We narrowed to 104 results for: PAM
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TypeBlog PostPublishedMarch 28, 2018, 6:52 p.m....and GAT PAMs. xCas9 3.7 Activity in Mammalian Cells Construct NGG PAM NGA PAM NGC PAM NGT PAM...alternative PAMs like NGAG and NGCG and SaCas9 with an NNGRRN PAM by mutagenizing the PAM-interacting ... PAM GAA PAM GAT PAM xCas9 3.7 41 (1) 32 (1.6) 13 (2.1) 38 (4.5) 7.2 (5.2) xCas9...short PAM sequence adjacent to the targeted sequence at the locus of interest. SpCas9’s 3’ NGG PAM occurs...genomes, but a PAM is not always available near the locus you’d like to modify. To tackle the PAM problem, ... far! Why do we need PAM flexibility? IDT estimates that there is an NGG PAM every 42 bases in the human...editing window about 15 nt upstream of the PAM. Even if there’s a PAM near your insertion site, the corresponding...
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Progress Towards a PAM-Free CRISPR
TypeBlog PostPublishedMarch 7, 2024, 2:39 p.m....research, the old PAM constraints just won’t cut it anymore. Say hello to PAM-free and PAM-flexible nucleases...Summary of PAM-flexible Cas enzymes Are we truly PAM-less? Have we reached an essentially PAM-free solution... Adjacent Motif (PAM) sequence. If the gRNA sequence is suitable, but there is no PAM next to the desired...the PAM requirement to allow flexibility in gRNA selection and subsequent editing. Identifying PAM-free...solution to the PAM problem seems simple, in theory: find a Cas enzyme or evolve one that uses a PAM with no ...Cas9 variants which utilize alternative PAMs. These alternative PAMs are not necessarily more flexible than...recognizes the PAM sequences of TTTV. While all of these enzymes certainly add more PAM options, none ... -
The PAM Requirement and Expanding CRISPR Beyond SpCas9
TypeBlog PostPublishedAug. 20, 2020, 2:30 p.m....of a Protospacer Adjacent Motif (PAM sequence). The 3-5 nucleotide PAM sequence serves as a binding signal...mediated DNA cleavage. The need for more PAM sequences While PAM sequences for the commonly used S. pyogenes...on the PAM site, check out this video from IGI!) Synthetic S. pyogenes Cas9s with novel PAM recognition...with altered PAM binding specificity: SpCas9 variant Mutations (relative to SpCas9) PAM sequence ...found in the REC2, REC3, and PAM interacting domains and allows for expanded PAM recognition as well as increased...understanding of their PAMs is shown in the table below. Cas9 species PAM sequence ’) Streptococcus...Cas9 species PAM sequence may not be characterized Non-SpCas9's bind a variety of PAM sequences, which... -
CRISPR 101: Cas9 Nickase Design and Homology Directed Repair
TypeBlog PostPublishedMarch 15, 2018, 12:59 p.m....either a PAM-in or PAM-out orientation. Just as the names imply, PAM-out designs have the PAM sequences...extremes of the targeted region, whereas PAM-in designs place the PAMs closer together in the middle of the... D10A and H840A total editing efficiency in PAM-in and PAM-out configurations with varied nick distances...results, it’s clear that editing is much higher in the PAM-out configuration. In addition, D10A editing efficiency...potent editors, but their indel profiles vary. In the PAM-out configuration, D10A tends to generate small deletions...5’ overhangs and H840A creates 3’ overhangs in a PAM-out design. Exploring nickases for homology directed... nicks? To find out, Schubert and Yan designed a PAM-out nickase experiment to insert an EcoRI site using... -
Choosing a CRISPR Nuclease: Site Accessibility, Specificity, and Sensitivity
TypeBlog PostPublishedNov. 5, 2019, 1:28 p.m....previous blog post The PAM Requirement and Expanding CRISPR Beyond SpCas9 described the PAM specificity of Cas9s... targeted by the Cas9. This is determined by the PAM sequence recognized by the nuclease. For the most...other species can recognize a variety of different PAM sequences. Researchers have also used experimental...experimental evolution to develop Cas9s that have a broader PAM specificity, allowing for the targeting of sites ...were previously unavailable. Figure 1: The PAM sequence that the Cas nuclease recognizes determines...determines site accessibility. Cas9s with a broader PAM specificity can target more sites. Created with BioRender.com...Cas9 variants that were able to target different PAM sites (NGG, NGAN, NGNG, NGAG, and NGCG). Since then... -
Components of CRISPR/Cas9
TypeBlog PostPublishedFeb. 2, 2016, 5 p.m....of the PAM sequence. Cas9 Species/Variants and PAM Sequences Species/Variant of Cas9 PAM Sequence... Adjacent Motif or PAM. In order for dsDNA to be cut by Cas9, it must contain a PAM sequence immediately...see table below) have different PAM requirements. These different PAM requirements allow researchers to... (for example, xCas9 is a variant with increased PAM flexibiliy and eSpCas9/SpCas9-HF1 have increased ...is upstream (5') of a protospacer adjacent motif (PAM) Cas9 endonuclease binding to the target genomic ...RNA. In the absence of either the guide RNA or a PAM sequence, Cas9 will neither bind nor cut the target...their prefered Cas9 variant (with the appropriate PAM sequence) to modify the desired genomic locus. ... -
A Needle in a Base-Stack: Cas9 Structural Biology
TypeBlog PostPublishedJune 4, 2024, 1:15 p.m.... role is recognizing the PAM on DNA, the CTD is also sometimes called the PAM-interacting (PI) domain.... ready to check for PAM sequencines. This helps explain why Cas9 can’t locate PAM sites until after RNA...the PAM-recognition residues in the CTD can get cozy with DNA. S. pyogenes Cas9 recognizes the PAM sequence...no adjacent PAM to anchor it. However, Cas9 only checks the non-target strand for the PAM sequence and...sequence with a nearby protospacer-adjacent motif (PAM)? Cas9 is becoming an ever more ubiquitous tool for...DNA non-target strand CTD (or PI) Recognize PAM REC REC I, II, and III Recognize guide RNA...Figure 2). The portion of the CTD that recognizes the PAM is so flexible in this state that it doesn’t appear... -
CRISPR 101: Which Cas9 Do I Choose for My CRISPR Experiment?
TypeBlog PostPublishedOct. 13, 2022, 1:45 p.m....be a NGG PAM site anywhere to be found. If you’re lucky enough to find a SpCas9 compatible PAM at your ...number of Cas9s with looser PAM requirements compared to SpCas9. xCas9 has a PAM requirement of NG, GAA, ...Information on even more alternative PAM Cas9s can be found in “The PAM Requirement and Expanding CRISPR ...immediately upstream of a Protospacer Adjacent Motif (PAM), the sequence NGG. If these conditions apply to...variant, discovered by the Kleinstiver group has a PAM of NGN (Walton et al., 2020). Further, this group...characterized a second Cas9 variant, SpRY, which cuts at NRN PAMs with high efficiency, as well as NYN, but with a...impaired Cas9 proteins (such as SpRY) with altered PAM requirements, giving it more flexibility. A consideration... -
CRISPR 101: Cas9 vs. The Other Cas(s)
TypeBlog PostPublishedDec. 8, 2022, 2:15 p.m....variants exist with unique cutting features and evolved PAM sites, making Cas9 an adaptable choice for many genome...blog post on choosing a Cas9 enzyme. Fast facts – PAM requirement: NGG and an expanding number of others...application potential as a result. Fast facts – PAM requirement: AAG or TTC Best for: very large deletions...conducive for targeting AT-rich genomic loci as the PAM does not require any G’s or C’s. One curious feature...made to increase cutting efficiency and diversify PAM sequences of Cas12a to further optimize it for therapeutic...therapeutic and laboratory usage. Fast facts – PAM requirement: TTN or TTTN. Best for: homology-directed...as single nucleotide polymorphisms. Fast facts – PAM requirement: none. Best for: high fidelity ssDNA... -
Cpf1: A New Tool for CRISPR Genome Editing
TypeBlog PostPublishedOct. 14, 2015, 2:30 p.m....assay to discover FnCpf1’s PAM sequence requirements. Cpf1’s preferred PAM is 5’-TTN, differing from that...cleaves relatively far away from the PAM, NHEJ might retain the PAM site. Therefore, if HDR does not initially...namely its blunt double stranded cleavage and G-rich PAM requirement. Zetsche et al. started from square one...Whereas Cas9 generates blunt ends 3 nt upstream of the PAM site, Cpf1 cleaves in a staggered fashion, creating...nucleotide 5’ overhang 18-23 bases away from the PAM. With this information, they turned to a cell culture... regions or AT-rich genomes that lack the 3’-NGG PAM sites favored by SpCas9. Since Cpf1 doesn’t require... (NHEJ). Cas9-mediated NHEJ usually destroys the PAM site due to its proximity to the cleavage site, preventing... -
CRISPR-mediated Plant Base Editors
TypeBlog PostPublishedJan. 3, 2019, 1:35 p.m....counting the ‘NGG’ PAM as 21-23 (Figure 3). If the target ‘A’ is closer to the PAM, i.e., positioned at...recognize PAM sequences other than NGG (Table-1). Type Nickase Cas9 (D10A) Deaminase PAM requirements... ‘A’ relative to the protospacer adjacent motif (PAM). ABE7.10 can edit target 'A' if it lies in a small...protospacer. And if the target cytosine is closer to the PAM site? CBE developed using the hAPOBEC3 deaminase ...stretched window ranging from 1-17 bp relative to the PAM sequence (Zong et al., 2018) (see CBE-3 in Figure...base editors. Plant CBE and ABE with expanded PAM compatibility All of the base editors mentioned ...nickase-based and depend on the presence of an ‘NGG’ PAM at a suitable distance from the base (C/A) to be ... -
Sensing Neuronal Dopamine
TypeBlog PostPublishedJuly 30, 2019, 12:59 p.m....What do we understand about Dopamine? DA is produced by specific dopaminergic neurons in a brain region ...developed several ways to sense dopamine. Methods for measuring Dopamine In vivo microdialysis The gold...brain’s reward circuits are generally linked to dopamine (DA), a well-known reward chemical and neurotransmitter...fluorescent-protein based DA sensors (Figure 2). The dLight1 dopamine sensor In 2018, Lin Tian’s lab has developed dLight1...live mice Find dLight sensor here! The GRABDA dopamine sensor Yulong Li’s lab has created the GRABDA ... Report endogenous DA release from a single dopaminergic fiber in mouse brain slices Demonstrate DA detection...species and while exhibiting complex behaviors. Find dopamine and other biosensors in our AAV vector inventory... -
Cpf1 Update: Comparison to Cas9 and NgAgo
TypeBlog PostPublishedJuly 14, 2016, 2:30 p.m....cleaves relatively far away from the PAM, NHEJ might retain the PAM site. Therefore, if HDR does not initially...overcome some of Cas9’s shortcomings. Cpf1’s preferred PAM is 5’-TTN, differing from that of Cas9 (3’-NGG) in...whereas Cas9 generates blunt ends 3 nt upstream of the PAM site, Cpf1 cleaves in a staggered fashion, creating...nucleotide 5’ overhang 18-23 bases away from the PAM. Cpf1’s staggered cleavage pattern opens up the possibility... (NHEJ). Cas9-mediated NHEJ usually destroys the PAM site due its proximity to the cleavage site, preventing...mediated cleavage, the continued presence of the PAM may give Cpf1 the ability to cleave again and possibly...editing post-HDR, repair templates should remove the PAM sequence. Many research and clinical applications... -
CRISPR/Cas9 FAQs Answered!
TypeBlog PostPublishedMarch 13, 2014, 4:08 p.m....There is no need to add the NGG PAM sequence. Because the 'NGG' of the PAM is used to select your genomic...target site sequence (protospacer+PAM) is located? If there are other PAMs in the region, will they also ...good way is to mutate the PAM 'NGG' sequence in the HR template. Since the PAM sequence is required for...including one from the Zhang group. Q2: Should I add the PAM sequence to the oligo when cloning my target spacers...targeted? A4: The Cas9 cuts 3–4 bp upstream of the PAM sequence. There can be some off-target DSBs using... (gRNA). These considerations only matter if the PAM sequence is immediately adjacent to the nearly-homologous...nearly-homologous target sites. The mere presence of additional PAM sequences should not be sufficient to generate off-target... -
CrispyCrunch: High-throughput Design and Analysis of CRISPR+HDR Experiments
TypeBlog PostPublishedFeb. 7, 2019, 2:16 p.m....typically advised to mutate the PAM to which the guide binds. However, if the PAM resides in a coding region...pairs of the PAM (NGG -> NCC, CCN -> GGN). This ends the mutation process. If the guide PAM is within the... optimal mutation in CrispyCrunch: If the guide PAM resides outside a coding region in a UTR, CrispyCrunch...sequence to every possible 23bp sequence (protospacer + PAM) in the target region after HDR. If the max CFD score...codons in the guide sequence, one by one, from the PAM outwards so that the DNA sequence is altered but ... -
Hot Plasmids - September 2019 - CRISPR, Auxin Inducible Degradation, MerMAID Channelrhodopsins, and Genome Looping
TypeBlog PostPublishedSept. 3, 2019, 1:15 p.m....specific PAM (protospacer adjacent motif) in order to bind the target sites for editing. PAM sequences...Streptococcus pyogenes Cas9 (SpCas9) requires an NGG PAM to recognize the target. Osamu Nureki’s lab engineered...with relaxed preferences for the third base of the PAM so that it now recognizes NG rather than NGG. In ...conversion in the target sites adjacent to an NG PAM in human cells. The increased versatility of the ... -
An “elegans” Approach to Better CRISPR/Cas9 Editing Efficiency
TypeBlog PostPublishedDec. 17, 2020, 1:30 p.m....single injected animal. PAM sequence considerations For changes 5’ to the PAM, sequences corresponding... strand as the PAM produced a higher editing efficiency, while for edits 3’ to the PAM sequences corresponding...orientation where the 5’ ends of the PAMs are facing outwards, ensuring the PAMs remain on the chromosome after...difficult to find an appropriate NGG PAM site to target. The (T)TTN PAM motif required by the Acidaminococcus...al., 2019). The Meyer lab also determined optimal PAM orientation for editing using two Cas9 targets. An... -
A New Generation of Adenine Base Editors Improves Editing in Primary Human Cells
TypeBlog PostPublishedMay 7, 2020, 1:15 p.m....in the ABE complex with PAM-variant Cas9 proteins: the S. pyogenes NG-Cas9 (PAM: NG) to create NG-ABE8....to contain a specific protospacer adjacent motif (PAM) made up of 5′-NGG-3′ (“N” can be any nucleotide ...ABEs as DNA sites that do not contain a suitable PAM cannot be edited efficiently. To expand the targeting...NG-ABE8.xm/d and the S. aureus Cas9 (PAM: NNGRRT) to create Sa-ABE8.x-m/d. With these variants, ABE8 could target...editor: ABE8e Read about xCas9, a CRISPR variant with PAM flexibility Resources on Addgene.org Get the basics... -
Build Your CRISPR Vocabulary
TypeBlog PostPublishedJuly 2, 2024, 1:15 p.m....target and nontarget DNA strands upstream of the PAM site found in the nontarget strand. Protein ...complementarity, its sequence matches the guide sequence. PAM: The “protospacer-adjacent motif” present in the ...proteins won’t cut DNA that doesn’t have their specific PAM, which is how they avoid chopping up their own CRISPR...Various labs have created Cas9 enzymes with looser PAM requirements, which are available from Addgene! ... -
Analyzing CRISPR Editing Results with ICE from Synthego
TypeBlog PostPublishedMay 8, 2018, 1 p.m....RNA, excluding the PAM sequence. PAM Sequence - The Protospacer Adjacent Motif (PAM) sequence for the ...the guide sequence, along with the red underlined PAM. The vertical black dotted line represents the cut...topic page xCas9: Engineering a CRISPR Variant with Pam Flexibility RNA Editing with Cas13 and REPAIR Resources... -
CRISPR 101: Making a Knock-In Cell Line
TypeBlog PostPublishedDec. 22, 2022, 2:15 p.m.... success (Yu et al., Nat Chem Biol). Mutate the PAM or sgRNA sequences Cas9 likely goes through multiple... of cleavage at the target site until either the PAM site or part of the guide’s recognition sequence ...mutation. By introducing a mutation in either the PAM or the guide recognition sequence in the donor DNA... the coding region of a gene, make sure that the PAM edit you introduce is a silent mutation, so you don...interest. Fig. 2: Stop re-cutting with PAM and guide RNA disrupting mutations in donor DNA ... -
CRISPR 101: Cytosine and Adenine Base Editors
TypeBlog PostPublishedFeb. 13, 2025, 2:15 p.m....-A4 and A8-A10 at NGG PAM and 4.2-fold higher editing efficiency at non-NGG PAM variants compared to ABE7.10...surrounding -18 position upstream of the PAM Kim et al., 2017 SaBE3, BE3 PAM variants, BE3 editing window variants...tightly constrained by PAM availability in the genome. So the development of near-PAMless Cas9 variants significantly...modifying a 3-5 base window 18 bases upstream of the PAM. David Liu’s lab generated BE3 variants with other...variants to develop five new base editors with distinct PAM sequences, expanding the number of available target...and confirmed that the fusion protein retained the PAM properties of the individual Cas9. They also mutagenized...7.10) or to BE4max Evolved SpCas9 with NRN or NYN PAM site Chen et al., 2023 Td-CBE Engineered TadA... -
3 Tips to Improve HDR Efficiency for CRISPR Editing in Human Cells
TypeBlog PostPublishedSept. 5, 2017, 1:58 p.m....silent CRISPR/Cas9 blocking mutations in either the PAM (changing one of the G’s to an A,T or C – but avoid...improve editing efficiency. But what’s better: PAM-blocking or guide RNA blocking mutations? This depends...silent. In our view, it’s always best to change the PAM site, however we have also demonstrated the efficiency...mutations. So if the locus does not allow blocking the PAM sequence (e.g. if it would lead to a missense or ...recommend changing several bases as close to the PAM as possible (see below to find out why). Please check... -
Prime Editing: Adding Precision and Flexibility to CRISPR Editing
TypeBlog PostPublishedJan. 13, 2025, 9:49 p.m....far from PAM sites, making it less constrained by PAM availability than other methods. The PAM-to-edit ... Advantages of prime editing Less constrained by PAM sequence location The prime editor extends the reach...can be over 30 base pairs for prime editing. Since PAM sites occur on average every ~8 base pairs on either...cannot edit within what Fyodor Urnov refers to as “PAM deserts” in the genome. More versatile and precise...is more efficient due to its lower dependence on PAM placement. Fewer byproducts and more efficient than... -
History of CRISPR Cas - A tale of survival and evolution
TypeBlog PostPublishedNov. 25, 2013, 10:12 p.m....the species-specific protospacer adjacent motif (PAM). Once the CRISPR/Cas complex binds to the foreign...functions using slightly different Cas proteins and PAM sequences. A total of eight evolutionarily conserved...defense by generating a single point mutation in the PAM sequence, preventing the Cas nucleases from re-identifying... -
Easi-CRISPR: Generating Knock-In and Conditional Mouse Models
TypeBlog PostPublishedApril 5, 2018, 12:42 p.m....adjacent PAM. Your knock-in design may naturally remove the gRNA sequence or place it far from the PAM; if ...Easi-CRISPR. Potential guide sequences (arrows) and their PAM (bold highlighted text) and cleavage sites (slashes...if not, you can add a silent PAM or guide mutation. Designing an Easi-CRISPR conditional allele The design...also separates the gRNA target sequences from their PAMs, preventing re-cutting after editing. How to use... -
CasPEDIA: A Functional Classification of Cas Enzymes
TypeBlog PostPublishedJan. 25, 2024, 2:15 p.m....Nuclease properties (CasID): Cis/trans activity, PAM requirement, gRNA, and multiplex ability Experimental... guided by a gRNA is useless without an adjacent PAM or protospacer-flanking sequence (PFS) in some cases...experiment? CRISPR 101: Cas9 The Other Cas(s) The PAM Requirement and Expanding CRISPR Beyond SpCas9 More... -
CRISPRainbow and Genome Visualization
TypeBlog PostPublishedFeb. 28, 2017, 3:30 p.m....is key: since each ortholog requires a different PAM sequence, a gRNA designed for one dCas9 should be...number of limitations. Since color is specified by PAM sequence, each color requires a different Cas9 ortholog...target sequence must be located adjacent to that PAM. To scale up fluorescent CRISPR labeling, they took... -
Hot Plasmids and Viral Preps - January 2021
TypeBlog PostPublishedJan. 5, 2021, 2:15 p.m....addition, Casɸ has a minimal PAM requirement. For instance, for Casɸ-2 the PAM sequence is 5’-TBN-3’ (where...Kim’s lab engineered prime editors to expand their PAM flexibility. Find the engineered prime editors here... -
How to Design Your gRNA for CRISPR Genome Editing
TypeBlog PostPublishedSept. 24, 2020, 1:15 p.m....usually few potential gRNAs. While SpCas9, with a PAM preference of NGG, is still the most widely-used ...and engineered variants thereof offers additional PAM options that can greatly expand gRNA options. ...edit must be in a 5 - 10 nt window relative to the PAM, and bystander edits are possible if there is another...nucleotide transitions but still requires a nearby PAM, although these are still early days for this technology... -
The CRISPR Software Matchmaker: A New Tool for Choosing the Best CRISPR Software for Your Needs
TypeBlog PostPublishedNov. 3, 2015, 3:30 p.m....design”, “empirical design”, “single-PAM design”, and “multi-PAM design”. Trends: By the end of 2014, ...designing exclusively for NGG PAM targets and began allowing for arbitrary PAM definitions. These newer tools...genome contains only 0.66 million targetable NGG PAM sites whereas the human genome has about 300 million... -
INTEGRATE: Bacterial Genome Engineering Using CRISPR-Transposons
TypeBlog PostPublishedDec. 7, 2020, 2:53 p.m....upstream 2-bp PAM sequence for recognition by QCascade; although 5’-CC-3’ is one of the best PAMs for VchINT...VchINT, many other PAMs are also efficiently recognized by the system. Guided by the crRNA, QCascade complexes... -
CRISPR 101: Targeting RNA with Cas13a (C2c2)
TypeBlog PostPublishedSept. 21, 2017, 2:07 p.m....Enzymes Name Enzymatic Domains Guide RNA Target PAM (PFS) Cleavage Mechanism Cas9 HNH, RuvC TracrRNA...sequence (PFS) for LshCas13a, which is analogous to the PAM sequence for Cas9, is located at the 3’ end of the... the spacer sequence and contain the appropriate PAM sequence. The non-specific cleavage is thought to... -
Hot Plasmids and Viral Preps - July 2021
TypeBlog PostPublishedJuly 27, 2021, 1:15 p.m....variants have improved activity on NAG PAMS and reduced activity on NGG PAMs relative to wild type. A new genome-wide... -
CRISPR Challenges: Standardization and Homology Directed Repair
TypeBlog PostPublishedFeb. 14, 2018, 2:36 p.m....Protocols.io. The PAM Requirement and Expanding CRISPR Beyond SpCas9 The closer your edit is to the PAM site, the... -
Some Like it Hot: Thermostable GeoCas9
TypeBlog PostPublishedSept. 14, 2017, 12:40 p.m.... SpCas9 GeoCas9 Size 1368 AA 1087 AA PAM Sequence NGG CRAA (R = A or G) Spacer Length...and a guide targeting a site with an overlapping PAM. In both cases, GeoCas9 and SpyCas had similar levels... -
Optimizing Donor DNA for Enhanced CRISPR Genome Editing
TypeBlog PostPublishedMarch 24, 2016, 2:30 p.m....in length, With 36bp on the PAM-distal side of the break and 91bp on the PAM-proximal side, consistently... -
CRISPR Guide Update
TypeBlog PostPublishedOct. 10, 2024, 1:15 p.m....101: Cas9 vs the Other Cas(s) Progress Towards a PAM-free CRISPR... -
SARS-CoV-2/COVID-19 Detection Methods Based on CRISPR/Cas
TypeBlog PostPublishedMay 5, 2020, 1:15 p.m....absence of cleavage. Highlights: To detect non-PAM regions, PAM can be engineered into the primers. This method...preferences at the target site, while Cas12a requires a PAM (Protospacer Adjacent Motif) for target cleavage.... -
CRISPR 101: Cytosine Transversion Editors
TypeBlog PostPublishedMarch 25, 2025, 1:15 p.m....protospacer-adjacent motif (PAM) on the opposite strand. Once it finds a PAM, Cas9 unwinds the adjacent...variants with other Cas9s that recognize different PAMs. Their computational tool for predicting CGBE editing... terms, this strand is edited by base editors! PAM Protospacer-Adjacent Motif A short sequence that ...