Abstract
Here, an efficient cloning strategy for large DNA fragments and for simultaneous assembly of multiple DNA fragments assembly is presented. This strategy is named OEPR (based on O verlap E xtension P CR and R ecombination in vivo). OEPR cloning is a seamless, restriction- and ligation-independent method. The method takes advantage of both homologous recombination enzymes in E. coli and overlap PCR. Using OEPR cloning, a long fragment (1â6âkb) or multiple fragments (2â4 fragments) can be easily constructed and simultaneously assembled into a target vector.
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Introduction
A basic and essential procedure in biological research is the cloning of DNA fragments into plasmids. Traditional cloning methods rely on digestion of DNA by Type II restriction enzymes and the in vitro ligation of DNA fragments to vectors. However, because the restriction and ligation steps are inefficient and time-consuming, the success rates of traditional cloning methods are low. In addition, by traditional cloning methods using restriction enzymes, unwanted nucleotide sequences may be added to inserts, which might result in undesired changes to the structure and activity of the translated products1. Consequently, seamless cloning methods (e.g., enzyme-free cloning2, hetero-stagger cloning3 and polymerase incomplete primer extension (PIPE) cloning4,5) have been developed, which utilize a compatible set of tailed and non-tailed primers to generate DNA fragments and linear vectors with cohesive ends. These DNA fragments and linear vectors can then be paired together and repaired after direct transformation into E. coli. Seamless cloning methods are restriction- and ligation-independent as well as easy to implement; however, seamless methods still require careful design of numerous primers to ensure successful amplification of DNA fragments and linearized vectors. Uracil DNA-glycosylase cloning (UDG)6,7 and Ligation-Independent Cloning (LIC)8, which take advantage of the 3â˛-5Ⲡexonuclease activities of uracil DNAâglycosylase and T4 DNA polymerase, respectively, are able to generate 12-base cohesive ends.
Based on the principle of QuickChangeTM site-directed mutagenesis9,10, restriction-free (RF) cloning11,12 is a straightforward, efficient and reliable method for inserting a single fragment into a vector; this method does not introduce any unwanted extra bases at DNA fragment/insertion site junctions. However, RF cloning suffers from low DNA product yields due to linear amplification and low efficiencies for inserts longer than 1âkb. Although Exponential Megapriming PCR (EMP) Cloning13 and Inverse Fusion PCR Cloning (IFPC)14 address the product yield issue by introducing reverse primers to ensure exponential amplification, the phosphorylation and ligation of the final, second-round PCR products add to the labor and cost required for these methods.
If homologous regions exist between the linear inserts and vectors, in vitro recombination can be performed using commercially available recombinant enzymes such as GatewayÂŽ (Invitrogen)15 and In-FusionTM (Clontech)16. Homologous recombination can also occur in E. coli in vivo via three different mechanisms: RecA-dependent, RecA-independent and Red/ET-dependent; these mechanisms require >1âkb, >12âbp and 30â50âbp of homology, respectively1. The RecA-dependent mechanism requires homology regions that are too long to be ideal for cloning and sub-cloning. Red/ET-dependent recombination, which is based on the function of 5â˛-3Ⲡexonuclease and single-stranded DNA annealing protein pairs, is an efficient approach. However, expression of the RedÎą/Redβ or the RecE/RecT protein pair is required for successful Red/ET-dependent recombination17,18,19. High efficiencies can also be achieved by integrating the Îť prophage Red recombination system into the E. coli genome20. In contrast, RecA-independent recombination occurs in RecA strains at low efficiencies. Recently, in vivo RecA-independent recombination-like cloning was demonstrated in RecA- strains, such as E. coli strains DH10B and JM10920,21,22. Although in vitro and in vivo homologous recombination is convenient, such mechanisms require expensive enzymes or specific strains. Inspired by the aforementioned cloning methods, we developed a hybrid seamless method based on O verlap E xtension P CR and R ecombination in vivo and named it OEPR cloning. With OEPR cloning, the assembly of large DNA fragments (1â6âkb) and simultaneous assembly of multiple fragments (up to 4) can be easily performed in a single day. Compared to homologous recombination, RF cloning or other similar methods, OEPR cloning is much more efficient and cost-effective for the insertion of longer fragments or the assembly of multiple fragments.
Results
Overview of OEPR cloning
The mechanism of OEPR cloning for insertion of single fragments is shown in Fig. 1. OEPR cloning requires three steps. (i) The first step of OEPR cloning is the exponential amplification of the target insert a using a primer pair with overhangs A and B (F1 and R1) (Fig. 1A). The resulting PCR product (M1) contains regions homologous to the insert part of the vector (overhangs A and B) (Fig. 1A). The 5Ⲡend of the reverse primer R1 contains the homologous arm (sky blue part B, Fig. 1A) used for overlap extension PCR (Tmâ=â68â70â°C). The 5Ⲡend of the forward primer (F1) contains the homologous region (orange part A, Fig. 1A) used for in vivo recombination. ii) In the second step, the PCR product M1 is used together with a short reverse primer (R) to exponentially amplify the target plasmid (Fig. 1B). As shown in Fig. 1B, a final PCR product containing homologous region A (in orange) is created after two rounds of PCR. iii) In the third step, the product of the second OEPR PCR round is digested with DpnI and then directly transformed into chemically competent E. coli TOP10Fâ cells (Fig. 1C). The overhangs (homologous region A, Fig. 1C) can be repaired in vivo via the homologous recombination mechanism in E. coli.
In addition, the mechanism of OEPR cloning for assembly of multi-fragments is shown in Fig. 2, by using the assembly of three inserts as an example. Three steps are similar to the OEPR cloning for insertion of single fragments. As shown in Fig. 2, the assembly of three fragments into the vector was used as an example. (i) In the first step, three genes (a, b and c) are amplified by using the primer pairs of F1 and R1, F2 and R2, and F3 and R3, respectively (Fig. 2A). (ii) In the second step, the 1st PCR products (M1, M2 and M3) and the vector anneal with their overlapping homologous regions (parts B, C and D, Fig. 2B) and are exponentially amplified by product M1 and reverse primer R (Fig. 2B). (iii) The final linearized plamid with homologous overhangs (part A, Fig. 2C) in both 5â˛- and 3â˛-termini can be repaired in vivo via the homologous recombination mechanism in E. coli (Fig. 2C).
Efficiency and fidelity of OEPR cloning with different overhangs
In the first series of experiments, we examined the effect of the end homology length of part A (Fig. 1) on OEPR cloning efficiency. A series of F1 primers containing different 5Ⲡoverhang lengths (5 to 35âbp) was used for the insertion of a 1âkb fragment into pGADT7 (7988âbp) (Fig. 3). Insert fragments (1âkb) were amplified in the first PCR (Fig. 3A), and the resulting products were used as primers for pGADT7 amplification (Fig. 3B). Obviously, more recombinant colonies (>300) and higher cloning efficiencies (>90%) were obtained with homology arms (part A in Fig. 1) longer than 15âbp (Fig. 3C,D). Interestingly, compared to other homologous region length groups, the group with the 15âbp homology region yielded the highest positive percentage (Fig. 3D, 100%).
Insertion of long fragments of different sizes
We next investigated the influence of insert size (1~6âkb) using 15 or 30âbp overhangs. Each fragment was inserted into the vector pGADT7 (7988âbp). As shown in Fig. 4A and B, the target bands were successfully amplified. In addition, it was found that if more purified insert fragment was used as template in the second PCR, more colonies were obtained on plates (Fig. 4C,D). For the 1âkb and 2âkb inserts, 15âbp overhangs tended to yield more recombinant colonies and positive percentages than 30âbp overhangs. For inserts larger than 2âkb (3âkb~6âkb), 30âbp overhangs tended to yield more recombinant colonies and positive percentages than 15âbp overhangs (Fig. 4C,D,E). Increasing insert length tended to reduce the number of observed colonies and the positive percentage; however, this behavior can be partially addressed by using longer homology arms (Fig. 4E).
Insertion of multiple fragments
The experiments described above demonstrated that OEPR cloning is an efficient and precise method for inserting large fragments into vectors. To develop OEPR cloning into a more powerful tool for molecular cloning, we investigated whether multiple DNA fragments could be simultaneously reassembled with a vector using OEPR cloning. Insert fragments of different lengths were tested (two 1âkb, two 2âkb, two 3âkb, three 1âkb, three 2âkb and four 1âkb fragments were inserted into pGADT7). Our OEPR cloning method performed these assemblies well.
More specifically, all fragments of interest were amplified in a first PCR step, then purified. Fragment a (500âng) and the other fragments (100âng each) were added to the second PCR as forward primer and templates, respectively. After the second PCR step, the final PCR product containing the desired homologous region (part A in Fig. 2) could be detected by agarose gel electrophoresis (Fig. 5A,B). It was shown that 30âbp overhangs yielded more recombinant colonies than 15âbp overhangs (Fig. 5C). With regard to positive percentages, the 15âbp overhangs were more suitable for the assembly of shorter and/or simple fragments (two 1âkb and three 1âkb of fragments), while 30âbp overhangs were preferable for the assembly of longer fragments (Fig. 5D).
Discussion
Similar strategies of OEPR cloning have been reported previously, such as RF cloning11, CPEC (Circular Polymerase Extension Cloning) cloning23,24, EMP cloning13 and IFPC cloning14. In our opinions, all the methods of CPEC, EMP, IFPC and our OEPR cloning are derivatives of the RF cloning. In RF cloning, the amplified inserts are as long as the primers to amplify the vector, without adding extra sequences. Additionally, in CPEC method, a derivative method of RF cloning, the linear vector and inserts could anneal with their overlapping regions and extend using each other as a template. The most significant drawback of CPEC or RF is non-exponential amplification. Although, due to the introduction of the reverse primer, exponential amplification can be finished in both EMP and IFPC methods, the expensive enzymes [T4 PNK (T4 Polynucleotide Kinase) and T4 DNA ligase] are indispensable. But our OEPR cloning, with introduction of homologous regions of primer F1 of inserts with the vector (Figs 1A and 2A), the target products can be exponentially amplified in vitro and it can be directly transferred to E. coli without using expensive enzymes. So, OEPR cloning take the advantages of both RF cloning and EMP cloning, low cost and exponential amplification, respectively. Even using the home-made chemical competent cells with low transformation efficiency (about 106âcfu/Îźg), the efficiency of OEPR cloning is still working well. In addition, the whole experiment of OEPR cloning, purification and transformation can be finished in one day (about 9â14âhours, Figs 1 and 2).
Overall, the most significant features of OEPR cloning are that it combines the advantages of both PCR-based strategies and recombinant enzyme-based methods and that it works well. OEPR cloning is an efficient, labor- and cost-saving strategy for the seamless insertion of large DNA fragments (up to 6âkb) or multiple DNA fragments (up to two 3âkb, three 2âkb and four 1âkb) into vectors (8âkb tested). In conclusion, OEPR cloning is a good choice for researchers who perform plasmid-based genetic manipulations such as gene mutation, gene chimeragenesis, and gene fusion.
Methods
Materials
E. coli TOP10Fâ (Invitrogen, RecA- strain) was used for cloning. Chemically competent TOP10Fâ cells were home-made (106âcfu/Îźg). All insert fragments generated from hNaV1.5 and rNaV1.4 were inserted into the plasmid pGADT7 (Clontech, 7988âbp). All primers were purchased from Sangon (Shanghai, China). The insert, insertion site, and primer sequences are provided in the Supplementary Table S1 and S2.
Design of primers for insertion of large fragments
In this part, the insertion of 1âkb of fragment into the vector was used as an example. As shown in Fig. 1, the target gene a (insert-1 in Supplementary Table S1) and vector are marked in black and reddish purple, respectively. The black parts of primers F1 (the non-underlined sequences of the primers of F1-15, F1-20, F1-25, F1-30 and F1-35 in Supplementary Table S2) and R1 (the non-underlined sequences of the primers of 1kb-R1 in Supplementary Table S2) are homologous with the target gene and have Tm values of approximately 68â70â°C. The orange part of primer F1 is a 15â30âbp vector-derived homology region (the underlined parts of the primers of F1-15, F1-20, F1-25 and F1-30 in Supplementary Table S2). The sky blue part of primer R1 (the underlined sequences of the primers of 1kb-R1 in Supplementary Table S2) is homologous with the vector with a Tm of approximately 68â70â°C.
Design of primers for assembly of multiple fragments
In this part, the assembly of three 1âkb of fragments (insert-10 in Supplementary Table S1) into the vector was used as an example. As shown in Fig. 2, three insert genes a, b and c, (the parts of insert-10 are shaded in yellow, azure and yellow respectively in Supplementary Table S1) are amplified using primer pairs F1 and R1, F2 and R2 and F3 and R3 (the primer pairs of 3âĂâ1k-F1-15/30 and 3âĂâ1k-R1, 3âĂâ1k-F2 and 3âĂâ1k-R2, 3âĂâ1k-F3 and 3âĂâ1k-R3 respectively in Supplementary Table S2), respectively in Fig. 2A. The target gene and the vector are marked in black and reddish purple in Fig. 2, respectively. The black parts of the primers F1, R1, F2, R2, F3 and R3 (the bold sequences of the primers of 3âĂâ1k-F1-15/30, 3âĂâ1k-R1, 3âĂâ1k-F2, 3âĂâ1k-R2, 3âĂâ1k-F3 and 3âĂâ1k-R3 in Supplementary Table S2) are homologous with the target gene and have a Tm of approximately 68â70â°C. The orange part of primer F1 (the underlined sequences of the primers of 3âĂâ1k-F1-15/30 in Supplementary Table S2) is a 15â30âbp vector-derived homology region. The sky blue, bluish green and vermilion parts (part B, C and D, respectively) (the italic sequences of the primers of 3âĂâ1k-R1, 3âĂâ1k-R2 and the underlined sequences of primer 3âĂâ1k-R3 in Supplementary Table S2) of primers R1, R2 and R3 are homologous with gene b, gene c and the vector insertion site, respectively, with Tm values of approximately 68â70â°C.
Synthesis of large inserts
DNA fragments of different sizes (1~6âkb) were amplified from hNaV1.5 using KOD-FX (TOYOBO) and 0.2âÎźM of each primer, 1âĂâreaction buffer, 0.4âmM dNTPs, 1âU DNA polymerase and 10âng template DNA in 50âÎźl reaction mixtures. Mixtures were first denatured at 94â°C for 2âmin, subjected to 25 cycles of denaturation at 98â°C for 10âs, annealing at 60â°C for 30âs and elongation at 68â°C for 25 cycles (1âkb/min), followed by a final 10âmin extension step at 68â°C. PCR products were analyzed by agarose gel electrophoresis, and target fragments were purified using a DNA purification Kit (BioSci, Hangzhou, China).
Insertion of large fragments
Fragments purified from the first PCR step and the reverse primer R were used to exponentially amplify the plasmid pGADT7 (as shown in Fig. 1). The PCR mixture contained 0.2âÎźM primers, 10âng recipient plasmid, 1âĂâPCR Buffer, 0.4âmM dNTPs and 1âU DNA polymerase in a 50âÎźl reaction mixture. Mixtures were pre-denatured at 94â°C for 2âmin, subjected to 25 cycles of denaturation at 98â°C for 10âs, annealing at 60â°C for 30âs and elongation at 68â°C for 25 cycles (1âkb/min), followed by a final 10âmin extension step at 68â°C. The resulting PCR products were purified using a DNA purification Kit (BioSci, Hangzhou, China). Following purification, PCR products were digested using DpnI as follows: purified products (8âÎźl) supplemented with 1âÎźl 10âĂâreaction buffer were digested with 1âÎźl FastDigestTM DpnI (Thermo Fermentas, Burlington, Canada) at 37â°C for 1âh.
Insertion of multiple fragments
As shown in Fig. 2, OEPR cloning can also be used to simultaneously insert multiple DNA fragments. First, each insert fragment (e.g., genes a, b and c, Fig. 2A) is amplified using KOD-FX and purified using a DNA purification kit (BioSci, Hangzhou, China). Second, 500âng of purified fragment M1 (which is used as the forward primer) and 100âng of the other fragments (M2 and M3, shown in Fig. 2B) are added with reverse primer R into a PCR mixture for exponential vector amplification (shown in Fig. 2B). 5Ⲡends of the inserts contains 15 or 30ânt of homology to the vector. Reverse primer R is homologous to the vector with a Tm of approximately 68â70â°C. The inserts (M1, M2 and M3) and the vector anneal with their overlapping homologous regions (parts B, C and D, Fig. 2B) and are exponentially amplified by product M1 and reverse primer R. After this second PCR step, linear products with homologous region A (Fig. 2C, indicated in orange), which can be directly transformed and repaired by E. coli in vivo (RecA- strain), are obtained. DNA products from the second PCR were purified using a DNA purification kit (BioSci, Hangzhou, China). Purified products (8âÎźl) were supplemented with 1âÎźl 10âĂâreaction buffer and digested using 1âÎźl FastDigestTM DpnI (Thermo Fermentas, Burlington, Canada) at 37â°C for 1âh.
Transformation, colony PCR and DNA sequencing
Aliquots (5âÎźl) of digested DNA products were directly transformed into 50âÎźl of chemically competent TOP10Fâ cells that were made in-house. All cells were spread onto Luria-Bertani (LB) plates containing 100âÎźg/mL of ampicillin sodium salt and incubated overnight. Colony numbers per plate were determined to estimate cloning efficiencies. Colony PCR was used to screen 24 colonies randomly picked from each group. The percentages of positive clones obtained via colony PCR were used to estimate cloning fidelity. Colony PCR was performed using DreamTaq DNA polymerase (Thermo Scientific, USA) according to the manufacturerâs instructions. Further DNA sequencing was performed by Sangon (Shanghai, China).
Additional Information
How to cite this article: Liu, C.-J. et al. OEPR Cloning: an Efficient and Seamless Cloning Strategy for Large- and Multi-Fragments. Sci. Rep. 7, 44648; doi: 10.1038/srep44648 (2017).
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Acknowledgements
This work was supported by the Research Programme of National University of Defense Technology (No. JC2006-02-01 to Prof. D.Y. Zhang and JC14-02-09 to Dr. L.Y. Zhu) and Lateral Research Funds (No. 1501020414029 to Dr. E. Meng). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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D.-Y.Z., E.M. and C.-J.L. designed the appropriate technology routes. C.-J.L. and H.J. conducted main experiments including primers design, cloning, colony PCR screening and data analysis. L.W. and L.-Y.Z. participated in colony PCR screening and data analysis. D.-Y.Z. and E.M. supervised the project and wrote the paper. All authors read and approved the final manuscript.
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Liu, CJ., Jiang, H., Wu, L. et al. OEPR Cloning: an Efficient and Seamless Cloning Strategy for Large- and Multi-Fragments. Sci Rep 7, 44648 (2017). https://doi.org/10.1038/srep44648
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DOI: https://doi.org/10.1038/srep44648
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