Oct 03, 2023
Version 2
Barcode Composition by Overlap-Extension PCR V.2
- 1Walter and Eliza Hall Institute of Medical Research
Protocol Citation: Mathew Chu 2023. Barcode Composition by Overlap-Extension PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.ewov1q2p7gr2/v2Version created by Mathew Chu
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: October 03, 2023
Last Modified: October 03, 2023
Protocol Integer ID: 88717
Keywords: diversity libraries of dna barcode, dna barcode, observed diversity of barcode, barcode sequence, barcode composition by overlap, barcode composition, ground truth of barcode sequence, barcode, random oligonucleotide, barcode unit, dna, extension pcr, diversity library, individual sequence, pcr, observed diversity
Abstract
Traditionally, DNA barcodes are synthesised as random oligonucleotides. However, this leads to uncertainty regarding the ground truth of barcode sequences in the experimental setting. Without reference sequences, it is impossible to determine with absolute confidence whether or not the observed diversity of barcodes is due to errors arising from sequencing itself or various cellular and molecular processes.
Here, we propose a modular way to assemble high-diversity libraries of DNA barcodes from units whose individual sequences are known a priori. Barcode units are amplified and then combinatorically spliced in vitro using overlap-extension PCR, yielding products that can be assembled into vectors for downstream applications.
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Materials
- Q5 DNA polymerase (NEB) or some other high-fidelity DNA polymerase
- NEBuilder HiFi DNA assembly cloning kit (NEB)
Single Stranded DNA Pools for Combinatorial Assembly
ssDNA oligos for combinatorial assembly can be ordered as a pool (oPool). For a final barcode of n units, each with m diversity, order a set of m different barcode sequences for each unit:
unit_i = [Li + barcode_1 + Ri, Li + barcode_2 + Ri, …, Li + barcode_m + Ri]
where unit i (1 ≤ i ≤ n) consists of m barcodes flanked by left (L) and right (R) homology sequences.
Homology sequences 1 to n should be 20 nt long and serve as both primer binding sites as well as junctions for the linear assembly of the barcode units. A set of orthogonal sequences for this purpose has been described and experimentally validated by Subramanian, Russ & Ranganathan (2018).
oPools should be divided into sets of 3-4 units to enable assembly of 3-4 oligo sets (barcode units) per reaction.
For each set of units, order primers for the left and rightmost homology sequences.
If the assembly will be performed in sets of 3, order primers for L1, R3, L3, R6, …
Stage 1 Assembly of Barcode Units
For each oPool, assemble 3-4 barcode units by performing 15 rounds of PCR using Q5 DNA polymerase (NEB). If relying on homology sequences from the literature cited above, use the following PCR parameters:
- Ta = 65 C
- extension time 10 s/kb (for the total length of the first stage assembly)
- reaction volume 100 uL
- 0.5 uM template
Remove the PCR reaction from the thermocycler and place immediately on ice.
For each assembly, add primers for the left and rightmost homology sequences at 0.5 uM directly to the reaction. Perform an additional 15 cycles of PCR.
Perform gel separation and extract the assembly product.
Hierarchical Assembly of Barcodes
Continue assembling barcodes in a hierarchical manner by combining 0.5 uM of products from the previous stage of assembly into a reaction with the above PCR parameters, adjusting the extension time at each stage.
In each stage, repeat the steps from the initial stage of assembly (15 initial rounds of PCR with template only, followed by 15 rounds of extension PCR) until n barcode units are assembled.
Sequencing and Cloning Barcode Libraries
Using overhang primers for the left and rightmost homology in the completed assembly (L1 and Rn), perform a final PCR with the same parameters to add adaptor sequences for next-generation sequencing. If deferring sequencing until after cloning is completed, skip this step.
To clone the assembled barcodes into a plasmid, design overhang primers with at least 20 nt homology to the linearized backbone at the desired cloning site. Using HiFi assembly (NEB), insert the barcodes as a single piece into the backbone. The resulting plasmid library can be sequenced on the Oxford Nanopore platform.
The theoretical diversity of the final barcode library is mn.
Protocol references
Subramanian, S. K., Russ, W. P., & Ranganathan, R. (2018). A set of experimentally validated, mutually orthogonal primers for combinatorially specifying genetic components. Synthetic Biology, 3(1), ysx008.