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Zhou X, Shi X, Fillon Y, Antia F, Pickel T, Yang J, Zhang W, Delavari A, Zhang J. Simplified Oligonucleotide Phosphorus Deprotection Process with Reduced 3-(2-Cyanoethyl) Thymidine Impurities. Nucleic Acid Ther 2024; 34:83-89. [PMID: 38315742 DOI: 10.1089/nat.2023.0060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
Oligonucleotides have emerged as valuable new therapeutics. Presently, oligonucleotide manufacturing consists in a series of stepwise additions until the full-length product is obtained. Deprotection of the phosphorus backbone before cleavage and deprotection (C&D) by ammonolysis is necessary to control the 3-(2-cyanoethyl) thymidine (CNET) impurity. In this study, we demonstrate that the use of piperazine as a scavenger of acrylonitrile allows phosphorus deprotection and C&D to be combined in a single step. This reduces solvent consumption, processing time, and CNET levels. Additionally, we showed that substitution of piperazine for triethylamine in the phosphorus deprotection step of supported-synthesis leads to reduced reaction times and lower levels of CNET impurities.
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Affiliation(s)
- Xuan Zhou
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts, USA
| | - Xianglin Shi
- Leal Therapeutics, Worcester, Massachusetts, USA
| | - Yannick Fillon
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts, USA
| | - Firoz Antia
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts, USA
| | - Thomas Pickel
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts, USA
| | - Jing Yang
- Intellia Therapeutics, Inc., Cambridge, Massachusetts, USA
| | - William Zhang
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts, USA
| | - Armin Delavari
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts, USA
| | - Jiabao Zhang
- Oligonucleotide Process Development, Biogen, Cambridge, Massachusetts, USA
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2
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Eguaogie O, Conlon PF, Vyle JS. Synthesis of nucleoside phosphoroselenolates via the efficient Michaelis–Arbuzov reaction of selenocyanates. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.09.096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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3
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Dellinger DJ, Timár Z, Myerson J, Sierzchala AB, Turner J, Ferreira F, Kupihár Z, Dellinger G, Hill KW, Powell JA, Sampson JR, Caruthers MH. Streamlined Process for the Chemical Synthesis of RNA Using 2′-O-Thionocarbamate-Protected Nucleoside Phosphoramidites in the Solid Phase. J Am Chem Soc 2011; 133:11540-56. [DOI: 10.1021/ja201561z] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Douglas J. Dellinger
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Zoltán Timár
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Joel Myerson
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Agnieszka B. Sierzchala
- Agilent Nucleic Acids Solutions Division, 5555 Airport Boulevard, Suite 100, Boulder, Colorado 80301, United States
| | - John Turner
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Fernando Ferreira
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Zoltán Kupihár
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Geraldine Dellinger
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Kenneth W. Hill
- Agilent Nucleic Acids Solutions Division, 5555 Airport Boulevard, Suite 100, Boulder, Colorado 80301, United States
| | - James A. Powell
- Agilent Nucleic Acids Solutions Division, 5555 Airport Boulevard, Suite 100, Boulder, Colorado 80301, United States
| | - Jeffrey R. Sampson
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Marvin H. Caruthers
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
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Kim EK, Choi H, Lee ES. Reactivity and suitability of t-Boc-protected thiophosphotyrosine intermediate analogs for the solid or solution phase peptide synthesis. Arch Pharm Res 1998; 21:330-7. [PMID: 9875453 DOI: 10.1007/bf02975297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
N-(tert-Butoxycarbonyl)-O-(dimethylthiophosphono)-L-tyrosine (6) and N-(tert-butoxycarbony)-O-(dicyanoethylthiophosphono)-L-tyros ine (15) were prepared as intermediates for the synthesis of thiophosphotyrosine-containing peptides. The reactivity and suitability of two compounds for the solid phase or solution phase peptide synthesis utilizing t-Boc chemistry were examined.
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Affiliation(s)
- E K Kim
- College of Pharmacy, Yeungnam University, Kyongsan, Korea
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6
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Barber I, Imbach JL, Rayner B. Solution-phase synthesis of phosphorothioate oligodeoxynucleosides by the phosphotriester method. ANTISENSE RESEARCH AND DEVELOPMENT 1995; 5:39-47. [PMID: 7613072 DOI: 10.1089/ard.1995.5.39] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A "phosphorothioate triester method" was investigated for the solution-phase synthesis of phosphorothioate oligonucleosides. Using fully protected 3'-phosphorothiolate thymidine bearing O-cyanoethyl and S-2,4-dichlorobenzyl groups as phosphorothioate protecting groups, decathymidine nonaphosphorothioate was efficiently assembled through a blockwise procedure. Two side reactions occurred during the deprotection steps: breakage of internucleoside linkages (1.8% per linkage) and formation of phosphate diester linkages (0.9%). Substitution of the dichlorobenzyl group by the more labile 4-nitrobenzyl S-protecting group reduced the extent of internucleoside bond breakage by one-half.
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Affiliation(s)
- I Barber
- Laboratoire de Chimie BIo-organique, Université de Montpellier II, France
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Kegler-Ebo DM, Docktor CM, DiMaio D. Codon cassette mutagenesis: a general method to insert or replace individual codons by using universal mutagenic cassettes. Nucleic Acids Res 1994; 22:1593-9. [PMID: 8202358 PMCID: PMC308034 DOI: 10.1093/nar/22.9.1593] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We describe codon cassette mutagenesis, a simple method of mutagenesis that uses universal mutagenic cassettes to deposit single codons at specific sites in double-stranded DNA. A target molecule is first constructed that contains a blunt, double-strand break at the site targeted for mutagenesis. A double-stranded mutagenic codon cassette is then inserted at the target site. Each mutagenic codon cassette contains a three base pair direct terminal repeat and two head-to-head recognition sequences for the restriction endonuclease Sapl, an enzyme that cleaves outside of its recognition sequence. The intermediate molecule containing the mutagenic cassette is then digested with Sapl, thereby removing most of the mutagenic cassette, leaving only a three base cohesive overhang that is ligated to generate the final insertion or substitution mutation. A general method for constructing blunt-end target molecules suitable for this approach is also described. Because the mutagenic cassette is excised during this procedure and alters the target only by introducing the desired mutation, the same cassette can be used to introduce a particular codon at all target sites. Each cassette can deposit two different codons, depending on the orientation in which it is inserted into the target molecule. Therefore, a series of eleven cassettes is sufficient to insert all possible amino acids at any constructed target site. Thus codon cassettes are 'off-the-shelf' reagents, and this methodology should be a particularly useful and inexpensive approach for subjecting multiple different positions in a protein sequence to saturation mutagenesis.
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Affiliation(s)
- D M Kegler-Ebo
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510
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Affiliation(s)
- E Sonveaux
- Laboratoire de Biochimie Physique et des Biopolymères, Louvain-La-Neuve, Belgium
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9
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Nikiforov TT, Cornolly BA. The synthesis of oligodeoxynucleotides containing 4-thiothymidine residues. Tetrahedron Lett 1991. [DOI: 10.1016/s0040-4039(00)79395-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Chapter 10 Nucleic Acids, Polynucleotides and Oligonucleotides. ACTA ACUST UNITED AC 1988. [DOI: 10.1016/s0301-4770(08)61450-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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11
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Cosstick R, Williams DM. An approach to the stereoselective synthesis of Sp-dinucleoside phosphorothioates using phosphotriester chemistry. Nucleic Acids Res 1987; 15:9921-32. [PMID: 3480505 PMCID: PMC306540 DOI: 10.1093/nar/15.23.9921] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
An approach to the stereoselective synthesis of Sp- dinucleoside phosphorothioates has been investigated which utilizes phosphotriester chemistry. The stereoselectivity of internucleotide bond formation between N4-benzoyl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxycytidine-3'-O-(S2-cyano-e thyl) phosphorothioate (3) and 3'-O-acetylthymidine has been studied using either mesitylenesulphonyl-5-(pyridin-2-yl)tetrazole (MSPy) or 1-mesitylenesulphonyl-3-nitro-1,2,4-triazole (MSNT) as the activating agent. The removal of the cyanoethyl group from the protected dinucleoside phosphorothioate has been studied, and conditions are reported which provide rapid deprotection without concomittant desulphurisation.
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Affiliation(s)
- R Cosstick
- Robert Robinson Laboratories, Department of Organic Chemistry, University of Liverpool, UK
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Furman TC, Epp J, Hsiung HM, Hoskins J, Long GL, Mendelsohn LG, Schoner B, Smith DP, Smith MC. Recombinant Human Insulin-Like Growth Factor II Expressed in Escherichia coli. Nat Biotechnol 1987. [DOI: 10.1038/nbt1087-1047] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Morvan F, Rayner B, Imbach JL, Thenet S, Bertrand JR, Paoletti J, Malvy C, Paoletti C. alpha-DNA II. Synthesis of unnatural alpha-anomeric oligodeoxyribonucleotides containing the four usual bases and study of their substrate activities for nucleases. Nucleic Acids Res 1987; 15:3421-37. [PMID: 3575096 PMCID: PMC340739 DOI: 10.1093/nar/15.8.3421] [Citation(s) in RCA: 117] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
This paper describes for the first time the synthesis of alpha-oligonucleotides containing the four usual bases. Two unnatural hexadeoxyribonucleotides: alpha-[d(CpApTpGpCpG)] and alpha-[d(CpGpCpApTpG)], consisting only of alpha-anomeric nucleotide units, were obtained by an improved phosphotriester method, in solution. Starting material was the four base-protected alpha-deoxyribonucleosides 3a-d. Pyrimidine alpha-deoxynucleosides 3a and 3b were prepared by self-anomerization reactions followed by selective deprotection of sugar hydroxyles, while the two purine alpha-deoxynucleosides 3c and 3d were prepared by glycosylation reactions. In the case of guanine alpha-nucleoside derivative a supplementary base-protecting group: N,N-diphenylcarbamoyl was introduced on O6-position in order to avoid side-reactions during oligonucleotide assembling. The hexadeoxynucleotide alpha-[d(CpApTpGpCpG)] was tested as substrate of selected endo- and exonucleases. In conditions where the natural corresponding beta-hexamer was completely degradated by nuclease S1 and calf spleen phosphodiesterase, the alpha-oligonucleotide remained almost intact.
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Hsiung HM, MacKellar WC. Expression of bovine growth hormone derivatives in Escherichia coli and the use of the derivatives to produce natural sequence growth hormone by cathepsin C cleavage. Methods Enzymol 1987; 153:390-401. [PMID: 3323805 DOI: 10.1016/0076-6879(87)53067-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Debart F, Rayner B, Imbach JL, Chang DK, Lown JW. Structure and conformation of the duplex consensus acceptor exon:intron junction d[(CpTpApCpApGpGpT). (ApCpCpTpGpTpApG)] deduced from high-field 1H-NMR of non-exchangeable and imino protons. J Biomol Struct Dyn 1986; 4:343-63. [PMID: 3271448 DOI: 10.1080/07391102.1986.10506354] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The complementary consensus acceptor exon:intron junction d(ApCpCpTpGpTpApG) has been synthesized by a modified phosphotriester method. The non self-complementary octamer exists in the random coil form in aqueous buffer at 20 degrees C as evidenced by temperature variable 1H-NMR and NOE measurements. The non-exchangeable proton assignments were secured using a combination of techniques including two-dimensional COSY, NOESY and 1H-1H-INADEQUATE. The octamer was annealed with the primary consensus sequence d(CpTpApCpApGpGpT). Confirmation of complete duplex formation was confirmed by detection and assignment of imino protons in D2O:H2O mixtures. Assignment of the non-exchangeable proton signals in the duplex consensus junction was then secured by a combination of two-dimensional COSY correlations, NOESY and NOE experiments. Determination of individual vicinal coupling constants in the component deoxyribose moieties permitted deduction of the population of S conformations in this sequence. It is concluded that the consensus acceptor junction exists in solution in a conformation belonging to the B family, and that the bases are oriented anti. In addition the deoxyribose moieties in the 5' regions exist predominantly in the S form (2'endo-3'exo) whereas those residues on or adjacent to the junction on the primary strand show more N character (2'exo-3'endo). The contiguous bases A5-G6 (adjacent to the junction) and A15-G16 are stacked more closely than the other neighbor bases in this duplex sequence. These subtle structural and conformational differences in the exon:intron junction may serve as recognition signals for these critical sites in the genome.
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Affiliation(s)
- F Debart
- Laboratoire de Chimie Bio-Organique, CNRS Université des Sciences et Techniques du Languedoc, Montpellier, France
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Morvan F, Rayner B, Imbach JL, Chang DK, Lown JW. alpha-DNA. I. Synthesis, characterization by high field 1H-NMR, and base-pairing properties of the unnatural hexadeoxyribonucleotide alpha-[d(CpCpTpTpCpC)] with its complement beta-[d(GpGpApApGpG)]. Nucleic Acids Res 1986; 14:5019-35. [PMID: 3725590 PMCID: PMC311508 DOI: 10.1093/nar/14.12.5019] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The novel deoxyribonucleotide alpha-[d(CpCpTpTpCpC)] and its complement beta-[d(GpGpApApGpG)] were synthesized by the phosphotriester method. 1H-NMR-NOE examination of the alpha-hexamer revealed that the cytosine and thymine bases appear to adopt anti conformations in this strand. In addition the deoxyribose of the thymidine moieties may adopt average conformations approximating to C3'-endo while the cytidine furanose groups are close to C2'-endo conformations. Both hyperchromicity in thermal melting and detection of base paired imino protons in 1H-NMR studies in H2O provide evidence for the annealing of alpha-d[CCTTCC] with its complement beta-d[GGAAGG] in potassium phosphate buffer pH 7.1 containing 10 mM magnesium chloride. Under these conditions thermal melting begins at 38 degrees C and its complete at approximately 45 degrees C. NOE experiments do not permit a decision on the polarity of annealing (predicted to be parallel) for this particular pair of sequences.
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Lown JW, Chang DK, Debart F, Rayner B, Imbach JL. 1H and 31P-NMR assignments of the non-exchangeable protons of the consensus acceptor exon:intron junction d(CpTpApCpApGpGpT). J Biomol Struct Dyn 1986; 3:1171-87. [PMID: 2856022 DOI: 10.1080/07391102.1986.10508493] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The consensus acceptor exon:intron junction d(CpTpApCpApGpGpT) has been synthesized by a modified phosphotriester method. The non-self complementary octamer exists in the single strand form in aqueous buffer at 20 degrees C as evidenced by temperature variable 1H-NMR and NOE measurements. The non-exchangeable proton assignments were secured using a combination of techniques including two-dimensional COSY, NOESY and the double quantum technique 1H-1H-INADEQUATE as well as inversion recovery T1 experiments. The new technique of 31P-1H shift correlation is particularly valuable in removing certain ambiguities in the sugar proton assignments. Characteristic chemical shifts for the base protons which are determined by their immediate molecular environments are also useful in assignments. The consensus acceptor exon:intron junction adopts a random coil conformation in solution under the experimental conditions employed.
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Affiliation(s)
- J W Lown
- Department of Chemistry, University of Alberta, Edmonton, Canada
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Urdea MS, Horn T. Solid-supported synthesis, deprotection and enzymatic purification of oligodeoxyribonucleotides. Tetrahedron Lett 1986. [DOI: 10.1016/s0040-4039(00)84683-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Sinha ND, Biernat J, McManus J, Köster H. Polymer support oligonucleotide synthesis XVIII: use of beta-cyanoethyl-N,N-dialkylamino-/N-morpholino phosphoramidite of deoxynucleosides for the synthesis of DNA fragments simplifying deprotection and isolation of the final product. Nucleic Acids Res 1984; 12:4539-57. [PMID: 6547529 PMCID: PMC318857 DOI: 10.1093/nar/12.11.4539] [Citation(s) in RCA: 741] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Various 5'O-N-protected deoxynucleoside-3'-O-beta-cyanoethyl-N,N-dialkylamino-/N- morpholinophosphoramidites were prepared from beta-cyanoethyl monochlorophosphoramidites of N,N-dimethylamine, N,N-diisopropylamine and N-morpholine. These active deoxynucleoside phosphates have successfully been used for oligodeoxynucleotide synthesis on controlled pore glass as polymer support and are very suitable for automated DNA-synthesis due to their stability in solution. The intermediate dichloro-beta- cyanoethoxyphosphine can easily be prepared free from any PC1(3) contamination. The active monomers obtained from beta-cyanoethyl monochloro N,N- diisopropylaminophosphoramidites are favoured. Cleavage of the oligonucleotide chain from the polymer support, N-deacylation and deprotection of beta-cyanoethyl group from the phosphate triester moiety can be performed in one step with concentrated aqueous ammonia. Mixed oligodeoxynucleotides are characterized by the sequencing method of Maxam and Gilbert.
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Effects of mutations at glycine residues in the hydrophobic region of the Escherichia coli prolipoprotein signal peptide on the secretion across the membrane. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)43155-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Arentzen R, Ripka WC. Introduction of restriction enzyme sites in protein-coding DNA sequences by site-specific mutagenesis not affecting the amino acid sequence: a computer program. Nucleic Acids Res 1984; 12:777-87. [PMID: 6320109 PMCID: PMC321092 DOI: 10.1093/nar/12.1part2.777] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Structure/function relationship studies of proteins are greatly facilitated by recombinant DNA technology which allows specific amino acid mutations to be made at the DNA sequence level by site-specific mutagenesis employing synthetic oligonucleotides. This technique has been successfully used to alter one or two amino acids in a protein. Replacement of existing DNA sequence coding for several amino acids with new synthetic DNA fragments would be facilitated by the presence of unique restriction enzyme sites in the region of interest. This computer program provides a means of searching the DNA sequence of interest for restriction enzyme sites that could be introduced by site-specific mutagenesis not affecting the amino acid sequence of the protein. Alternately, the program will also allow single amino acid changes to be made.
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