Method for producing DNA vectors from molecular bricks containing sequences of interest
Disclosed is a method for producing, in one step, “made to measure” double-stranded DNA vectors from molecular bricks including sequences of interest in the presence of a one and only type IIs restriction enzyme.
1. A method for producing a circular double-stranded DNA vector comprising at least six sequences of interest, said method consisting of:
(a) a step of simultaneously contacting at equimolar ratio at least six molecular building blocks, which are different from one another, in the presence of a single type IIs restriction enzyme and a ligase,
each molecular building block consisting of an isolated linear double-stranded DNA molecule and containing:
(i) a sequence of interest with no specific recognition site of the aforementioned type IIs restriction enzyme,
(ii) two double-stranded DNA adapters, flanked upstream and downstream of said sequence of interest, each double-stranded DNA adapter comprising a sequence of at least 12 nucleotides, which sequence contains:
a single and only recognition site of the aforementioned type IIs restriction enzyme,
the recognition site of the aforementioned type IIs restriction enzyme of the adapter upstream of said sequence of interest and the recognition site of the aforementioned type IIs restriction enzyme of the adapter downstream of said specific sequence being convergent,
(b) a step of incubation of the mixture obtained in step a) at a temperature ranging from 20° C. to a temperature of 55° C., during a period ranging from 2 minutes to a period of 30 minutes, which step leads:
to the elimination by cleaving of the recognition sites of the type IIs restriction enzyme used,
to the formation of a cohesive single-stranded suture of at least 2 nucleotides at each of the ends of said sequence of interest,
said cohesive single-stranded suture of at least 2 nucleotides upstream of one of the at least six sequences of interest being complementary to said cohesive single-stranded suture of at least 2 nucleotides downstream of another sequence of interest,
to the pairing by nucleotide complementarity of the aforementioned cohesive single-stranded sutures of at least 2 nucleotides, and
to the positioning of the sequences of interest contiguously with one another in an order and a single and defined direction,
said cohesive single-stranded suture of at least 2 nucleotides upstream and downstream of the sequence of interest is selected for assembly using a scoring matrix where each pairing of two sequences of four non-palindromic nucleotides is attributed a score ranging from 0 to 10, where 0 corresponds to a total absence of complementarity (0%) and 10 indicates total complementarity (100%) and each suture selected has a score of complementarity equal to 0, 1 or 2 compared to other sutures selected for assembly,
(c) a step of ligation of said selected cohesive single-stranded sutures of at least 2 nucleotides, said step being performed at a temperature ranging from 10° C. to a temperature of 40° C. during a period ranging from 2 min to a period of 30 min to obtain a circular double-stranded DNA vector
said step (b) and (c) being repeated from 1 to 49 times,
said method also comprising:
(d) at least one step of incubation at a temperature from 41 to 60° C. during a period ranging from 0.5 to 15 min; and
wherein said steps (a), (b), (c) and (d) are performed in the same reaction mixture.
2. The method according to claim 1 , in which the type IIs restriction enzyme is a type IIs restriction enzyme selected from BsaI, Eco31I, BbsI, BpiI, BsmBI, Esp3I, BspMI, BfuAI and BveI.
3. The method according to claim 1 , in which the double-stranded DNA adapter, downstream or upstream of said sequence of interest, further comprises at least one recognition site of a type IIp restriction enzyme.
4. The method according to claim 1 , in which the double-stranded DNA adapters upstream and downstream of said sequence of interest do not have a site of recognition of a type IIs restriction enzyme other than that of the type IIs restriction enzyme present in the step of simultaneously contacting at least six molecular building blocks, which are different from one another.
5. The method according to claim 1 , in which the cohesive single-stranded suture of at least 2 nucleotides at each of the ends upstream and downstream of the sequence of interest comprises 2 to 10 nucleotides.
6. The method according to claim 1 , in which each cohesive single-stranded suture of at least 2 nucleotides produced from a molecular building block pairs with a cohesive single-stranded suture of at least 2 nucleotides produced from another molecular building block.
7. The method according to claim 1 , in which the cohesive single-stranded suture of at least 2 nucleotides produced at each of the ends downstream and upstream of the sequence of interest comprises a sequence of 42 possible combinations excluding the z*z combinations which result in a DNA palindrome, in which z is between 2 and 10 and z is the number of nucleotides of the single-stranded suture.
8. The method according to claim 1 , in which the cohesive single-stranded suture of at least 2 nucleotides upstream and downstream of the sequence of interest is designed with the aid of a scoring matrix.
9. The method according to claim 1 , in which said type IIs restriction enzyme cleaves the DNA at a distance ranging from 2 to 15 nucleotides, 2 to 14, 2 to 13, 2 to 12, 2 to 11, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4 or 2 to 3 nucleotides from the specific recognition site of said type IIs enzyme.
10. The method according to claim 1 , comprising, before the step of simultaneously contacting at least six molecular building blocks, a step of preparing each of the molecular building blocks by chemical synthesis or by a step of amplification by PCR of the sequence of interest contained in a building block with the aid of a forward primer comprising, from 5′ to 3′, a sequence corresponding to the sequence of the adapter and at least 14 nucleotides of the sequence of interest, and a reverse primer comprising, from 5′ to 3′, at least 14 nucleotides of the sequence of interest and at least one sequence corresponding to the sequence of the adapter.
11. The method according to claim 1 , which further comprises a step (e) of incubation at a temperature from 61 to 90° C. during a period ranging from 0.5 to 15 minutes.
12. The method according to claim 3 , wherein the double-stranded DNA adapter, downstream or upstream of said sequence of interest, further comprises two recognition sites of restriction enzymes selected from KpnI and AgeI, EcoRI and BstBI, SalI and MluI.
13. The method according to claim 5 , in which the cohesive single-stranded suture of at least 2 nucleotides at each of the ends upstream and downstream of the sequence of interest comprises 2 to 5 nucleotides.
14. The method according to claim 1 , wherein step (a) comprises the simultaneously contacting of an equimolar ratio of at least eight molecular building blocks.