CA1295558C - Synthesis of long chain dna - Google Patents

Abstract

ABSTRACT OF THE INVENTION

Long chain DNA which can carry information for the synthesis of specific proteins is synthesized by utilizing blocks of 4-8 base sequences using the solid base method i.e. triester method with aminated CPG as a support.

Description

The present invention relates to a novel method of synethsizing long chain DNA carrying information for synthesis of specific proteins and, more particularly, it relates to a method of synthesizing long chain DNA purely chemically, i.e. without the use 6 of enzymes, by a so-called solid phase method using blocks of 4 to 8 base sequences and using aminated CPG as a carrier.
It has been known that the synthesis of polypeptides using a synthetic gene is possible by the steps of (1) synthesis of a structural gene; (2) recombination of the gene into a suitable plasmid;
(3) transformation of a suitable host by the formed chimera plasmid;
and (4) obtaining the desired polypeptide by culturing the transformed substance.
Recently, development of a DNA probe has attracted public at-tention as a novel means for gene technology. This is a method of identifying unknown DNA and RNA which is a transcribed product by a hybridization of single stranded DNA and RNA which are known in the art by utilizing the properties of DNA and RNA whereby they can form duplexes, as in the relationship of a template and a casting. Since very sensitive and prompt identification is possible by utilizing the hybridization method, this method can be used for diagnosis of diseases by finding the specific DNA and RNA in a gene level from the blood and cells of patients and pathogenic bacteria. Accordingly, ~.

1~955~i8 DNA has an important value as a diagnostic agent by virtue of its utilization as a DNA probe.

When DNA is used as structural gene or a DNA probe, it has known that the longer the base sequence of the DNA, the better it functions as an information source or DNA probe. However, it has also been know that the longer the base sequence, the more difficult it is to synthesize DNA.
It is an object of the present invention to provide a simplified process for synthesizing long chain DNA.

The conventional method for synthesizing DNA is as follows.
First, comparatively short DNA fragments with 10 to 20 basis residues (i.e., base pairs) are chemically synthesized, and then they are combined to prepare fragments having a total structure of double stranded DNA having the desired information for peptide synthesis, then the fragments are combined using an enzyme called DNA ligase.

However, by such a method, only comparatively short fragments with 1 (monomer), 2 (dimer) or 3 (trimer) bases are manufactured prior to block condensation and it is not possible to synthesize long chain DNA with 80 residues or the like.

In addition, in that method it is essential to use an enzyme called DNA ligase. Therefore, in synthesizing double stranded DNA as a gene, it is necessary that all base sequences constituting double stranded DNA are synthesized at one time.
Accordingly, the above method is not so effective in a process of synthesizing double stranded DNA.

The present inventors overcame the above technical difficulty and succeeded in synthesizing DNA with approximately 46 bases by utili-'.~

~ `` lZ~55~8 zing a method called a triester method (among the so-called solid methods) in which 1% polystyrene is used as a support and the compounds of 4 (tetramer) or 5 (pentamer) bases are subjected to a repeated condensation.
Even by such a method, however, the base numbers in the re-sulting DNA are 50 at the largest and there is still a difficulty in synthesizing DNA with chains of as long as 80 to 150 residues.
Following this success, the present inventors have further carried out studies paying their attention to (1) the synthesis of long chain DNA carrying as much gene information as possible and (2) the synthesis under re advantageous conditions. The present invention represents the culmination of those studies.
Characteristic features of the present invention are as follows:
(1) ~nit numbers prior to bloc~ condensation are 4 to 8 (Octamer) bases;

(2) among the so-called solid phase methods,"triester method" is used; and (3) aminated CPG carrier is used as a support.
2~ The present invention will be further illustrated as here-under:

i5~58 Each block prior to the condensation can be obtained in the conventional way in which each base is subjected to a liquid phase synthesis.

Animated CPG (controlled pore glass) (cf. Tetrahedron, 24, 747-750, 1983) used in the present invention is used as a carrier in the solid phase method. To the amino group of this substance is combined deoxythymidine which is changed to 3'-succinate by usual method. This is used as a carrier for nucleoside. Each desired block is extended, on this resin, to the direction of 5'-terminal successively. Mesitylene sulfonyl-3-nitrotriazolide (MSNT) is used as a condensation agent. The resulting DNA is single stranded and the complimentary strand DNA which is necessary for preparation of duplet DNA can be easily obtained in a similar way. Alternatively, each duplet DNA can be very easily obtained by the use of DNA polymerase using short fragment (10 b.p. or so) which is complimentary with the 3'-terminal region of the resulting single stranded DNA. The fact that DNA polymerase can be used is one of the most advantageous aspects of the present invention for the condensation reaction can be accomplished without the aid of DNA ligase which has been widely used in conventional methods.

The resulting duplet DNA is combined to give vector plasmid by the known method, then transformed to bacteria such as Escherichia coli, and the strain is cultured to afford the desired polypeptide. In the above steps, various gene technological means which have been already established can be applied.

., 129~5~8 It is possible in accordance with the present invention to synthesize DNA with as long as 80 to 150 residues and, therefore, polypeptides with 15 to 30 amino acids can be synthesized by the known gene technological means. For instance, the following polypeptides can be synthesized. They are growth hormone-release inhibiting factor (Somatostatin, containing 14 amino acids), stomach acid secreting stimulant (Gastrin, containing 17 amino acids), duodenum ulcer remedy (Secretin, containing 27 amino acids), stimulant for secretion of growth hormone, insuline and blood sugar level increase (Glucagon, containing 29 amino acids), morphine like agent (beta-Endorphin, containing 31 amino acids), and hypercalcemia remedy (Calcitonin, containing 32 amino acids), and the like.

In addition, the long chain DNA of the present invention is applied not only for DNA base sequences of structural gene parts but also for the manufacture of general DNA including regulatory sites and specific sequences as well as for long chain DNA probe recognizing their structures. Accordingly the present invention can be positively applied for development of diagnostic agents.

According to the present invention, long chain DNA can be synthesized simply and in large quantities. The long chain DNA of the present invention can be effectively utilized as (1) a gene information source concerning polypeptide synthesis and (2) a source for application of the DNA probe in gene technology.

Production of DNA has been 0.1 OD (1 OD is equivalent to about 50 micrograms~ per one lot at best. However, in accordance with the present invention, it is now possible to manufacture in quantities as large as 30 to 50 OD per lot. Consequently, ex-pansion of the utilizable field of long chain DNA as a gene and as a DNA probe is now possible.
The following non-limitative exa~es describe the synthesis of endorphin whose physiological activities such as central nervous analgesic action and endocrine hormone action have been known.
(1) Synthesis of each block constituting base sequences including endorphin gene.
The amino acid sequence of endorphins has been known and the DNA base sequence corresponding thereto can be freely selected by ~;
referring t~ a table of coden usage. They are given as hereunder to-gether with their relation between each block constituting DNA base sequences used in the present invention. The upper, middle and lower columns are each block (figures therein are block numbers), base sequence~and corresponding amino acid sequence, respectively. Re-stricted enzyme sites are given at both terminals of DNA base sequences.
Said sites are used in inserting plasmids.

129SS~8 O a - Endolph ~
~13 12 11 ~ 10 5' ACCTGCAGCC CGT CGC TAC GGT GGT TTC ATG
I
Pst I Arg Arg Tyr Gly Gly Phe Met ACT TCT GAG AAG TCT CAA ACT CCA TTG GTG
Thr Ser Glu Lys Ser Gln Thr Pro Leu Val 5_-4 3 ACT TAA TAG GGCTGCAGGT
I
Thr STOP STOP Pst I

0a - [ Leu' ] - Endolphin --13 ~ 16 15 10 5 ' ACCTGCAGCC ATG TAC GGT GGT TTC TTG
I
Pst I Met Tyr Gly Gly Phe Leu ~9 8 7 6 ACT TCT GAG AAG TCT CAA ACT CCA TTG GTG
Thr Ser Glu Lys Ser Gln Thr Pro Leu Val 5_--4_~3 ACT TAA TAG GGCTGCAGGT
Thr STOP STOP Pst I

lZ955~8 O- [Leu~ ] - Eodo~
-- 13 ~16 15 ~ 10 5 ' ACCTGCAGCC ATG TAC GGT GGT TTC TTG
I
Pst I Met Tyr Gly Gly Phe Leu 9 ~8 - 7 ~ 6 ~--ACT TCT GAG AAG TCT CAA ACT CCA TTG GTG

5_---17_-3 ~
ACT TTG TAG GGCTGCAGGT
I
Thr Leu STOP Pst I

O y - Eodo~oio --13 ~ 12 ~ 11 ~ 10 5 ' ACCTGCAGCC CGT CGC TAC GGT GGT TTC ATG
I
Pst I Arg Arg Tyr Gly Gly Phe Met --9 ~ - 8 7 _~6 ACT TCT GAG AAG TCT CAA ACT CCA TTG GTG
Thr Ser Glu Lys Ser Gln Thr Pro Leu Val 5 ~17_-3 ACT TTG TAG GGCTGCAGGT
I
Thr Leu STOP Pst I

Among the blocks constituting the above endorphin genes, the block 7 was synthesized by the steps as given below.

.,~.

bz bz ( I ) d (DMTr) Ae Ae CE
TEA bz bz ( II ) d (DMTr) Ae Ce CE
d (DMi r) Ae Ae o~ ¦ d (DMTr) Te Ce CE ( III ) bz bz TEA bz( bIzV ) d IAe Ce CE d (DMTr) Ce Ae CE
¦ MSNT bzBSA
d (DMTr) Te Ce o-bz bz bz bz ( YII 1 d (DMTr) Ae Ae Ae ce CE ~ I ~Z bz I TEA ( IX ) d lce Ae CE

bz bz bz bz d (DMTr) Ae Ae A~ Ce 0- . bz bz bz ( XI ) d (DMTr) Te Ce Ce Ae CE
¦ BSA ( X ) bz bz bz d Te Ce Ce Ae CE
~ I ( XII ) ¦ MSNT ( XIII ) bz bz bz bz bz bz bz d (DMTr) Ae Ae Ae Ce Te ce Ce Ae CE
¦ TEA ( XIV ) bz bz bz bz bz bz bz d (DMTr) Ae Ae Ae Ce Te Ce Ce Ae O~ ~ Block 7 DMTr: 4,4 - Dimethoxytolityl bAZ N-Benzoyladenosyl bcz N-Benzoylcytidylyl T: Tymidylyl e o-Chlorophenyl phosphate BSA: Benzenesulfonic acid TEA: Triethylamine ,~,.

lZ9~5X8 - 9a -The accompanying drawings illustrate the present invention.
In particular:

Fig. 1 is X-ray autoradiogram showing the result of 20%
polyacryamide electrophoresis of deoxy 80 mer containing alpha-endorphin gene synthesized after determination by Maxam-Gilbert method.
Fig. 2 is X-ray autoradiogram showing the result of 8%
polyacrylamide electrophoresis of deoxy 80 mer containing alpha-endorphin gene synthesized after determination by Maxam-Gilbert method.
Fig. 3 shows the result of high performance liquid chromatography (Nucleosil 300-7*C18) of deoxy 80 mer containing alpha-endorphin gene synthesized after determination by Maxam-Gilbert method. Ordinate and abscissa show absorbency and time, respectively. Solvent system used was triethylamine acetate-acetonitrile and the flowing speed was 1.0 ml/min. Nucleosil 300-7 is a registered trademark.

Other blocks (1-6, and 8-17) constituting endorphin type genes can be synthesized by similar way. Each yield is given as hereunder.
Blocks Base Sequences Yield (%) . _ 25 (2) Endorphins genes synthesis:
alpha-Endorphin gene (deoxy 80 mer) containing restricted enzyme sites was synthesized by a solid phase method as follows:
1. Deoxytymidine CPG resin is washed with CH2C12/MeOH.
2. Detritylation is conducted with 2% BSA/CH2C12 (this was 30 conducted repeatedly and promptly until colorization disappears) 3. Subjected to azeotropic drying after substituted with pyridine.

lZ955~8 A solution of each block is added, subjected to azeotropic drying, and MSNT and pyridine for the reaction are added. Allowed to stand at room temperature and washed with pyridine.
4. O.lM Dimethylaminopyridine/pyridine solution and acetic anhydride are added, allowed to stand at room temperature, and washed with pyridine.

The above procedure is conducted repeatedly, for 13 times in total. Average yield of this reaction was 84~. Then the resin is deprotected, at room temperature, with a solution of O.lM tetramethylguanidine-pyridine aldoxime (cf. C. B. Reese, et al: Tetrahedron Lett., 2727, 1978) in dioxane-water, then washed with pyridine-water, the washing is concentrated in vacuo, concentrated ammonia water is added thereto and the mixture is warmed. Ammonia is evaporated therefrom and a part of the residue is taken using dimethoxytrityl group as a target to calculate the yield of the final stage.

The residual reaction solution is subjected to a reversed phase (Clg silica gel for Prep 500*manufactured by Waters), ion exchange (DEAE-20 toyopal)*, and reversed phase (Clg silica gel, TSK-Gel*10-20 micrometers) open chromatographies to afford pure alpha-endorphin gene (containing restricted enzyme sites) (-deoxy 80 mer). Prep 500, DEAE-toyopal and TSK-Gel are registered trademarks.
Purity was confirmed by HPLC (Nucleosil 300-7*Clg) and by electrophoresis and its base sequences were confirmed by Maxam-Gilbert method. The result is given in Fig. 1 to Fig. 3.
Nucleosil 300-7 is a registered trademark.

12~SS58 Similarly prepared were alpha-(Leu5)-endorphin gene (containing restrictive enzyme site) (deoxy 77 mer), gamma-(Leu5)- endorphin gene (containing restrictive enzyme site) (deoxy 77 mer) and gamma-endorphin gene (containing restrictive enzyme site) (deoxy 80 mer).
(3) Svnthesis of duplex DNA and its combination with vector plasmid Each one mole of deoxy 80 mer and synthetic nucleotide primer which is complimentary with 3'-terminal of the former were mixed, heated at 65-C, and cooled to room temperature to anneal the deoxy 80 mer and the primer. Then E.coli polymerase I (Klenow fragment) was added by conventional means and 10 made to rect at 37~C for 30 minutes so that DNA was converted into double stranded.
DNA was recovered as a precipitate in ethanol, made to react at 37~C for 30 minutes using T~ polynucleotidekinase, and both 5'-terminals of the double stranded DNA were phosphorylated.
Then the vector plasmid pUC 8 DNA was scissored with a restrictive enzyme Pst 1, added to the above double stranded DNA solution, made to react at 16'C overnight with T~ DNA ligase, and the double stranded d 80 mer DN~ was combined with the vector plasmid.
(4) Clonina of ~lasmids containinq endor~hin aenes.
The plasmid prepared as above described was transformed into E. coli JM
103 strain by conventional procedure, then selected using a deficiency `~D
~.

1%95~8 of beta-galactosidase activity present in the pUC 8 as a target, and plasmid molecules were collected by cloning from the strain.
It has been confirmed that plasmid in which endorphin gene S was inserted into the correct orientation and position as desired in accordance with Maxam-Gilbert method.

(5) Obtaining of endorphins.

Transformed E. coli JM 103 strain was precultured overnight in an LB medium, planted in 2YT medium, and subjected to a shake culture at 37C.

IPTG was added to the logarithmic productive phase stages (initial, medium and final stages) to make it 0.5mM and synthesis of endorphin was induced. After being induced by IPTG, fused protein was extracted, and analyzed by HPLC whereupon it was found that adequate quantity of protein production was observed (1-5.0 x 105 molecules per cell) when induction was applied at the initial stage of logarithmic productive phase.

The natural type alpha-endorphin and gamma-endorphin having methionine residue in a molecule were treated with trypsin by conventional procedures. Alpha-(Leu5)-endorphin and gamma-(Leu5)-endorphin having leucine residue in place of methionine were treated with BrCN. Each of the desired endorphin proteins was subjected to a column chromatography according to the general purification method of proteins whereupon each of them was separated and purified.
The fact that each of the resulting endorphin molecules exhibits desired amino acid sequence was confirmed by the fact that they were identical with the samples already obtained by the peptide synthesis by testing with HPLC using a reverse phase carrier.

.~

Claims (3)

The embodiments of the invention in which an exclusive property or privilege is claimed are defined as follows:
1. Claim 1. A method of synthesizing long chain DNA
   carrying gene information having chains of at least 80 base pairs which comprises chemically synthesizing by condensation such long chain DNA by the phosphate triester method using units of at least 4-8 bases and animated controlled pore glass as a carrier support.
2. Claim 2. A method as defined in claim 1 wherein deoxythymidine is combined with the amino group of the aminated controlled pore glass.
3. Claim 3. A method as defined in claim 1 wherein a suitable condensation agent is used.