Jul 03, 2023
Version 3
A Programmable DNA Roadblock System Using dCas9 and Multivalent Target Sites V.3
Peer-reviewed method
- priceal 1,
- ekmatozel 1,
- parzialest 1
- 1Emmanuel College
- Emmanuel College
- Spotlight series
External link: https://doi.org/10.1371/journal.pone.0268099
Protocol Citation: priceal , ekmatozel , parzialest 2023. A Programmable DNA Roadblock System Using dCas9 and Multivalent Target Sites. protocols.io https://dx.doi.org/10.17504/protocols.io.36wgq422kvk5/v3Version created by parzialest
Manuscript citation:
Matozel EK, Parziale S, Price AC (2022) A programmable DNA roadblock system using dCas9 and multivalent target sites. PLOS ONE 17(5): e0268099. https://doi.org/10.1371/journal.pone.0268099
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: June 29, 2023
Last Modified: July 03, 2023
Protocol Integer ID: 84237
Keywords: sgRNA, RNA, cas9, CRISPR, dcas9, roadblock, PCR, EcoRI, BtgI, NdeI, restriction endonuclease, translocation, single molecule, DNA cleavage, programmable dna roadblock system, crispr effector nuclease cas9, dna roadblock, dna roadblocks on the translocation, translocation of other dna binding protein, other dna binding protein, introduced protein roadblock, dna binding, protein roadblock form, synthetic gene, protein roadblock, multivalent target site, programmable roadblock, gene expression, restriction endonuclease ndei, dna, using dcas9, complete binding of the roadblock, internal restriction site, significant effects on gene expression, binding site, deficient mutant, protein, roadblock
Abstract
A protein roadblock forms when a protein binds DNA and hinders translocation of other DNA binding proteins. These roadblocks can have significant effects on gene expression and regulation as well as DNA binding. Experimental methods for studying the effects of such roadblocks often target endogenous sites or introduce non-variable specific sites into DNAs to create binding sites for artificially introduced protein roadblocks. In this work, we describe a method to create programmable roadblocks using dCas9, a cleavage deficient mutant of the CRISPR effector nuclease Cas9. The programmability allows us to custom design target sites in a synthetic gene intended for in vitro studies. These target sites can be coded with multivalency—in our case, internal restriction sites which can be used in validation studies to verify complete binding of the roadblock. We provide full protocols and sequences and demonstrate how to use the internal restriction sites to verify complete binding of the roadblock. We also provide example results of the effect of DNA roadblocks on the translocation of the restriction endonuclease NdeI, which searches for its cognate site using one dimensional diffusion along DNA.
(The last step in this version contains a supplemental video with extra context and tips, as part of the protocols.io Spotlight series, featuring conversations with protocol authors.)
Materials
Step 1:
- Nuclease-free water
- Q5 Master Mix (New England Biolabs)
- Forward and Reverse primers (10 uM) (See below)
- synthetic template DNA (See below)
- Sterile microcentrifuge tubes and PCR tubes
- PCR thermocycler
The sequence of the synthetic template DNA used:
CCAACTTAAT CGCCTTGCGC CGCCAGCTGG CGTAATAGCG AAGAGGCCCG CACCGATCGC CCTTCCCAAC GTTGCGCAG CCTGAATGGC GAATGGCGCT TTGCCTGGTA TCCTGCACCA GGAGCGCTGC CGGAAAGCTG GCTGGAGTGC ATCTTCCTG AGGCCGATAC TGTCGTCGTC CCCTCAAACT GGCAGATGCA CGGTTACGAT GCGCCCATCT ACACCAACGT GACCTATCCC ATTACGGTCA ATCCGCCGTT TGTTCCCACC TAGAATCCGA CGGGTTGTTA CTCGCTCACA TTTAATGTTG ATGAAAGCTG GCTACAGGAA GGCCAGACGC GAATTATTTT TGATGGCGTT CCTATTGGTT AAAAAATGGATATCGATCCACGGATCCAGG TGCGAATTTT AACAAAATAT TTACGGTTAC AATTTGGGTA TTTGCTTATA CAATCTTCCT GTTTTTGGGG CTTTTCTGAT TATCAACCGG GGTACATATG AATTCCATGC TAGTTTTACG ATTACCGTTC TTCGTTTCTC TTGTTTGCTC CAGACTCTCA GGCAATGACC TGATAGCCTT TGTAGATCTC TCAAAAATAG GGATATCGATCCACGGATCC TGGTCAGCTA GAACGGTTGA ATATCATATT GATGGTGATT TGACTGTCTC CGGCCTTTCT CACCCTTTTG AATCTTTACC TACACATTAC TCAGGCATTG CAGGGAAAAT ATATGAGGGT TCTAAAAATT TTTATCCTTG CGTTGAAATA AAGGCTTCTC CCGCAAAAGT ATTACAGGGT CATAATGTTT TTGGTACAAC CGATTTAGCT TTATGCTCTG AGGCTTTATT GCTTAATTTT GCTAATTCTT TGCCTTGCCT GTATGATTTA TTGGATGTTA ATGCTACTAC TATTAGTAGA ATTGATGCCA CCTTTTCAGC TCGCGCCCCA AATGAAAATA TAGCTAAACA GGTTATTGAG CGAAATGTAT CTAATGGTCA
The forward primer sequence: 5’-CGCGTTGGCCGATTC-3’
The reverse primer sequence: 5’-AGGGTGAGAAAGGCC-3’.
Step 6:
- PCR product from Step 5
- Qiagen PCR clean up kit (with spin columns and all reagents)
- Microcentrifuge tube for storage of purified DNA
Step 8:
- Purified DNA from Step 7
- Water or EB buffer from PCR cleanup kit
- Nanodrop spectrophotometer
Step 14:
- Sterile nuclease-free microfuge tubes
- Nuclease-free water
- EnGen 2X sgRNA Reaction Mix, S. pyogenes
- Target-specific DNA oligo (1 µM) (see below)
- Create by adding 1 µL oligo into 99 µL RNase free water
- DTT (0.1 M)
- EnGen sgRNA Enzyme Mix
The sequence of the target specific DNA oligo:
TTCTAATACGACTCACTATAGGATATCGATCCACGGATCCGTTTTAGAGCTAGA
Step 20:
- RNA product from Synthesis protocol above
- Monarch RNA Cleanup Kit (50 µg)
- ≥ 95% Ethanol
- Microcentrifuge tube for storage of purified RNA
Step 22:
- Sterile nuclease-free microcentrifuge tubes
- Nuclease-free Water
- NEBuffer 3.1
- 500 nM sgRNA
- Dilute product from sgRNA synthesis with nuclease-free water
- 1 µM dCas9, S. pyogenes
- Substrate DNA
- Glycerol
PCR Preparation
Gather the materials used in Step 1 (See Materials section). Thaw components before use. Keep all on ice.
Dilute the primers for (See Materials) to 10 uM before using.
PCR reaction
Combine the components from Step 1 into PCR tube(s) in order, for the desired final volume. Use Table 1 for reference.
| A | B | C | D | E | F | |
| Component | Stock Concentration | 4x Amount | 2x Amount | 1x Amount | Final Concentration | |
| Nuclease-free Water | - | 78 μL | 39 μL | 19 μL | - | |
| Q5 Master Mix | 2x | 100 μL | 50 μL | 25 μL | 1x | |
| Forward primer (DnnnnF) | 10 μM | 10 μL | 5 μL | 2.5 μL | 500 nM | |
| Reverse primer (BnnnnR) | 10 μM | 10 μL | 5 μL | 2.5 μL | 500 nM | |
| Template DNA | 4 µg/mL | 2 μL | 1 μL | 1 μL | 0.2 - 0.4 µg/mL | |
| Total Volume | 200 μL | 100 μL | 50 μL |
Table 1: Q5 Master Mix
Perform PCR using Table 2 for parameters
| A | B | C | |
| Step | Temperature (°C) | Time (Seconds) | |
| Denaturation | 98 | 30 | |
| Melt | 98 | 10 | |
| Anneal | 60 | 30 | |
| Extend | 72 | 30 | |
| Final Extend | 72 | 120 | |
| Infinite Hold | 4 | - |
Table 2: PCR Protocol
Advance to purification steps
Purification of PCR Product
Gather the materials used in Step 6 (See Materials section).
Perform Qiagen PCR purification kit by following the printed protocol inside the kit. Make sure pure ethanol (200 Proof) has been added to the correct buffer.
For 1x volume (50 uL total), you must use a blank centrifuge tube with water to counterbalance the spin column.
For 2x volume (100 uL total), use two spin columns and add 50 uL to each column. This will produce the same concentration as 1x protocol, but twice the volume (2x the amount of DNA).
For 4x volume (200 uL total), use two spin columns and add 100 uL (two PCR tubes) to each column. This will produce twice the concentration of the 1x protocol, and twice the volume (4x the amount of DNA).
Store on ice after purification.
Determination of DNA Concentration
Gather the materials used in Step 8 (See Materials section).
Use a nanodrop or similar UV absorbance instrument for measurements.
Blank with Buffer EB or dd H2O, depending on how you elute in your PCR purification kit.
Collect concentrations 2 times each.
Take the average of your 2 readings for each DNA sample.
Convert ng/uL to nM using the formula below. Record both ng/uL and nM numbers.
Concentration [nM] = 1.62 × Concentration [ng/uL]
Preparation of sgRNA
Gather the materials used in Step 14 (See Materials section).
Thaw EnGen 2X sgRNA Reaction Mix, S. pyogenes, and the customer-supplied target-specific oligo (1 µM). Mix and pulse each component in microfuge prior to use for 10 seconds. Store enzyme mix on ice.
Assemble the reaction at room temperature in the order listed below. Add the enzyme last to each reaction.
| A | B | |
| Reagent | Amount | |
| Nuclease-free Water | 2 μL | |
| EnGen 2X sgRNA Reaction Mix, S. pyogenes | 10 μL | |
| Target-specific DNA oligo (1 µM) | 5 μL | |
| DTT (0.1 M) | 1 μL | |
| EnGen sgRNA Enzyme Mix | 2 μL | |
| Total Volume | 20 μL |
Table 4: EnGen 2X sgRNA Reaction Mix
Mix thoroughly and pulse-spin in a microfuge for 10 seconds. Incubate at 37°C for 30 minutes.
Transfer reaction to ice.
For DNase treatment, bring volume to 50 µL by adding 30 µL of nuclease-free water. Add 2 µL of DNase I, mix and incubate at 37°C for 15 minutes.
Gather the materials used in Step 20 (See Materials section).
Use Monarch RNA Cleanup Kit (50 µg) or similar RNA purification kit. From here, follow the protocol printed inside of the kit. Ensure that ethanol has been added to the correct buffer.
Activation of dCas9 and Binding to DNA
Gather the materials used in Step 22 (See Materials section).
Thaw NEBuffer 3.1, 500 nM sgRNA, and 1 µM dCas9. Mix and pulse each component in microfuge prior to use. Store tubes on ice.
Assemble the reaction below, in order, at room temperature. The final concentration of both the dCas9 and sgRNA should be 60 nM.
| A | B | |
| Reagent | Amount | |
| Nuclease-free Water | 19.14 µL | |
| NEBuffer 3.1 | 3 μL | |
| 500 nM sgRNA | 3.24 µL | |
| 1 µM dCas9, S. pyogenes | 1.62 µL | |
| Total Volume | 27 μL |
Table 5: dCas9 System Reaction Mix
Mix thoroughly by pipetting mixture up and down gently. Pulse-spin in a microfuge. Incubate at 25°C for 10 minutes.
Add enough DNA to reaction tube so that the final concentration of DNA is 3 nM. The ratio of dCas9:sgRNA:DNA should be 20:20:1.
- Ex. Add 1.12 µL of 75 nM stock DNA to reaction tube
Mix thoroughly by pipetting mixture up and down gently. Pulse-spin in a microfuge. Incubate at 37°C for 15 minutes.
Transfer reaction to ice.
Add enough glycerol to tube so that it is equal to total reaction volume. Mix thoroughly by pipetting mixture up and down.
- Ex. Add 28.12 µL glycerol to 28.12 µL reaction mixture
Roadblocks are now bound to programmed sites on DNA. Store in freezer.
Spotlight video