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A theoretical model for template-free synthesis of long DNA sequence
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Research Article
A theoretical model for template-free synthesis of long DNA sequence
S. M. Minhaz Ud-Dean1, 2 
| (1) |
Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh |
| (2) |
Ashtabhuj Systems, 77 Basupara Main Road, Khulna, Bangladesh |
Received: 31 December 2008 Revised: 17 March 2009 Accepted: 18 March 2009 Published online: 3 April 2009
Abstract This theoretical scheme is intended to formulate a potential method for high fidelity synthesis of Nucleic Acid molecules
towards a few thousand bases using an enzyme system. Terminal Deoxyribonucleotidyl Transferase, which adds a nucleotide to
the 3′OH end of a Nucleic Acid molecule, may be used in combination with a controlled method for nucleotide addition and degradation,
to synthesize a predefined Nucleic Acid sequence. A pH control system is suggested to regulate the sequential activity switching
of different enzymes in the synthetic scheme. Current practice of synthetic biology is cumbersome, expensive and often error
prone owing to the dependence on the ligation of short oligonucleotides to fabricate functional genetic parts. The projected
scheme is likely to render synthetic genomics appreciably convenient and economic by providing longer DNA molecules to start
with.
Keywords Long DNA synthesis - Enzyme system modelling - Synthetic gene - pH regulated synthesis - Terminal deoxyribonucleotidyl transferase - Genetic parts fabrication
References
Agarwal KL, Buchi H, Caruthers MH, Gupta N, Khorana HG, Kleppe K, Kumar A, Ohtsuka E, Rajbhandary UL, Van de Sande JH et al
(1974) Total synthesis of the gene for an alanine transfer ribonucleic acid from yeast. Nature 227:27–34. doi:10.1038/227027a0
|
| |
Aksnes G, Libanu FO (1991) Temperature dependence of ester hydrolysis in water. Acta Chem Scand 45:463–468. doi:10.3891/acta.chem.scand.45-0463
|
| |
Baedeker M, Schulz GE (1999) Overexpression of a designed 2.2 kb gene of eukaryotic phenylalanine ammonia-lyase in Escherichia coli. FEBS Lett 457:57–60. doi:10.1016/S0014-5793(99)01000-5
|
| |
| Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D (2007) BRENDA, AMENDA and FRENDA: the enzyme information system
in 2007. Nucleic Acids Res. doi:10.1093/nar/gkl972
|
| |
| Bollum FJ (1974) Terminal deoxynucleotidyl transferase. In: Boyer PD (ed) The enzymes, vol 10, 3rd edn. Academic Press, New
York, pp 145–171
|
| |
Bollum FJ (1978) Terminal deoxynucleotidyl transferase: biological studies. Adv Enzymol Relat Areas Mol Biol 47:347–374
|
| |
| Carr PA, Park JS, Lee YJ, Yu T, Zhang S, Jacobson JM (2004) Protein-mediated error correction for de novo DNA synthesis. Nucleic
Acids Res. doi:10.1093/nar/gnh160
|
| |
Caruthers MH (1985) Gene synthesis machines: DNA chemistry and its uses. Science 230:281–285. doi:10.1126/science.3863253
|
| |
Cello J, Paul AV, Wimmer E (2002) Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of
natural template. Science 297:1016–1018. doi:10.1126/science.1072266
|
| |
Chalmers FM, Curnow KM (2001) Scaling up the ligase chain reaction-based approach to gene synthesis. Biotechniques 30:249–252
|
| |
Coleman MS (1977) Terminal deoxynucleotidyl transferase: characterization of extraction and assay conditions from human and
calf tissue. Arch Biochem Biophys 182:525–532. doi:10.1016/0003-9861(77)90533-1
|
| |
Deng GR, Wu R (1983) Terminal transferase: use in the tailing of DNA and for in vitro mutagenesis. Methods Enzymol 100:96–116.
doi:10.1016/0076-6879(83)00047-6
|
| |
Dickson KS, Burns CM, Richardson JP (2000) Determination of the free-energy change for repair of a DNA phosphodiester bond.
J Biol Chem 275:15828–15831. doi:10.1074/jbc.M910044199
|
| |
Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403:335–338. doi:10.1038/35002125
|
| |
| Endy D (2005) Foundations for engineering biology. Nature doi:10.1038/nature04342
|
| |
Eschenfeldt WH et al (1987) Homopolymeric tailing. Methods Enzymol 152:337–342. doi:10.1016/0076-6879(87)52040-7
|
| |
Frohman MA et al (1988) Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific
oligonucleotide primer. Proc Natl Acad Sci USA 85:8998–9002. doi:10.1073/pnas.85.23.8998
|
| |
| Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire
MA, et al (2008) Complete chemical synthesis, assembly and cloning of a Mycoplasma genitalium genome. Science doi:10.1126/science.1151721
|
| |
| Glick BR, Pasternak JJ (2003) Molecular biotechnology: principles and applications of recombinant DNA, 3rd edn. ASM Press,
Washington DC, p 81
|
| |
Gorczyca W et al (1993) Detection of DNA strand breaks in individual apoptotic cells by the in situ terminal deoxynucleotidyl
transferase and nick translation assays. Cancer Res 53:1945–1951
|
| |
Haas H, Redl B, Leitner E, Stöffler G (1991) Penicillium chrysogenum extracellular acid phosphatase: purification and biochemical characterization. Biochim Biophys Acta 1074:392–397
|
| |
Hoover DM, Lubkowski J (2002) DNA works: an automated method for designing oligonucleotides for PCR-based gene synthesis.
Nucleic Acids Res 30:e43. doi:10.1093/nar/30.10.e43
|
| |
Hutchison CA, Peterson SN, Gill SR, Cline RT, White O, Fraser CM, Smith HO, Venter JC (1999) Global transposon mutagenesis
and a minimal Mycoplasma genome. Science 286:2165–2169. doi:10.1126/science.286.5447.2165
|
| |
Igloi GL, Schiefermayr E (1993) Enzymatic addition of fluorescein- or biotin-riboUTP to oligonucleotides results in primers
suitable for DNA sequencing and PCR. Biotechniques 15:486–497
|
| |
| Khorana HG (1968) Nucleic acid synthesis in the study of the genetic code. In: Nobel lectures: physiology or medicine (1963–1970).
Elsevier Science Ltd, Amsterdam, pp 341–369
|
| |
Kleppe K, Ohtsuka E, Kleppe R, Molineux I, Khorana HG (1971) Studies on polynucleotides XCVI. Repair replications of short
synthetic DNA’s as catalyzed by DNA polymerases. J Mol Biol 56:341–361. doi:10.1016/0022-2836(71)90469-4
|
| |
Kodumal SJ, Patel KG, Reid R, Menzella HG, Welch M, Santi DV (2004) Total synthesis of long DNA sequences: synthesis of a
contiguous 32-kb polyketide synthase gene cluster. Proc Natl Acad Sci USA 101:15573–15578. doi:10.1073/pnas.0406911101
|
| |
Kormelink FJM, Lefebvre B, Strozyk F, Voragen AGJ (1993) Purification and characterization of an acetyl xylan esterase from
Aspergillus niger. J Biotechnol 27:267–282. doi:10.1016/0168-1656(93)90090-A
|
| |
Kumar A et al (1988) Nonradioactive labeling of synthetic oligonucleotide probes with terminal deoxynucleotidyl transferase.
Anal Biochem 169:376–382. doi:10.1016/0003-2697(88)90299-0
|
| |
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W et al (2001) Initial
sequencing and analysis of the human genome. Nature 409:860–921. doi:10.1038/35057062
|
| |
| Luo Y-R (2007) Comprehensive handbook of chemical bond energies. CRC Press, Boca Raton, pp 255–338
|
| |
Martin VJ, Pitera DJ, Withers ST, Newman JD, Keasling JD (2003) Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol 21:796–802. doi:10.1038/nbt833
|
| |
Mehl RA, Anderson JC, Santoro SW, Wang L, Martin AB, King DS, Horn DM, Schultz PG (2003) Generation of a bacterium with a
21 amino acid genetic code. J Am Chem Soc 125:935–939. doi:10.1021/ja0284153
|
| |
| Ratliff RL (1981) Terminal deoxyribonucleotidyl transferase. In: Boyer PD (ed) The enzymes, vol 14, 3rd edn. Academic Press,
New York, pp 105–118
|
| |
Richmond KE, Li MH, Rodesch MJ, Patel M, Lowe AM, Kim C, Chu LL, Venkataramaian N, Flickinger SF, Kaysen J et al (2004) Amplification
and assembly of chip-eluted DNA (AACED): a method for high-throughput gene synthesis. Nucleic Acids Res 32:5011–5018. doi:10.1093/nar/gkh793
|
| |
Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification
of DNA with a thermostable DNA polymerase. Science 239:487–491. doi:10.1126/science.2448875
|
| |
| Sambrook J, Russel D (2001) Molecular cloning: a laboratory manual, vol 2, 3rd edn. Cold Harbor Laboratory Press, Cold Spring
Harbor, pp 8.18–8.25
|
| |
| Scheele G, Fukuoka S-I (1992) Synthesis of full-length double-stranded DNA from a single-stranded linear DNA template. US
Patent 5162209
|
| |
| Scheele G, Fukuoka S-I (1997) Synthesis of full-length double-stranded DNA from a single-stranded linear DNA template. US
Patent 5643766
|
| |
Schomburg I, Chang A, Schomburg D (2002) BRENDA, enzyme data and metabolic information. Nucleic Acids Res 30:47–49. doi:10.1093/nar/30.1.47
|
| |
Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D (2004) BRENDA, the enzyme database: updates and major
new developments. Nucleic Acids Res 32:D431–D433. doi:10.1093/nar/gkh081
|
| |
| Sitnitsky AE (2006) Dynamical contribution into enzyme catalytic efficiency. Physica A doi:10.1016/j.physa.2006.03.039
|
| |
Smith HO, Hutchison CA, Pfannkoch C, Venter JC (2003) Generating a synthetic genome by whole genome assembly: ΦX174 bacteriophage
from synthetic oligonucleotides. Proc Natl Acad Sci USA 100:15440–15445. doi:10.1073/pnas.2237126100
|
| |
| Sprinzak D, Elowitz MB (2005) Reconstruction of genetic circuits. Nature. doi:10.1038/nature04335
|
| |
Tian J, Gong H, Sheng N, Zhou X, Gulari E, Gao X, Church GM (2004) Accurate multiplex gene syntheses from programmable DNA
chips. Nature 432:1050–1053. doi:10.1038/nature03151
|
| |
Tu C-PD, Cohen SN (1980) 3’-end labeling of DNA with [alfa-32P]cordycepin-5’-triphosphate. Gene 10:177–183. doi:10.1016/0378-1119(80)90135-3
|
| |
Vainonen JP, Vorobyeva NN, Rodina EV, Nazarova TI, Kurilova SA, Skoblov JS, Avaeva SM (2005) Metal-free PPi activates hydrolysis
of MgPPi by an Escherichia coli inorganic pyrophosphatase. Biochemistry (Mosc) 70:69–78
|
| |
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA et al (2001) The sequence
of the human genome. Science 291:1304–1351. doi:10.1126/science.1058040
|
| |
Vincent C et al (1982) Synthesis of 8-(2, 4-dinitrophenyl-2, 6-aminohexyl)aminoadenosine-5’-triphosphate: biological properties
and potential uses. Nucleic Acids Res 10:6787–6796. doi:10.1093/nar/10.21.6787
|
| |
| Voet D, Voet JG (2004) Biochemistry, 3rd edn. Wiley, New York, p 566
|
| |
Withers-Martinez C, Carpenter EP, Hackett F, Ely B, Sajid M, Grainger M, Blackman MJ (1999) PCR-based gene synthesis as an
efficient approach for expression of the A + T-rich malaria genome. Protein Eng 12:1113–1120. doi:10.1093/protein/12.12.1113
|
| |
|
|
|
|
|
|