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Biomimetic Approaches in Synthetic Biology

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Advances in Synthetic Biology

Abstract

Biomimetics is an advanced method to create full or partial replicates in stimulating biological system at macro and nanoscale. There are several inspired innovations that are developed to resolve the biological problems in efficient method. This chapter briefs development of engineering designs for recognition of biological phenomena accelerating the synthetic biology research. In addition, we describe the strategies for finding potential analogies in biological phenomena, including searching functional repertoire across multiple levels of organization, from the molecule to the biosphere. In addition, initial efforts at finding appropriate analogies are documented using an example.

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References

  • Ames BN, Durston WE, Yamasaki E, Lee FD (1973) Carcinogens are mutagens: a simple test system combining liver homogenates for activation and bacteria for detection. Proc Natl Acad Sci U S A 70(8):2281–2285

    CAS  PubMed  PubMed Central  Google Scholar 

  • Andrianantoandro E, Basu S, Karig DK, Weiss R (2006) Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2. 2006.0028

    Google Scholar 

  • Baeumner AJ, Schlesinger NA, Slutzki NS, Romano J, Lee EM, Montagna RA (2002) Biosensor for dengue virus detection: sensitive, rapid, and serotype specific. Anal Chem 74(6):1442–1448

    CAS  PubMed  Google Scholar 

  • Benner SA, Sismour AM (2005) Synthetic biology. Nat Genet 6:533–543

    CAS  Google Scholar 

  • Bensaude-Vincent B (2009) Biomimetic chemistry and synthetic biology: a two-way traffic across the borders. Hyle Int J Philos Chem 15(1):31–46

    CAS  Google Scholar 

  • Bhatia P, Chugh A (2013) Synthetic biology based biosensors and the emerging governance issues. Curr Synth Syst Biol 1(1):1–7

    Google Scholar 

  • Buranachai C, Thavarungkul P, Kanatharana P (2012) A novel reconfigurable optical biosensor based on DNA aptamers and a DNA molecular beacon. J Fluoresc 22(6):1617–1625

    CAS  PubMed  Google Scholar 

  • Checa SK, Zurbriggen MD, Soncini FC (2012) Bacterial signaling systems as platforms for rational design of new generations of biosensors. Curr Opin Biotechnol 23:766–772

    CAS  PubMed  Google Scholar 

  • Chen X, Ellington AD (2009) Design principles for ligand-sensing, conformation-switching ribozyme. PLoS Comput Biol 5(12):e1000620

    PubMed  PubMed Central  Google Scholar 

  • Chianella I, Piletsky SA, Tothill IE, Chen B, Turner APF (2003) MIP-based solid phase extraction cartridges combined with MIP-based sensors for the detection of microcystin-LR. Biosens Bioelectron 18:119–127

    CAS  PubMed  Google Scholar 

  • Choffnes ER, Relman DA, Pray L, IOM (Institute of Medicine) (2011) The science and applications of synthetic and systems biology. The National Academies Press, Washington, DC

    Google Scholar 

  • David PC, Nanette JP (2016) Biotechnology, 2nd edn. Elsevier, Amsterdam

    Google Scholar 

  • Dennis AM, Rhee WJ, Sotto D, Dublin SN, Bao G (2012) Quantum dot-fluorescent protein FRET probes for sensing intracellular pH. ACS Nano 6(4):2917–2924

    CAS  PubMed  PubMed Central  Google Scholar 

  • Effendi L, Nielsen D, Solomon K, Prather KJ (2008) Engineering microbes with syntheticbiology frameworks. Trends Biotechnol 26(12):674–681

    Google Scholar 

  • Enander K, Choulier L, Olsson AL, Yushchenko DA, Kanmert D, Klymchenko AS, Demchenko AP, Mely Y, Altschuh D (2008) A peptide-based ratiometric biosensor construct for direct fluorescence detection of a protein analyte. Bioconjug Chem 19:1864–1870

    CAS  PubMed  Google Scholar 

  • Franck P, Paulasova P (2004) The peptide nucleic acids, efficient tools for molecular diagnosis. Int J Mol Med 13(4):521–525

    Google Scholar 

  • Gómara MJ, Fernández L, Pérez T, Ercilla G, Haro I (2010) Assessment of synthetic chimeric multiple antigenic peptides for diagnosis of GB virus C infection. Anal Biochem 396:51–58

    PubMed  Google Scholar 

  • Gu X, TrybiÅ‚o M, Ramsay S, Jensen M, Fulton R, Rosser S, Gilbert D (2010) Engineering a novel self-powering electrochemical biosensor. Syst Synth Biol 4:203–214

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hartig JS, Famulok M (2008) Screening of molecular interactions using reporter hammerhead ribozymes. Methods Mol Biol 429:251–263

    CAS  PubMed  Google Scholar 

  • Isaacs FJ, Dwyer DJ, Collins JJ (2006) RNA synthetic biology. Nat Biotechnol 24:545–554

    CAS  PubMed  Google Scholar 

  • Jampasa S, Wonsawat W, Rodthongkum N, Siangproh W, Yanatatsaneejit P, Vilaivan CO (2014) Electrochemical detection of human papillomavirus DNA type 16 using a pyrrolidinyl peptide nucleic acid probe immobilized on screen-printed carbon electrodes. Biosens Bioelectron 54:428–434

    CAS  PubMed  Google Scholar 

  • Kanwar JR, Roy K, Maremanda NG, Subramanian K, Veedu RN, Bawa R, Kanwar RK (2015) Nucleic acid-based aptamers: applications, development and clinical trials. Curr Med Chem 22(21):2539–2557

    CAS  PubMed  Google Scholar 

  • Karimian N, Vagin M, Zavar MHA, Chamsaz M, Turner APF, Tiwari A (2013) Label-free biosensing: advanced materials, devices and applications. Biosens Bioelectron 50:492–498

    CAS  PubMed  Google Scholar 

  • Kellenberger CA, Chen C, Whiteley AT, Portnoy DA, Hammond MC (2015) RNA-based fluorescent biosensors for live cell imaging of second messenger cyclic di-AMP. J Am Chem Soc 137:6432–6435

    CAS  PubMed  PubMed Central  Google Scholar 

  • Khalil AS, Collins JJ (2010) Synthetic biology: applications come of age. Nat Genet 11:367–379

    CAS  Google Scholar 

  • Kindschy L, Alocilja E (2007) Development of a molecularly imprinted biomimetic electrode. Sensors 7(8):1630–1642

    CAS  PubMed Central  Google Scholar 

  • Kobayashi H, Kærn M, Araki M, Chung K, Gardner TS, Cantor CR, Collins JJ (2004) Programmable cells: interfacing natural and engineered gene networks. PNAS 101(22):8414–8419

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kong RM, Zhang XB, Chen Z, Meng HM, Song ZL, Tan W, Yu RQ (2011) Unimolecular catalytic DNA biosensor for amplified detection of L-histidine via anenzymatic recycling cleavage strategy. Anal Chem 83(20):7603–7607

    CAS  PubMed  Google Scholar 

  • Kwakye S, Baeumner A (2003) A microfluidic biosensor based on nucleic acid sequence recognition. Anal Bioanal Chem 376:1062–1068

    CAS  PubMed  Google Scholar 

  • Lee GN, Na J (2013) Future of microbial polyesters. Microb Cell Fact 12:54

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lee J, Park IS, Jung E, Lee Y, Min DH (2014) Biosens Bioelectron 62:140–144

    CAS  PubMed  Google Scholar 

  • Lepora NF, Verschure P, Prescott TJ (2013) The state of the art in biomimetics. Bioinspir Biomim 8:1–11

    Google Scholar 

  • Levesque MV, Levesque D, Briere FP, Perreault JP (2010) Investigating a new generation of ribozymes to target HCV. PLoS One 5(3):e9627

    PubMed  PubMed Central  Google Scholar 

  • Liang R, Zhang R, Qin W (2009) Biomedical nanomaterials. Sens Act B Chem 141(2):544–550

    CAS  Google Scholar 

  • Liu Y, Zhu L, Zhang Y, Tang H (2012) Sens Act B Chem 171:1151–1158

    Google Scholar 

  • Lu TK, Khalil AS, Collins JJ (2009) Next-generation synthetic gene networks. Nat Biotechnol 27(12):1139–1150

    CAS  PubMed  PubMed Central  Google Scholar 

  • Marner WD (2009) Practical application of synthetic biology principles. Biotechnol J 4:1406–1419

    CAS  PubMed  Google Scholar 

  • Marx S, Zaltsman A, Turyan I, Mandler D (2004) Parathion sensor based on molecularly imprinted sol−gel films. Anal Chem 76:120–126

    CAS  Google Scholar 

  • Mascini M (2008) Analytical applications of aptamers. J Biol Chem 36(4):273–282

    Google Scholar 

  • Michener K, Thodey K, Liang JC, Smolke CD (2012) Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metab Eng 14:212–222

    CAS  PubMed  Google Scholar 

  • Neumann H, Neumann-Staubitz P (2010) Synthetic biology approaches in drug discovery and pharmaceutical biotechnology. Appl Microbiol Biotechnol 87:75–86

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nicholls IA, Adbo K, Andersson HS, Andersson PO, Ankarloo J, Hedin-Dahlström J, Jokela P, Karlsson JP, Olofsson L, Rosengren J, Shoravi S, Svenson J, Wikman S (2001) Can we rationally design molecularly imprinted polymers? Anal Chim Acta 435:9–18

    CAS  Google Scholar 

  • Ogawa A (2011) Rational design of artificial riboswitches based on ligand-dependent modulation of internal ribosome entry in wheat germ extract and their applications as label-free biosensors. RNA 17:478–488

    CAS  PubMed  PubMed Central  Google Scholar 

  • Okumoto S, Looger LL, Micheva KD, Reimer RJ, Smith SJ, Frommer WB (2005) Detection of glutamate release from neurons by genetically encoded surface-displayed FRET nanosensors. PNAS 102(24):8740–8745

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pardieu E, Cheap H, Vedrine C, Lazerges M, Lattach Y, Garnier F, Remita S, Pernelle C (2009) Molecularly imprinted conducting polymer based electrochemical sensor for detection of atrazine. Anal Chim Acta 649:236–245

    CAS  PubMed  Google Scholar 

  • Peeters M, Troost FJ, van Grinsven B, Horemans F, Alenus J, Murib MS,... Wagner P (2012) MIP-based biomimetic sensor for the electronic detection of serotonin in human blood plasma. Sensor and Actuat B-Chem 171:602–610

    Google Scholar 

  • Pei R (2011) Aptamer-based biosensors through target-induced strand release. In: International Conference on Nanotechnology and Biosensor IPCBEE, 2. IACSIT Press, Singapore

    Google Scholar 

  • Peter EN, Michael E (1999) An introduction to peptide nucleic acid. Curr Iss Mol Biol 1(2):89–104

    Google Scholar 

  • Piletsky SA, Piletska EV, Bossi A, Karim K, Lowe P, Turner AP (2001a) Substitution of antibodies and receptors with molecularly imprinted polymers in enzyme-linked and fluorescent assays. Biosens Bioelectron 16(9–12):701–707

    Google Scholar 

  • Piletsky SA, Alcock S, Turner AP (2001b) Molecular imprinting: at the edge of the third millennium. Trends Biotechnol 19(1):9–12

    Google Scholar 

  • Prasuhn DE, Feltz A, Blanco-Canosa JB, Susumu K, Stewart MH, Mei BC, Yakovlev AV, Louko C, Mallet JM, Oheim M, Dawson PE, Medintz IL (2010) Quantum dot peptide biosensors for monitoring Caspase 3 proteolysis and calcium ions. ACS Nano 4(9):5487–5497

    CAS  PubMed  Google Scholar 

  • Prindle A, Samayoa P, Razinkov I, Danino T, Tsimring LS, Hasty J (2012) A sensing array of radically coupled genetic ‘biopixels’. Nature 481:39–44

    CAS  Google Scholar 

  • Quintero A, Garcia S, Guevara C, Rincon C, Ospina C, Guevara P, Cuero R (2007) A microbial biosensor device for iron detection under UV irradiation. IET Synth Biol 1(1–2):71–73

    Google Scholar 

  • Ryoo SR, Lee J, Yeo J, Na HK, Kim YK, Jang H, Min DH (2013) Quantitative and multiplexed microRNA sensing in living cells based on peptide nucleic acid and nano graphene oxide (PANGO). ACS Nano 7(7):5882–5891

    CAS  PubMed  Google Scholar 

  • Saeidi N, Wong CK, Lo TM, Nguyen HX, Ling H, Leong SSJ, Poh CL, Chang MW (2011) Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen. Mol Syst Biol 7:521–532

    PubMed  PubMed Central  Google Scholar 

  • Sarikaya M, Tamerler C, Jen AKY, Schulten K, Baneyx F (2003) Molecular biomimetics: nanotechnology through biology. Nat Mater 2:577–585

    CAS  PubMed  Google Scholar 

  • Scognamiglio V (2013) Nanotechnology in glucose monitoring: advances and challenges in the last 10 years. Biosens Bioelectron 47:12–25

    CAS  PubMed  Google Scholar 

  • Scognamiglio V, Stano P, Polticelli F, Antonacci A, Lambreva MD, Pochetti G, Giardi MT, Rea G (2013) Design and biophysical characterization of atrazine-sensing peptides mimicking the Chlamydomonas reinhardtii plastoquinone binding niche. Chem Phys 15:13108–13115

    CAS  Google Scholar 

  • Sergeyeva TA, Slinchenko OA, Gorbach LA, Matyushov VF, Brovko OO, Pi-letsky SA, Sergeeva LM, Elska GV (2010) Catalytic molecularly imprinted polymer membranes: development of the biomimetic sensor for phenols detection. Anal. Chim. Acta 659:274–279

    CAS  PubMed  Google Scholar 

  • Sismour AM, Benner SA (2005) Synthetic biology. Expert Opin Biol Ther 5(11):1409–1414

    CAS  PubMed  Google Scholar 

  • Siuti P, Yazbek J, Lu TK (2013) Synthetic circuits integrating logic and memory in living cells. Nat Biotechnol 31(5):448–453

    CAS  PubMed  Google Scholar 

  • Subrahmanyam S, Piletsky SA, Piletska EV, Chen B, Karim K, Turner APF (2001) `Bite-and-Switch' approach using computationally designed molecularly imprinted polymers for sensing of creatinine. Biosens Bioelectron 16:631–637

    CAS  PubMed  Google Scholar 

  • Sun C, Liu X, Feng K, Jiang J, Shen G, Yu R (2010) An aptazyme-based electrochemical biosensor for the detection of adenosine. Anal Chim Acta 669:87–93

    CAS  PubMed  Google Scholar 

  • Suravajhala P, Burri HVR, Heiskanen A (2014) Combining aptamers and in silico interaction studies to decipher the function of hypothetical proteins. Eur Chem Bull 3(8):809–810

    Google Scholar 

  • Teo WS, Chang MW (2015) Bacterial XylRs and synthetic promoters function as genetically encoded xylose biosensors in Saccharomyces cerevisiae. Biotechnol J 10:315–322

    CAS  PubMed  Google Scholar 

  • Tombelli S, Minunni M, Mascini M (2007) Aptamers-based assays for diagnostics, environmental and food analysis. Biomol Eng 24:191–200

    CAS  PubMed  Google Scholar 

  • Valero-Navarro A, Salinas-Castillo A, Fernández-Sánchez JF, Segura-Carretero A, Mallavia R, Fernández-Gutiérrez A (2009) The development of a MIP-optosensor for the detection of monoamine naphthalenes in drinking water. Biosens Bioelectron 24:2305–2311

    CAS  PubMed  Google Scholar 

  • Villiers M-B, Cortay J-C, Cortès S, Bloquel B, Brichler S, Brakha C, Kay A, Falah N, Zoulim F, Marquette C, Marche PN, Dény P (2015) Protein-peptide arrays for detection of specific anti-hepatitis D virus (HDV) genotype 1, 6, and 8 antibodies among HDV-infected patients by surface plasmon resonance imaging. J Clin Microbiol 53(4):1164–1171

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ye L, Haupt K (2004) Molecularly imprinted polymers as antibody and receptor mimics for assays, sensors and drug discovery. Anal Bioanal Chem 378(8):1887–1897

    CAS  PubMed  Google Scholar 

  • Zhao J, Jedlicka SS, Lannu JD, Bhunia AK, Rickus JL (2006) Liposome-doped nanocomposites as artificial-cell-based biosensors: detection of listeriolysin.Biotechnol Prog 22(1):32–37

    CAS  PubMed  Google Scholar 

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Acknowledgements

The authors wish to thank Dr. Prashanth Suravajhala for providing the suggestions, encouragement, and fruitful discussion during preparation of this chapter.

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Correspondence to Renuka Suravajhala .

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Suravajhala, R., Kumar, A., Burri, H.R., Malik, B. (2020). Biomimetic Approaches in Synthetic Biology. In: Singh, V. (eds) Advances in Synthetic Biology. Springer, Singapore. https://doi.org/10.1007/978-981-15-0081-7_6

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