CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

Summary

Here, we present chimera assembly by plasmid recovery and restriction enzyme site insertion (CAPRRESI), a protocol based on the insertion of restriction enzyme sites into synonym DNA sequences and functional plasmid recovery. This protocol is a fast and low-cost method for fusing protein-coding genes.

Abstract

Here, we present chimera assembly by plasmid recovery and restriction enzyme site insertion (CAPRRESI). CAPRRESI benefits from many strengths of the original plasmid recovery method and introduces restriction enzyme digestion to ease DNA ligation reactions (required for chimera assembly). For this protocol, users clone wildtype genes into the same plasmid (pUC18 or pUC19). After the in silico selection of amino acid sequence regions where chimeras should be assembled, users obtain all the synonym DNA sequences that encode them. Ad hoc Perl scripts enable users to determine all synonym DNA sequences. After this step, another Perl script searches for restriction enzyme sites on all synonym DNA sequences. This in silico analysis is also performed using the ampicillin resistance gene (ampR) found on pUC18/19 plasmids. Users design oligonucleotides inside synonym regions to disrupt wildtype and ampR genes by PCR. After obtaining and purifying complementary DNA fragments, restriction enzyme digestion is accomplished. Chimera assembly is achieved by ligating appropriate complementary DNA fragments. pUC18/19 vectors are selected for CAPRRESI because they offer technical advantages, such as small size (2,686 base pairs), high copy number, advantageous sequencing reaction features, and commercial availability. The usage of restriction enzymes for chimera assembly eliminates the need for DNA polymerases yielding blunt-ended products. CAPRRESI is a fast and low-cost method for fusing protein-coding genes.

Introduction

Chimeric gene assembly has been widely used in molecular biology to elucidate protein function and/or for biotechnological purposes. Different methods exist for fusing genes, such as overlapping PCR product amplification¹, plasmid recovery², homologous recombination³, CRISPR-Cas9 systems⁴, site-directed recombination⁵, and Gibson assembly⁶. Each of these offers different technical advantages; for example, the flexibility of overlapping PCR design, the in vivo selection of constructions during plasmid recovery, or the ....

Protocol

1. CAPRRESI Protocol

NOTE: Figure 1 represents the overall CAPRRESI protocol. This technique is based on an in silico design and the subsequent construction of the desired chimeras.

1. Selection of the cloning plasmid, pUC18 or pUC19.
   1. Select the pUC vector that best fits technical demands.
      NOTE: Both vectors have the same sequence, except for the orientation of the multiple cloning site. This is important for the design of oligonucleotides and the PCR plasmid disruption.
2. In silico analysis of the wildtype genes and pUC18/19 seque....

Results

Figure 1 depicts CAPRRESI. Using this method, two chimeric genes were assembled by exchanging the domains of two bacterial primary sigma factors (i.e., E. coli RpoD and R. etli SigA). The DNA sequences of the rpoD and sigA genes were obtained using the Artemis Genome Browser¹⁴ from GenBank genome files NC_000913 and NC_007761, respectively. The DNA sequence of the pUC18 vector was obtained from the nucleotide dat.......

Discussion

CAPRRESI was designed as an alternative to the PRM². The original PRM is a powerful technique; it allows for the fusion of DNA sequences along any part of the selected genes. For PRM, wildtype genes should be cloned into the same plasmid. After that, oligonucleotides are designed inside wildtype and antibiotics resistance genes found on the plasmid. Plasmid disruption is achieved by PCR using blunt-ended, high-fidelity DNA polymerases and previously designed oligonucleotides. The ligation of compl.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Platinum Taq DNA polymerase High Fidelity	Thermo Fisher	11304011	Produces a mix of blunt/3’-A overhang ended PCR products
High pure plasmid isolation kit	Roche	11754785001	Used for all plasmid purification reactions
High pure PCR product purification kit	Roche	11732676001	Used for all PCR purification reactions from agarose gels
AflII restriction enzyme	New England Biolabs	R0520L	Recognizes sequence 5’-CTTAAG-3’ and cuts at 37 °C
KpnI-HF restriction enzyme	New England Biolabs	R3142L	Recognizes sequence 5’-GGTACC-3’ and cuts at 37 °C
SpeI-HF restriction enzyme	New England Biolabs	R3133L	Recognizes sequence 5’-ACTAGT-3’ and cuts at 37 °C
XbaI restriction enzyme	New England Biolabs	R0145L	Recognizes sequence 5’-TCTAGA-3’ and cuts at 37 °C
Ampicillin sodium salt	Sigma Aldrich	A0166-5G	Antibiotics
Nalidixic acid	Sigma Aldrich	N8878-5G	Antibiotics
Yeast Extract	Sigma Aldrich	Y1625-1KG	Bacterial cell culture
Casein peptone	Sigma Aldrich	70171-500G	Bacterial cell culture
NaCl	Sigma Aldrich	S9888-1KG	Sodium chloride
Agar	Sigma Aldrich	05040-1KG	Bacterial cell culture
XbaI restriction enzyme	Thermo Fisher	FD0684	Fast digest XbaI enzyme
KpnI restriction enzyme	Thermo Fisher	FD0524	Fast digest KpnI enzyme
Quick Ligation Kit	New England Biolabs	M2200S	Fast DNA ligation kit
AflII restriction enzyme	Thermo Fisher	FD0834	Fast digest AflII enzyme
SpeI restriction enzyme	Thermo Fisher	FD1253	Fast digest SpeI enzyme