"In vitro" method of assembling a synthetic gene

Without prior in vitro enzymatic ligation a DNA duplex was assembled successfully by directly transforming competent cells with a mixture containing six synthetic complimentary oligodeoxyribonucleotides and a linearized plasmid. One out of 100 transformants was positive in colony hybridization with one of the synthetic fragment probe. The sequence of the DNA duplex inserted into the plasmid was confirmed by dideoxy sequencing method.     

A rellable mapping method for sequence determination of oligodeoxyribonucleotides by mobility shift analysis

The method for sequence analysis of large oligodeoxyribonucleotides based on the characteristic mobility shifts of their sequential partial degradation products on two-dimensional homochromatography has been perfected using a large number of synthetic oligodeoxyribonucleotides of defined sequences as standards. Flat bed electrophoresis with careful temperature control gave entirely reproducible mobilities in the first dimension. Using this information, an accurate formula has been derived for calculating the relative electrophoretic mobilities of oligodeoxyribonucleotides of any composition. This formula is used to calculate the mobility shifts between two consecutive oligodeoxyribonucleotides in a series of partial products of an unknown oligomer distributed in the two-dimensional homochromatogram which differ by one nucleotide in length. This is compared with the observed mobility shift value to identify the added nucleotide. This provides a direct and rapid method for obtaining the unambiguous sequence of an entire oligodeoxyribonucleotide up to 15 nucleotides in length.     

Site-localized mutagenesis directed by phosphotriester analogs of oligonucleotides

17- and 20-mer oligodeoxyribonucleotides and their analogues, containing one to four phosphate groups esterified with ethyl alcohol in different positions of oligonucleotide chain, were synthesized by modified triester method. Ethylated di- and trinucleotide blocks were prepared by transesterification method from chlorophenyl derivatives. The structures of the oligonucleotides were confirmed by Maxam-Gilbert sequencing method. Oligonucleotides were not totally complementary to the N-terminal region of lac Z'gene (coding for N-terminal fragment of beta-galactosidase) of phage M13mpB DNA and induced the formation of the proposed deletion mutant DNA M13mp1 delta T. Phosphotriester analogues were more effective mutagens as compared to phosphodiester oligonucleotides due to their stability to nucleases. The use of E. coli DNA-polymerase I provided the increase in the mutant yields in case of the phosphotriester analogues. The stability of the analogues to 5'----3'----5'-endonuclease action, the specificity of oligonucleotide: DNA binding and the structure of mutant DNA were studied by the Sanger sequencing method.     

Synthetic oligodeoxyribonucleotide probes for detection of Listeria monocytogenes.

A 500-base-pair DNA fragment of a presumptive beta-hemolysin gene of Listeria monocytogenes has been used to identify this organism by a modified colony hybridization technique. We have cloned this DNA fragment into M13 bacteriophage vectors and sequenced it by a dideoxynucleotide sequencing technique. From this sequencing information, several oligodeoxyribonucleotides were synthesized and used as synthetic probes to identify L. monocytogenes. The probes were specific for L. monocytogenes and did not react with any other Listeria strains in a colony hybridization assay. In particular, one of these probes (AD07) was used to detect L. monocytogenes in artificially contaminated raw-milk and soft-cheese samples.     

Synthetic oligodeoxyribonucleotide probes for detection of Listeria monocytogenes

A 500-base-pair DNA fragment of a presumptive beta-hemolysin gene of Listeria monocytogenes has been used to identify this organism by a modified colony hybridization technique. We have cloned this DNA fragment into M13 bacteriophage vectors and sequenced it by a dideoxynucleotide sequencing technique. From this sequencing information, several oligodeoxyribonucleotides were synthesized and used as synthetic probes to identify L. monocytogenes. The probes were specific for L. monocytogenes and did not react with any other Listeria strains in a colony hybridization assay. In particular, one of these probes (AD07) was used to detect L. monocytogenes in artificially contaminated raw-milk and soft-cheese samples.     

Solid-phase methods for sequencing of nucleic acids I. Simultaneous sequencing of different oligodeoxyribonucleotides using a new, mechanically stable anion-exchange paper.

A solid-phase method for simultaneous sequencing of large numbers of oligodeoxyribonucleotides has been developed using a new, mechanically stable anion-exchange paper. The excellent mechanical properties of the polymer allow the processing of several paper segments in one reaction vessel or to carry out all necessary operations on a larger area of the paper. In addition, DNA material can be chemically eluted from the new carrier during the piperidine reaction, thus avoiding salt elution of DNA and subsequent ethanol precipitation steps - a prerequisite for sequencing oligonucleotides. The approach involves 7 operations including: i) immobilization; ii) washing; iii) modification; iv) washing; v) sorting of the papers; vi) piperidine reaction and chemical elution and vii) lyophilization. All steps can be carried out in 4 to 5 hours independently of the number of oligonucleotides to be sequenced. It is also possible to sequence small oligonucleotides with 3 to 4 base pairs. The method can be fully automated.     

A method of determining the primary structure of oligodeoxyribonucleotides

Sanger method was modified to fulfill the requirements of sequencing of oligodeoxyribonucleotides. E. coli DNA polymerase I Klenow fragment was used for all the reactions. The method consists of three steps made in succession in one tube: 1. Optional hydrolysis of a 5'-labeled oligodeoxyribonucleotide primer in order to get a set of primers of different lengths. 2. Elongation of the produced set of primers in the presence of a template, natural dNTPs and chain terminating dNTP analogs. 3. Hydrolysis of the products of the previous step in order to remove the unterminated molecules. Change of steps in achieved just by varying the reaction conditions without any product purification. The method in insensitive to the presence of admixture of oligonucleotides which is not complementary to the primer or to the template.     

An efficient method for the sequence analysis of oligodeoxyribonucleotides

Modifications of the chemical method of DNA sequence analysis that permit rapid and reliable sequence determination of single-stranded oligodeoxyribonucleotides as short as 4 nucleotides in length are reported. The principal changes made were increasing the level of chemical modification and optimizing the conditions for recovery of the chemically modified oligodeoxyribonucleotides. This method includes two approaches to the removal of [γ-³²P]ATP from ³²P-labeled oligodeoxyribonucleotides and is especially useful in the determination of the sequence of chemically synthesized oligodeoxyribonucleotides, which are generally between 4 and 20 nucleotides in length.     

Preferential modification of guanine bases in DNA by dimethyldioxirane and its application to DNA sequencing

From gel sequencing experiments with 32P-end-labelled oligodeoxyribonucleotides, it is shown that treatment of DNA with the powerful oxidant dimethyldioxirane, followed by heating in piperidine, causes selective strand scission at the sites of guanine bases. The same specificity for cleavage at guanine was observed with a 45-mer labelled at either the 3'- or 5'-end and with a single and double stranded 34-mer. On account of its speed and operational simplicity, modification with dimethyldioxirane is proposed as a practicable alternative to conventional chemical sequencing procedures for locating guanine bases in DNA.     

Application of new catalytic phosphate protecting groups for the highly efficient phosphotriester oligonucleotide synthesis.

An effective procedure for the synthesis of oligonucleotides by the phosphotriester method has been developed. The procedure is based on the use of phosphate protecting groups enabling O-nucleophilic intramolecular catalysis in the reaction of internucleotide bond formation under the action of arylsulfonyl chlorides and their derivatives. Using this new procedure, the time needed to perform one elongation step on polymer support is 7-8 min. The effectiveness of the methodology has been demonstrated in the synthesis of many oligodeoxyribonucleotides of different length with high yields.     

Ligation-free gene synthesis by PCR: synthesis and mutagenesis at multiple loci of a chimeric gene encoding OmpA signal peptide and hirudin.

A unique kination and ligation-free method that allows de novo synthesis of a gene through a novel application of polymerase chain reaction (PCR) involving stepwise elongation of sequence (SES) is described. SES-PCR is simple and efficient. Optimal utilization of nucleotides, ability to use only partially purified oligodeoxyribonucleotides, and elimination of kination and ligation of intermediates make SES-PCR-mediated gene synthesis more economical in terms of time, labour and money. Site-directed mutagenesis and/or gene fusion by SES-PCR is not limited by the prior availability of the gene(s) in question. The potentials of this novel method in gene synthesis, mutagenesis at multiple loci of DNA and gene fusion have been demonstrated using a chimeric gene encoding fusion between OmpA signal peptide and hirudin, as an example. The SES-PCR product was cloned and sequencing of positive clones demonstrated the presence of genes with expected sequence and bearing only the desired mutations. A nearly 100% efficiency of mutation was easily achieved by the design of the method.     

A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA.

A method is presented for choosing optimal oligodeoxyribonucleotides as probes for filter hybridization, primers for sequencing, or primers for DNA amplification. Three main factors that determine the quality of a probe are considered: stability of the duplex formed between the probe and target nucleic acid, specificity of the probe for the intended target sequence, and self-complementarity. DNA duplex stability calculations are based on the nearest-neighbor thermodynamic values determined by Breslauer et al. [Proc. Natl. Acad. Sci. U.S.A. (1986), 83: 3746]. Temperatures of duplex dissociation predicted by the method described here were within 0.4 degrees C of the values obtained experimentally for ten oligonucleotides. Calculations for specificity of the probe and its self-complementarity are based on a simple dynamic algorithm.     

One-lane sequence analysis of oligodeoxyribonucleotides

Treatment of 5'-end 32P-labeled oligodeoxyribonucleotides with 0.4 M aqueous piperidinium formate, pH 2, at 37 degrees C for 6 h, followed by treatment with 1 M aqueous piperidine at 90 degrees C for 6 h, produces, after electrophoresis through 27% polyacrylamide sequencing gels, one-dimensional distributions of radioactivity from which the base sequences can be deduced. The order of intensities for the bands signaling the various bases is G greater than A greater than C greater than T. The spacing from a given band to the next higher band in the ladder was base characteristic, the order of band spacings being G greater than T greater than or equal to A greater than C. In contrast to the one-cleavage one-lane DNA sequencing method reported earlier (B. J. B. Ambrose and R. C. Pless, 1985, Biochemistry 24, 6194-6200), which was based on treatment of end-labeled DNA with hot aqueous piperidine in the presence of sodium chloride, the present method produces a salt-free hydrolysate, thus minimizing electrophoretic irregularities in the fastest moving bands.     

T4 RNA ligase catalyzed synthesis of base analogue-containing oligodeoxyribonucleotides and a characterization of their thermal stabilities.

Self-complementary oligodeoxyribonucleotides containing the base analogues 2-aminopurine, 2,6-diaminopurine, N6-methyladenine, uracil, and 5-bromouracil were synthesized by a general method that allows incorporation of the analogues at specific positions. The method uses chemically synthesized partial sequences but circumvents the need for protected base analogues by incorporating their unprotected 3',5'-bisphosphate derivatives enzymatically. T4 RNA ligase was used to add the analogues to the oligodeoxyribonucleotides with yields from 54 to greater than 95 percent. Oligodeoxyribonucleotides were joined to the oligodeoxyribonucleotides containing the analogues at their 3'-termini in yields from 22 to 81 percent. The high yields obtained in these joinings suggest that RNA ligase should be of general use for the specific incorporation of other deoxyribonucleotide analogues into oligodeoxyribonucleotides. The oligodeoxyribonucleotides containing the base analogues were characterized by their mobilities during HPLC, nucleoside compositions, sequences, and thermal stabilities.     

Rapid analysis of 3'-ends of DNA fragments by terminal 32P-labeling

A fast method of analysis of the 3′ ends of oligodeoxyribonucleotides is described. Basically the method involves: (a) Labeling of the 3′ ends of oligodeoxyribonucleotides with the terminal deoxynucleotidyl transferase and [α-³²P] ATP as donor; (b) hydrolysis of the labeled fragments to 3′ deoxymononucleotides by acid DNase and spleen exonuclease; (c) unidimensional separation on polyethylene imine cellulose thin-layer plates of the four 3′ deoxyribomononucleotides, 3′ riboadenylic acid, and ATP.     

Cleavage of oligodeoxyribonucleotides from controlled-pore glass supports and their rapid deprotection by gaseous amines.

A novel method for the deprotection of oligodeoxyribonucleotides has been developed. Gaseous amines such as ammonia or methylamine were employed under pressure to achieve mild and rapid deprotection conditions. For example, oligodeoxyribonucleotides having a (tert-butyl)phenoxyacetyl group for the protection of the exocyclic amino function of cytosine, adenine and guanine were released from controlled-pore glass supports and fully deprotected by ammonia or methylamine under gas phase conditions, at room temperature, within 35 or 2 min respectively.     

Efficient synthesis of double dye-labeled oligodeoxyribonucleotide probes and their application in a real time PCR assay.

A fast cleaving non-nucleosidic tetramethylrhodamine dye-labeled support has been developed for automated synthesis of double dye-labeled oligodeoxyribonucleotides in high yield. A mixture (1:1:2) of t-butylamine:methanol:water is used for cleavage and deprotection of dye-labeled oligodeoxyribonucleotides without any degradation or modification of dyes and nucleobases. The cleavage rate of oligodeoxyribonucleotides is significantly increased by using a diglycolate ester linkage instead of the commonly used succinate linkage. These double dye-labeled probes are used in PCR for real time detection of a specific PCR product. Using a 5'-exonuclease assay, detected on the ABI PRISM 7700 Sequence Detection System, there was no distinguishable difference in performance of probes synthesized using the dye-labeled support compared with traditional post-synthetic attachment of rhodamine.     

Incorporation by chemical synthesis and characterization of deoxyribosylformylamine into DNA.

2-deoxyribosylformylamine is a major oxidative DNA damage type which occurs upon the action of ionizing radiation on DNA. The protected 2-deoxyribosylformylamine phosphoramidite was synthesized and used in conjunction with previously reported alkali labile base protected phosphoramidites ('PAC phosphoramidites') for the preparation of oligodeoxyribonucleotides containing this lesion. Final deprotection of the oligonucleotides was performed under mild alkaline conditions to preserve the integrity of the fragile defect. The presence of formylamino deoxyribosyl residue was confirmed by FAB mass spectrometry sequencing. Oligonucleotides bearing deoxyribosyl formylamine were used as templates for studying in vitro replication. They direct the insertion of guanine or induce a deletion opposite the lesion.