Use of In Vivo Assembly for High-efficiency Plasmid Construction

Summary

In vivo assembly is a ligation-independent cloning method that relies on intrinsic DNA repair enzymes in bacteria to assemble DNA fragments by homologous recombination. This protocol is both time and cost-effective, as few reagents are required, and cloning efficiency can be as high as 99 %.

Abstract

In vivo assembly (IVA) is a molecular cloning method that uses intrinsic enzymes present in bacteria that promote intermolecular recombination of DNA fragments to assemble plasmids. This method functions by transforming DNA fragments with regions of 15-50 bp of homology into commonly used laboratory Escherichia coli strains and the bacteria use the RecA-independent repair pathway to assemble the DNA fragments into a plasmid. This method is more rapid and cost-effective than many molecular cloning methods that rely on in vitro assembly of plasmids prior to transformation into E. coli strains. This is because in vitro methods require the purchase of specialized enzymes and the performance of sequential enzymatic reactions that require incubations. However, unlike in vitro methods, IVA has not been experimentally shown to assemble linear plasmids. Here we share the IVA protocol used by our laboratory to rapidly assemble plasmids and subclone DNA fragments between plasmids with different origins of replication and antibiotic resistance markers.

Introduction

Molecular cloning encompasses a series of laboratory techniques needed to produce plasmids containing specific recombinant DNA¹. These ubiquitous techniques often act as a bottleneck in the experimental workflow². Many molecular cloning techniques rely on the assembly of DNA fragments in vitro using a series of enzymatic reactions prior to transformation into a host strain (e.g., Escherichia coli DH5a) for amplification^3,4,5,6,7. As in vi....

Protocol

1. Design primers or DNA fragments with homologous ends

1. Use a word processing software or specialized DNA analysis software to artificially assemble the desired plasmid.
   NOTE: It is often helpful to color-code DNA fragments from different sources and to highlight homologous regions that will be used in downstream assembly steps. In addition, it is also helpful to color-code homologous DNA to ensure directional assembly.
2. Design primers that bind to each DNA fragment and contain 15-50 bp of the homologous DNA sequence (Figure 1)^2,15.

Discussion

The most critical step for successful IVA cloning is the DNA fragment and primer design. IVA efficiency is greatly improved when homologous fragments are designed to be at least 15 bp in length with a melting temperature of approximately 47-52 °C. A detailed study exploring the optimization of IVA fragment design has been published¹⁶. Another important step for having high cloning efficiency is to use as little template DNA as possible in PCR amplification steps. To further reduce the carryov.......

Materials

Name	Company	Catalog Number	Comments
1 kb Plus DNA ladder	FroggaBio	DM015-R500	DNA molecular weight marker
AccuReady M Single Channel 0.5-10 µL	Bulldog Bio	BPP020	Pipettes for transferring liquid
AccuReady M Single Channel Pipettor Kit	Bulldog Bio	BPK100	Pipettes for transferring liquid
Agar	BioShop Canada	AGR003.1	Solidifying agent for growth medium
Agarose	Biobasic	D0012	Make agarose gels for DNA electrophoresis
Biometra TOne	Analytikjena	846-2-070-301	Thermocycler
Caps for glass culture tubes	Fisher Scientific	14-957-91	Reusable caps for glass culture tubes
DNA primers	Integrated DNA Technologies	N/A	Bind and amplify template DNA in PCR reaction
DpnI	New England Biolabs	R0176S	Cleave methylated template DNA following PCR amplification
EcoRI	New England Biolabs	R3101L	Restriction enzyme, comes with appropriate buffer
Eppendorf microtubes 1.5 mL	Sarstedt	72.690.300	Microtube, 1.5 mL, conical base, PP, attached flat cap, molded graduations and frosted writing space
Ethidium bromide	Fisher Scientific	AAL0748203	DNA visualization/intercalating agent, toxic
EZ-10 Spin Column Plasmid DNA Miniprep Kit	Biobasic	BS614	Isolate plasmid DNA from overnight bacterial cultures
GelDoc Go-Gel system	Bio-Rad	12009077	Imaging DNA gels
Glass culture tubes	Fisher Scientific	14-925E	Glass culture tubes
myGel Mini Electrophoresis System	Sigma-Aldrich	Z742288	System used for gel electrophoresis
NanoDrop One	Thermo Fisher	ND-ONE-W	Determine DNA concentration
PCR Clean Up for DNA Sequencing	Biobasic	BT5100	Purify PCR products
Petri dish	Sarstedt	82.1473.011	Petri dish 92 x 16 mm, PS, transparent, with ventilation cams
Pipette tip, 1000 µL	Sarstedt	70.305	Pipette tips for 100-1000 µL
Pipette tip, 2.5 µL	Sarstedt	70.3010.265	Pipette tips for up to 2.5 µL
Pipette tip, 20 µL	Sarstedt	70.3020.200	Pipette tips for up to 20 µL
Pipette tip, 200 µL	Sarstedt	70.3030.020	Pipette tips for 1-200 µL
Salt (NaCl)	Fisher Scientific	S271-10	Component of bacterial growth medium (10 g/L)
Single 0.2 mL PCR tubes with flat cap	FroggaBio	TF-1000	PCR tubes
Tryptone (Bacteriological)	BioShop Canada	TRP402.5	Component of bacterial growth medium (10 g/L)
VeriFi DNA polymerase	PCR Biosystems	PB10.42-01	High fidelity polymerase, the PCR buffer containing Mg2+ and dNTPs is provided with purchase
Xba I	New England Biolabs	R0145S	Restriction enzyme, comes with appropriate buffer
Yeast extract	BioShop Canada	YEX401.205	Component of bacterial growth medium (5 g/L)