 23 . http://doi.org/10.1155/2010/409310

Hasnip, P.., Refson, K.., Probert, Matt., Yates, J.., Clark, S.., & Pickard, C.. (2014). Density functional theory in the solid state. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences , 372 . http://doi.org/10.1098/rsta.2013.0270

He, Yanan., Wang, Bo., Dukor, R.., & Nafie, L.. (2011). Determination of Absolute Configuration of Chiral Molecules Using Vibrational Optical Activity: A Review. Applied Spectroscopy , 65 , 699 - 723 . http://doi.org/10.1366/11-06321

Heidari, A.. (2016). A Bio-Spectroscopic Study of DNA Density and Color Role as Determining Factor for Absorbed Irradiation in Cancer Cells. , 2016 , 1-3 . http://doi.org/10.4172/2472-0429.1000E102

Heng, Siow-Chin., Morrissey, O.., Chen, S.., Thursky, K.., Manser, R.., Nation, R.., Kong, D.., & Slavin, M.. (2015). Utility of bronchoalveolar lavage fluid galactomannan alone or in combination with PCR for the diagnosis of invasive aspergillosis in adult hematology patients: A systematic review and meta-analysis. Critical Reviews in Microbiology , 41 , 124 - 134 .

http://doi.org/10.3109/1040841X.2013.804033

Hong, Jindui., Xia, X.., Wang, Yongsheng., & Xu, R.. (2012). Mesoporous carbon nitride with in situ sulfur doping for enhanced photocatalytic hydrogen evolution from water under visible light. Journal of Materials Chemistry , 22 , 15006-15012 . http://doi.org/10.1039/C2JM32053C

Hooper, S., & Munro, K. (2013). Physical and Methodological Perspectives on the Optical Properties of Biological Samples: A Review. MDPI Photonics, 8(12), 540. https://doi.org/10.3390/photonics8120540

Jonkman, J.., Cathcart, Judith A.., Xu, Feng., Bartolini, Miria E., Amon, Jennifer E., Stevens, K.., & Colarusso, P.. (2014). An introduction to the wound healing assay using live-cell microscopy. Cell Adhesion & Migration , 8 , 440 - 451 . http://doi.org/10.4161/cam.36224

Kim, Dohyun., & Herr, A.. (2013). Protein immobilization techniques for microfluidic assays.. Biomicrofluidics , 7 4 , 41501 . http://doi.org/10.1063/1.4816934

Kimmel, Danielle W.., LeBlanc, G.., Meschievitz, Mika E., & Cliffel, D.. (2012). Electrochemical sensors and biosensors.. Analytical chemistry , 84 2 , 685-707 . http://doi.org/10.1021/ac202878q

Ko, J.., Seok, H.., Cho, S.., Ha, Y.., Baek, J.., Kim, So Hyun., Kim, Yae-Jean., Park, Jin Kyeong., Chung, C.., Kang, E.., Cho, D.., Müller, M.., Drosten, C.., Kang, C.., Chung, D.., Song, Jae-Hoon., & Peck, K.. (2018). Challenges of Convalescent Plasma Infusion Therapy in Middle East Respiratory Coronavirus Infection: A Single Centre Experience. Antiviral Therapy , 23 , 617 - 622 . http://doi.org/10.3851/IMP3243

Krämer, Joana., Kang, Rui., Grimm, L.., Cola, L. De., Picchetti, Pierre., & Biedermann, Frank. (2022). Molecular Probes, Chemosensors, and Nanosensors for Optical Detection of Biorelevant Molecules and Ions in Aqueous Media and Biofluids. Chemical Reviews , 122 , 3459 - 3636 . http://doi.org/10.1021/acs.chemrev.1c00746

Kronik, L.., Stein, T.., Refaely-Abramson, S.., & Baer, R.. (2012). Excitation Gaps of Finite-Sized Systems from Optimally Tuned Range-Separated Hybrid Functionals.. Journal of chemical theory and computation , 8 5 , 1515-31 . http://doi.org/10.1021/ct2009363

Kumar, R.., Sharma, Amit., Singh, Hardev., Suating, Paolo., Kim, Hyeong Seok., Sunwoo, Kyoung., Shim, Inseob., Gibb, B.., & Kim, Jong Seung. (2019). Revisiting Fluorescent Calixarenes: From Molecular Sensors to Smart Materials.. Chemical reviews . http://doi.org/10.1021/acs.chemrev.8b00605

Leeflang, M.., Debets-Ossenkopp, Y.., Wang, Junfeng., Visser, C.., Scholten, R.., Hooft, L.., Bijlmer, H.., Reitsma, J.., Zhang, Mingming., Bossuyt, P.., & Vandenbroucke-Grauls, C.. (2015). Galactomannan detection for invasive aspergillosis in immunocompromised patients.. The Cochrane database of systematic reviews , 12 , CD007394 . http://doi.org/10.1002/14651858.CD007394.pub2

Lerner, E.., Cordes, T.., Ingargiola, Antonino., Alhadid, Yazan., Chung, SangYoon., Michalet, X.., & Weiss, S.. (2018). Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer. Science , 359 . http://doi.org/10.1126/science.aan1133

Lin, Yang-Wei., Huang, Chih-Ching., & Chang, Huan‐Tsung. (2011). Gold nanoparticle probes for the detection of mercury, lead and copper ions.. The Analyst , 136 5 , 863-71 . http://doi.org/10.1039/c0an00652a

Lindl, J.., Landen, O.., Edwards, J.., & Moses, E.. (2014). Review of the National Ignition Campaign 2009-2012. Physics of Plasmas , 21 , 020501 . http://doi.org/10.1063/1.4865400

Liu, Dongqing., Shadike, Zulipiya., Lin, Ruoqian., Qian, Kun., Li, H.., Li, Kaikai., Wang, Shuwei., Yu, Qipeng., Liu, Ming., Ganapathy, S.., Qin, X.., Yang, Quan-hong., Wagemaker, M.., Kang, F.., Yang, Xiao‐Qing., & Li, Baohua. (2019). Review of Recent Development of In Situ/Operando Characterization Techniques for Lithium Battery Research. Advanced Materials , 31 . http://doi.org/10.1002/adma.201806620

Luchansky, Matthew S.., & Bailey, R.. (2012). High-Q optical sensors for chemical and biological analysis.. Analytical chemistry , 84 2 , 793-821 . http://doi.org/10.1021/ac2029024

Millot, M.., Hamel, S.., Rygg, J. R.., Celliers, P.., Collins, Gilbert W.., Coppari, F.., Fratanduono, D.., Jeanloz, R.., Swift, D.., & Eggert, J.. (2018). Experimental evidence for superionic water ice using shock compression. Nature Physics , 14 , 297-302 . http://doi.org/10.1038/S41567-017-0017-4

Nasir, M.., Nawaz, Mian Hasnain., Latif, Usman., Yaqub, Mustansara., Hayat, A.., & Rahim, A.. (2017). An overview on enzyme-mimicking nanomaterials for use in electrochemical and optical assays. Microchimica Acta , 184 , 323-342 . http://doi.org/10.1007/s00604-016-2036-8

Oba, F.., Choi, Minseok., Togo, A.., & Tanaka, I.. (2011). Point defects in ZnO: an approach from first principles. Science and Technology of Advanced Materials , 12 . http://doi.org/10.1088/1468-6996/12/3/034302

Papkovsky, D.., & Dmitriev, R.. (2013). Biological detection by optical oxygen sensing.. Chemical Society reviews , 42 22 , 8700-32 . http://doi.org/10.1039/c3cs60131e

Picetti, R.., Shakur-Still, H.., Medcalf, R.., Standing, J.., & Roberts, I.. (2019). What concentration of tranexamic acid is needed to inhibit fibrinolysis? A systematic review of pharmacodynamics studies. Blood Coagulation & Fibrinolysis , 30 , 1 - 10 . http://doi.org/10.1097/MBC.0000000000000789

Qiu, Zhenli., Shu, Jian., & Tang, D.. (2017). Bioresponsive Release System for Visual Fluorescence Detection of Carcinoembryonic Antigen from Mesoporous Silica Nanocontainers Mediated Optical Color on Quantum Dot-Enzyme-Impregnated Paper.. Analytical chemistry , 89 9 , 5152-5160 . http://doi.org/10.1021/acs.analchem.7b00989

Shekhar, Prashant., Atkinson, J.., & Jacob, Z.. (2014). Hyperbolic metamaterials: fundamentals and applications. Nano Convergence , 1 . http://doi.org/10.1186/s40580-014-0014-6

Singh, Arunima K.., Mathew, K.., Zhuang, H.., & Hennig, R.. (2015). Computational Screening of 2D Materials for Photocatalysis.. The journal of physical chemistry letters , 6 6 , 1087-98 . http://doi.org/10.1021/jz502646d

Spadavecchia, F.., Cappelletti, G.., Ardizzone, S.., Ceotto, M.., & Falciola, L.. (2011). Electronic Structure of Pure and N-Doped TiO2 Nanocrystals by Electrochemical Experiments and First Principles Calculations. Journal of Physical Chemistry C , 115 , 6381-6391 . http://doi.org/10.1021/JP2003968

Strauss, V.., Margraf, Johannes T.., Dolle, C.., Butz, B.., Nacken, Thomas J.., Walter, J.., Bauer, W.., Peukert, W.., Spiecker, E.., Clark, T.., & Guldi, D.. (2014). Carbon nanodots: toward a comprehensive understanding of their photoluminescence.. Journal of the American Chemical Society , 136 49 , 17308-16 . http://doi.org/10.1021/ja510183c

Trizio, Luca De., Gaspari, Roberto., Bertoni, G.., Kriegel, I.., Moretti, L.., Scotognella, F.., Maserati, L.., Zhang, Yang., Messina, G.., Prato, M.., Marras, S.., Cavalli, A.., & Manna, L.. (2015). Cu3-xP Nanocrystals as a Material Platform for Near-Infrared Plasmonics and Cation Exchange Reactions. Chemistry of Materials , 27 , 1120 - 1128 . http://doi.org/10.1021/cm5044792

Trpković, A.., Resanović, I.., Stanimirovic, J.., Radak, D.., Mousa, S.., Cenić-Milosević, D.., Jevremović, D.., & Isenovic, E.. (2015). Oxidized low-density lipoprotein as a biomarker of cardiovascular diseases. Critical Reviews in Clinical Laboratory Sciences , 52 , 70 - 85 . http://doi.org/10.3109/10408363.2014.992063

Tsuji, K.., & Müller, Stefan C. (2021). Physiology and. Physics and Music . http://doi.org/10.1007/978-3-030-68676-5_11

Weber, Judith., Beard, P.., & Bohndiek, S.. (2016). Contrast agents for molecular photoacoustic imaging. Nature Methods , 13 , 639-650 . http://doi.org/10.1038/nmeth.3929

Wiederseiner, S.., Andreini, N.., Epely-Chauvin, G.., & Ancey, C.. (2011). Refractive-index and density matching in concentrated particle suspensions: a review. Experiments in Fluids , 50 , 1183-1206 . http://doi.org/10.1007/S00348-010-0996-8

Zhang, Lei., Li, Yang., Li, Dawei., Jing, Chao., Chen, Xiaoyuan., Lv, Min., Huang, Qing., Long, Yitao., & Willner, I.. (2011). Single gold nanoparticles as real-time optical probes for the detection of NADH-dependent intracellular metabolic enzymatic pathways.. Angewandte Chemie , 50 30 , 6789-92 . http://doi.org/10.1002/anie.201102151

Zhao, Yufei., Jia, Xiaodan., Waterhouse, Geoffrey I N., Wu, Lizhu., Tung, C.., O′Hare, D.., & Zhang, Tierui. (2016). Layered Double Hydroxide Nanostructured Photocatalysts for Renewable Energy Production. Advanced Energy Materials , 6 . http://doi.org/10.1002/aenm.201501974