https://www.thebaileylab.org/posts daily 0.75 2022-12-07 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1572384287437-WISRXG3TQ7KEZXBWCIGY/spiral+darkened.jpg Posts https://www.thebaileylab.org/posts/kaitlin-johnson-leaves-bailey-lab monthly 0.5 2022-07-28 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1572040789737-RPE93NYAE38ZYU7JJ9ST/Kaitlin+Johnson.jpg Posts - Dr. Kaitlin Johnson leaves Bailey Lab to join UC Boulder Kaitlin Johnson stands in front of a wall, smiling. https://www.thebaileylab.org/posts/what-makes-a-match monthly 0.5 2022-10-17 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1572534993446-WCJUPOFXR9LCUWGRAF3X/Johnson+et+al+Figure1.PNG Posts - What makes a match? For CRISPR type III-B, it depends on location Figure showing the alignment of a crRNA and RNA target, with a dashed line box around the left side, leading to two different zoomed-in views. The aligned sequences have horizontal bars, with vertical bars extending toward each other, a little like combs with the teeth facing each other and aligned. The top sequence is the crRNA, labeled with 5' at the left and 3' at the right. The left most section labeled "crRNA tag,” is short and colored light blue, a horizontal bar with four vertical bars pointing down on the right half. To the right the figure is green and labeled "spacer." The spacer has bars reaching down with gaps like where the tooth of a comb is broken. Starting at the left there are six groups of five bars, and then the spacer ends with a single vertical bar. Below the crRNA is a purple RNA target, labeled 3' at the left and 5' at the right. The left most section is dark purple bar labeled PFS, lined up with the crRNA tag above. To the right is the light purple RNA protospacer, which has bars pointing up, aligned and in the same pattern as the spacer above. The RNA target extends to the right with a short, dark purple 5' flank. A dashed box around the light blue crRNA tag and dark purple PFS has lines leading to two boxes below showing the individual bases, with the positions labeled -8 at the left to -1 at the right. Both have the same crRNA sequence – black letters surrounded by blue, with the letters at the -5 through -2 positions offset so that they are slightly lower than the others. The sequence is AUG GAAA G. In the left box, the lower sequence is labeled “noncomplementary,” white letters surrounded by dark green, with the same sequence as the tag above. In the box on the right, the lower sequence is labeled “anti-tag,” sequence, black letters surrounded by red, with a sequence complementary to the blue tag above – UACCUUUG. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1572535140536-G0YZDYUHLCP0LX1VJCX7/Johnson+et+al.PNG Posts - What makes a match? For CRISPR type III-B, it depends on location Figure showing the alignment of a crRNA and RNA target, with regulatory and binding segments marked and activating and deactivating conditions identified. The same crRNA and target alignment from Figure 1 is shown – the crRNA with a short blue stretch with four bars pointing down, the PFS, followed by a longer green stretch with six segments of five bars pointing down, and the target all purple – the first and last sections dark purple, and center light purple with pars point upward, aligned with the green section of the crRNA. Boxes label the PFS and the first segment of paired vertical bars on the left as “regulation,” and the segments that follow “Binding, segments 2-6;” the 5’ dark purple tail of the target is not inside a box. Heavy dashed line boxes surround the PFS and first segment in the regulation box, leading to arrows showing two conditions – “activating” on top, and “deactivating” on the bottom. In the activating pair, on the left the PFS is shown with the noncomplementary sequence, with no connections indicated, while on the right Segment 1 is shown with matching bars from both the crRNA and target strands. In the deactivating pair, the PFS is shown with the “anti-tag” sequence, with four bars connecting the complementary base from each strand, and on the right Segment 1 is shown with straight green and purple lines, with no connecting bars. https://www.thebaileylab.org/posts/2016-frontier-award monthly 0.5 2022-07-28 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1572556546454-D209QKHAZPK24NWTY6GL/_JHU7522cropped+%281%29.jpg Posts - President's Frontier Award Scott Bailey speaks in front of a screen https://www.thebaileylab.org/posts/new-cryo-em-at-johns-hopkins-beckman-center monthly 0.5 2022-07-28 https://www.thebaileylab.org/posts/bailey-lab-wins-bmb-gingerbread-contest-with-a-very-crispr-christmas monthly 0.5 2022-07-28 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1576523975026-IHI5XN7MOP622QPUTMMO/Bailey+lab+gingerbread+winners.jpg Posts - Bailey Lab wins BMB gingerbread contest with “A Very Crispr Christmas” The Bailey lab with their winning gingerbread contest entry of a cell using Crispr to fight off a bacteriophage infection. From left to right: Anita Ramachandran, Morgan Beckett, Scott Bailey, Haobo Wang, Katelyn Jackson, John Mallon, Elvar Bjarkason. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1576525046219-DAAI5V93EVWSNR3B4H1E/gingerbread+crispr+front.jpg Posts - Bailey Lab wins BMB gingerbread contest with “A Very Crispr Christmas” A geometric “phage,” made of gingerbread, frosting, pretzels and candy sits atop a gingerbread dome “bacterium” with a flat cross section showing DNA gummy strands and piped icing Crispr proteins. Two cookies read”A Very Crispr Christmas” https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1576525061414-6CVH8YCV5F9HIEZEXWBX/gingerbread+crispr+back.jpg Posts - Bailey Lab wins BMB gingerbread contest with “A Very Crispr Christmas” The back of the domed gingerbread “cell” with geometric “phage” on top - drawn in white frosting are two eyes and a round mouth, saying “oh no!” https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1576525064341-P6PORUL9EG4FMUX3FTQZ/CRISPR+labels+and+lines.jpg Posts - Bailey Lab wins BMB gingerbread contest with “A Very Crispr Christmas” Close-up of the Crispr cut-away with added labels. Red gummy candy strands labeled “phage DNA” lead down from the top. A green icing blob, labeled “Cascade complex” surrounds a section where the strand splits in two. The strand inside Cascade runs along side another short strand labeled “crRNA.” The other end surrounded by a red icing blob labeled Cas3. To the left a short pair of gummy strands is surrounded by a red blob, Cas2 dimer, flanked by two green dots on either side, Cas1 dimers. Below a row of short strands of yellow, green and red gummy candy is labeled “Crispr array” https://www.thebaileylab.org/posts/crispr-spacers-asymmetry-and-orientation monthly 0.5 2022-10-17 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1579815205255-EVSE29DKFLIQYUUVFM4K/Model+part+one+updated.jpg Posts - CRISPR spacers - asymmetry and orientation A figure showing the first part of the proposed model. DNA sequences are depicted with horizontal bars, and areas of double stranded DNA are connected by thin vertical lines. At the top the pre-processed pre-spacer is depicted on top of a light gray shape labeled Cas1-Cas2. Cas1-Cas2 is in the general shape of a dumbbell. The pre-processed pre-spacer shows an offset DNA strand - the center is double-stranded, with the top strand's overhang extending further to the right, and the lower strand's overhang extending to the left. Both ends are labeled with "OH" and 3', and both extend past the edge of Cas1-Cas2. In the double-stranded section, the top non-PAM strand is green and the bottom PAM-strand is purple. The start of both overhangs match the center color before becoming gray near the edge of Cas1-Cas2. On the bottom strand, the PAM sequence, TTC, is shown in orange letters between the purple and gray overhang sections. An arrow points down, to the same diagram, but with yellow "Pac-Man" shapes labeled DnaQ on either end of the now shorter gray overhangs, trailed by small gray squares. An arrow points down to the diagram with text to the left: "Protection of PAM by Cas1-Cas2 [arrow] Trimming of Pam Strand stalled". The bottom strand overhang has a short section of gray in addition ot the PAM and purple overhang and is labeled "9 or 10 nt". The top strand overhang is reduced to just the green section, labeled "5 nt - Optimal length of integration. Below is a CRISPR array, shown as double stranded DNA with a red leader sequence (bound by a blue shape labeled IHF - Integration Host Factor), a gray repeat and then a blue spacer. From the prespacer above, two thin arrows curve down from the OH 3' at the end of the top green strand, pointing to two different locations on a CRISPR array below. One arrow, with a red X, points to the lower strand of the array, between the repeat and spacer - the red X is labeled "Spacer side integration of Non-PAM strand blocked". The other arrow points to the top strand between the leader and repeat An arrow points down to a diagram showing the prespacer angled at the top of the array, with the green overhang connected to the left edge of the top repeat strand. There is a gap between the top strand of the red leader sequence and the repeat. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1579814355803-JJ3FL0AXFCB12TZWUIZ7/Orientation%2Bcorrected.jpg Posts - CRISPR spacers - asymmetry and orientation A model showing how spacer orientation determines functionality with two side-by-side schematics – “Correctly Oriented (Functional) Spacer” (left) and “Incorrectly Oriented (Non-functional) Spacer” (right). Both start with a CRISPR array, the DNA depicted with two horizontal bars connected by thin vertical lines - at the left the top bar is labeled 5' and the lower 3'. Both have five labeled sections, from left to right: Leader (red), Repeat (gray), New Spacer (Green and Purple), Repeat (gray) and Spacer (blue). The orange letters of a single base pair are inserted on one side of the new spacer. The two arrays show a different orientation for the "New Spacer" - in the Functional array the top strand the base pair is on the left, with the G connected to the top green strand and the C connected to the lower purple strand. This is flipped in the Non-functional array – the top purple strand ends in a C on the right, above a green strand ending in a G. Below each array an arrow points to a crRNA diagram – with a 3’ gray bar on the left angled down to meet a colored horizontal bar with a gray hairpin on the right. The Functional side shows a green center section, with a G on the left, and the Non-Functional side shows a purple center section, with a C on the right. Arrows point down again to the crRNA bound to a yellow lobed shape labeled Cascade, and target sequence diagram with the PAM marked about a fifth of the way from the left side - TTC in the top purple strand and AAG on the lower green strand. In the functional side, the target strand is “unzipped” at the center, starting at the PAM sequence, and the the top purple strand is base-paired to the green crRNA bound to Cascade, and the lower green strand has two yellow shapes labeled Cas3 - below an arrow points to "Immunity" On the non-functional side, Cascade is bound to the purple crRNA, but not the target sequence. A label reads "Target Recognition Impaired" and an arrow below points to "No Immunity" https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1579815301542-5FFBKHYG89JS8JHCSX69/model+part+2.jpg Posts - CRISPR spacers - asymmetry and orientation A continuation of the model above. The prespacer is still connected to the array at an angle. The gray overhang of the purple strand has been removed, leaving only the “C” from the PAM sequence. An arrow points from the "C" to the lower strand of the array, between the repeat and spacer. A down arrow points to the spacer integrated into the array, which now has two gray single-stranded repeats flanking the new spacer, which has the green non-PAM strand on top and the purple PAM strand below. The left spacer has only the lower strand and the right spacer has only the upper strand. An arrow points down to the same array with the repeats filled in with double stranded DNA, labeled "New spacer in the correct direction" https://www.thebaileylab.org/posts/walder-foundation-funds-bailey-lab monthly 0.5 2022-07-28 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1580918065747-ADPF9075HCNER3HE5LV4/Bailey-and-walder Posts - Walder Foundation funds Bailey Lab research and communications Three people face a desk with a pair of computer monitors on the left. Scott Bailey leans forward, reaching to point at the computer screen. Behind him to the left, Elizabeth Walder stands, looking down at section of the screen that Bailey is pointing at. On the right, in front of Bailey, postdoctoral fellow Evan Worden sits, head turned toward the screen. https://www.thebaileylab.org/posts/anita-ramachandran-thesis-defense monthly 0.5 2022-07-28 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/4fb4d4da-7bc5-49d0-909a-169588dd7dd6/Anita+and+compass+cas1cas2.jpg Posts - Congratulations to Anita on her thesis defense! - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.thebaileylab.org/posts/farewell-john-mallon monthly 0.5 2022-07-28 https://www.thebaileylab.org/posts/crispr-primer-launches-with-walder-foundation-support monthly 0.5 2022-07-28 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596549298132-AX3N792950S7NENQ3P4S/Cascade.png Posts - CRISPR Primer launches with Walder Foundation support Cartoon diagram of Cascade complex cleaving DNA. Cascade is a grey elongated globular arch. It contains a crRNA, a thick black line with the middle section a green arch that is had double bonds the top strand of a piece of DNA. A red bean-shaped Cas3 is docked on Cascade, bound to the lower DNA strand and clipping the DNA into small pieces. https://www.thebaileylab.org/posts/crispr-researchers-charpentier-and-doudna-win-chemistry-nobel-prize monthly 0.5 2022-07-28 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1603207806578-1Z65Q4CI9PLTUQSRY64R/chemistry-2020-figure1-m-copy.jpg Posts - CRISPR researchers Charpentier and Doudna win chemistry Nobel Prize https://www.thebaileylab.org/posts/2020-johns-hopkins-discovery-awards monthly 0.5 2022-07-28 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1607553434154-9Y28PWIINT26PH1YRGK7/2020+discovery+awards.png Posts - 2020 Johns Hopkins Discovery Awards include Bailey Lab project https://www.thebaileylab.org/posts/a-look-at-a-cas3-hd-domain monthly 0.5 2022-10-17 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1615590967280-XK4O9D0TKEPDK1M6H3QB/1b.jpg Posts - A look at a Cas3 HD domain A ribbon structure model of the Cas3 HD domain. [11] coiled ribbons form a globular structure surrounding a black sphere at the center; portions of five coils are colored. At the top left there is a C label and the bottom right has a N label; at the C label are two flattened arrows. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1615591075910-SE7XS0BC0FEDQVXKS2L9/5a.jpg Posts - A look at a Cas3 HD domain A agarose gel - a ladder on the far left and then 42 lanes of controls and experimental products; the top labels identify the lanes for controls and then additions of different metal ions at different concentrations. Most of the lanes have a clear, dark band in the same location, others have lighter smears in lower positions. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1616592052254-91RVD3RQO1NVUH67367D/Cas3HD%2Bcropped.jpg Posts - A look at a Cas3 HD domain Structure of Cas3 HD domain light blue barrels connected by thin orange cords surround a small green sphere - near the center five molecular structures with dark blue, white and red sections extend from barrels toward the sphere, five beaded red lines lead from the sphere, four connecting to the extended molecules; at the far right the are a pair of flattened purple arrows https://www.thebaileylab.org/posts/crispr-primer-expands-with-type-ii-sections monthly 0.5 2022-07-28 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1621189819109-XWS6G20DSM7LEY23L2BV/Cas9+cleaving+DNA Posts - CRISPR Primer expands with Type II sections - Make it stand out A cartoon style diagram of the Cas9 complex cleaving DNA. The blue globular Cas9 structure with a sgRNA sits on a stretch of double-stranded DNA. A small region of the DNA within the complex is “open,” with the green portion of the sgRNA bound to the corresponding green section of the DNA just to the left of the red section indicating the PAM region. Each strand of the open DNA section has a gap at the same distance from the PAM, with pairs of blue arrows pointing at each at the cleavage sites. https://www.thebaileylab.org/posts/bailey-lab-welcomes-new-phd-student-elvar-bjarkason monthly 0.5 2022-07-28 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1626267674093-4K4W71RPOQX68Q4ET9IS/ElvarBjarkason.jpg Posts - Bailey Lab welcomes new PhD student Elvar Bjarkason! - Make it stand out Elvar Bjarkason https://www.thebaileylab.org/posts/viewing-a-cascade monthly 0.5 2022-10-17 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1630701059330-GKCNOKBM0X0WJDE9GIRE/Cascade.png Posts - Viewing a Cascade - Make it stand out Two views of the Cascade structure, rotated 90 degrees along the vertical axis; a legend below identifies subunits and nucleic acids by color. Proteins are represented as colored tubes and flat arrows connected by thinner wires, crRNA and ssDNA as space-filling balls. The structure looks like a top-heavy seahorse, a fat head curving into the body with a stubby tail. The green crRNA and orange ssDNA spiral down in a wide loop, with light and medium blue Cas7 subunits forming a backbone around the nucleic acids. The top is capped by a pink Cas6e, the tail is made of a purple Cse1, and the red Cas5 is at the bottom of the crRNA, just above the tip of the tail. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1630701632941-HQ7PI6R64CFK1NBC0FMV/crRNA.png Posts - Viewing a Cascade - Make it stand out Two views of the crRNA-ssDNA. Left, a space filling model, a loose spiral in a side view similar to the above structure. The green crRNA, which extends further than the orange ssDNA on either end, is labeled 3’ handle at top and 5’ handle at bottom. The two strands have short 5-bp segments where they are base paired, with small 1-bp gaps in between – four gaps are visible; the top curve of the spiral obscures any pairing gaps in that region. Right, a top-down ribbon structure with the same colors shows the two lined up in a scalloped curve, almost a complete circle with a gap at the bottom. Five asterisks where the scalloped edges pinch in indicate the location of the flipped-out bases. At the gap, the left side end of the crRNA is labeled 5’ and the right 3’. https://www.thebaileylab.org/posts/solving-a-targeting-puzzle monthly 0.5 2022-10-17 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/9fb9fb2f-e5c7-4a64-a236-ecf3f098b5a4/Screen+Shot+2021-12-14+at+2.10.14+PM.png Posts - Solving a targeting puzzle: Type III-B DNA cleavage - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.thebaileylab.org/posts/crispr-comparisons monthly 0.5 2022-07-28 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1639081238857-PKKJ5TVOXJCQVGY8OXUV/bitmap.png Posts - How do different types of CRISPR compare? Find out in our Primer! - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.thebaileylab.org/posts/bailey-lab-welcomes-scm-student-brynn-durecki monthly 0.5 2022-07-28 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/5b3090a5-5805-4ab6-a980-359b364dc8a6/Brynn+Durecki.jpg Posts - Bailey lab welcomes ScM student Brynn Durecki! - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.thebaileylab.org/posts/molecular-biophysics-phd-student-zoe-hutchinson-joins-the-bailey-lab monthly 0.5 2022-08-04 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/92ef1ba3-0866-41ef-99b9-53f016577b79/Zoe-Hutchinson-3x2.jpg Posts - Molecular Biophysics PhD Student Zoë Hutchinson Joins The Bailey Lab! - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.thebaileylab.org/posts/farewell-to-katelyn-jackson monthly 0.5 2022-09-02 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/9ab2d5db-bbf0-4244-b584-5e646e049747/Katelyn-and-Scott.jpg Posts - Farewell to Katelyn Jackson! - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.thebaileylab.org/posts/congratulations-to-dr-haobo-wang monthly 0.5 2022-09-30 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/6d4c1b89-3fae-4efb-8cad-9fe9dfda31d8/Scott-and-Haobo.jpg Posts - Congratulations to Dr. Haobo Wang! - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.thebaileylab.org/posts/congratulations-to-bailey-labs-morgan-beckett-on-winning-the-2022-bmb-sharon-krag-award monthly 0.5 2022-12-07 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/996bac97-5e35-4c65-b537-4209f33d7809/Morgan-presenting-B.jpg Posts - Congratulations to Bailey lab’s Morgan Beckett on receiving the 2022 BMB Sharon Krag award! - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.thebaileylab.org/posts/tag/news monthly 0.5 https://www.thebaileylab.org/posts/tag/what+makes+a+match monthly 0.5 https://www.thebaileylab.org/posts/tag/complex+target+interactions monthly 0.5 https://www.thebaileylab.org/posts/tag/cryoEM monthly 0.5 https://www.thebaileylab.org/posts/tag/Walder+Foundation monthly 0.5 https://www.thebaileylab.org/posts/tag/student monthly 0.5 https://www.thebaileylab.org/posts/tag/primer monthly 0.5 https://www.thebaileylab.org/posts/tag/congratulations monthly 0.5 https://www.thebaileylab.org/posts/tag/acquisition+paper monthly 0.5 https://www.thebaileylab.org/posts/tag/team monthly 0.5 https://www.thebaileylab.org/posts/tag/type+i monthly 0.5 https://www.thebaileylab.org/posts/tag/type+i+paper monthly 0.5 https://www.thebaileylab.org/posts/tag/type+iii+paper monthly 0.5 https://www.thebaileylab.org/posts/tag/award monthly 0.5 https://www.thebaileylab.org/posts/tag/paper monthly 0.5 https://www.thebaileylab.org/posts/tag/asymmetry+and+orientation monthly 0.5 https://www.thebaileylab.org/posts/tag/Solving+a+targeting+puzzle monthly 0.5 https://www.thebaileylab.org/posts/tag/type+iii monthly 0.5 https://www.thebaileylab.org/posts/tag/cascade+structure monthly 0.5 https://www.thebaileylab.org/posts/tag/cleavage+mechanisms monthly 0.5 https://www.thebaileylab.org/posts/tag/welcome monthly 0.5 https://www.thebaileylab.org/posts/tag/farewell monthly 0.5 https://www.thebaileylab.org/home daily 1.0 2022-07-20 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1658349012695-GPMC1GCK2V6ZAGSLNMPI/Our-Research-button.png Home - Our Research https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1658349254816-US4OJX4R620CW935I3NH/CRISPR-Primer-button.png Home - CRISPR Primer https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1658349266487-3AF9PLESMMRM7JQU7OYY/Our-Team-button.png Home - Our Team https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1607541197437-5HPWJL8BZ4GZIUSHZ7MO/Home%2BBanner.jpg Home https://www.thebaileylab.org/crispr-primer daily 0.75 2021-11-29 https://www.thebaileylab.org/crispr-primer/type-iii-tools monthly 0.5 2022-10-14 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596209005566-6OVHD4F6XKH9CE7KH0M0/type-iii-tools-cell-death CRISPR Primer - Type III Tools - Cell Death Pathway The potential for cyclic oligoadenylate production to trigger high enough levels of Csm6 RNA cleavage to cause extensive RNA damage leading to death is a disadvantage for some tools, but can also be used as a highly-selective antimicrobial tool. crRNAs can be created that are specific to a pathogenic species in population, or even to a particular gene, such as an antibiotic resistance gene. Type III systems only target actively transcribed genes, providing a level of control, as only cells actively expressing the genes would be affected. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1605909578524-O85326CJXY6NDNHFRGY9/Cascade%252Bmodule%252Badditions.jpg CRISPR Primer - Type III Tools - Type I Tools https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1621451879613-18Y3BF1ATRPYJDJ5MZYE/Cas9+with+fusion+thumbnail.jpg CRISPR Primer - Type III Tools - Type II Tools https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596553583710-JP19MOCN4R6KXZS5RMU2/What+is+CRISPR.png CRISPR Primer - Type III Tools - What is CRISPR? https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1605909173500-G531CIC6N2PXPFAHT29E/Type%2BIII%2Binterference.jpg CRISPR Primer - Type III Tools - Type III Interference https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596208034985-LLFAH1P10HEYF0OQUP0I/type-iii-tools-amplified CRISPR Primer - Type III Tools - Amplified RNA Cleavage When Type III CRISPR complexes are bound to a transcript they produce cyclic oligoadenylates (cOA), which are secondary messengers that activate the RNA cleavage activity of Csm6, and each new cOA produced while the complex is bound amplifies the amount of RNA cleavage. This activity can be coupled to other systems to amplify RNA cleavage. This feature been used in a nucleic acid detection system called SHERLOCK V2, where the readout signal is based on the cleavage of RNA reporters - when the detector protein binds a target sequence, it begins cleaving the RNA reporter, triggering Csm6 to amplify the RNA cleavage signal output. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596206238287-ACBFJ1N1XRWSD1S2BAPG/type-iii-tools-rna-targeting CRISPR Primer - Type III Tools - Programed RNA Targeting The ability of Type III systems guided by crRNA to bind and cleave RNAs provides a method to “knock-down” the levels of specific RNAs in a controlled manner when the DNA cleavage activities are disabled. Programed degradation of RNA has been demonstrated in cells with their own Type III systems by providing crRNAs. Delivery and expression of Type III system components in cells that do not have a Type III system could be used in a similar way. https://www.thebaileylab.org/crispr-primer/type-i-tools monthly 0.5 2022-10-14 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1594931202288-CI2R1A2VP1SF4JYKNPQR/type-i-tools-abundance CRISPR Primer - Type I Tools - Abundance Type I CRISPR systems are the most abundant in nature, found in a large number of both bacterial and archaeal genomes, including strains of interest to humans – from pathogens to industrially useful strains involved in food and drug production. This raises the possibility of “reprogramming” cells with an endogenous Type I systems by simply providing a new crRNA. This could have several applications. A crRNA that targets the genome can result in cell death, potentially useful as antimicrobial tool. crRNAs delivered along with a repair template could be used for gene editing. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1594931961250-DZMN9S0LUM7NN7AITPFF/type-i-tools-processive CRISPR Primer - Type I Tools - Processive Cleavage Cas3 is has both nuclease and helicase activities, which allows it to unwind double-stranded DNA and degrade the non-target strand in a 3’ to 5’ direction. While this is a problem for precise cuts, researchers have begun to take advantage of this capability to introduce large deletions in eukaryotic and prokaryotic genomes. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1595257675763-HJKIWH2C98Z5DSTADKZ3/type-i-tools-subunits CRISPR Primer - Type I Tools - Subunit Modules Cascade’s multiple subunits and relatively large size makes it unsuited for applications that require streamlined systems, but that modularity may offer more opportunities to engineer additional functions by modifying domains or attaching proteins with useful activities. For example, adding transcriptional activators and repressors could be used for targeted gene expression regulation, while adding proteins that make DNA alterations could be used for targeted genetic and epigenetic editing. For example, Cascade-FokI endonuclease fusions have been used to generate double stranded breaks for gene editing applications. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1621451813227-0TJLOTCQ4SS0I7A06QZV/Cas9+with+fusion+thumbnail.jpg CRISPR Primer - Type I Tools - Type II Tools https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596491759325-KXETTEH9A856IRB522AN/Type+III+fragment+release.png CRISPR Primer - Type I Tools - Type III Tools https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596553532453-5XP8ZS4Z1D4KYV50SQOS/What+is+CRISPR.png CRISPR Primer - Type I Tools - What is CRISPR? https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596491809073-U0L5MLO3LRLHDWU0UQ7A/Cascade.png CRISPR Primer - Type I Tools - Type I Interference https://www.thebaileylab.org/crispr-primer/type-i-interference monthly 0.5 2022-10-14 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1595006212911-OGBDCYBG22E2D590P0MZ/type-i-degredation CRISPR Primer - Type I Interference After the Cascade binds the target strand, Cascade recruits Cas3, a protein with both a nuclease and a helicase domain. Cas3 nicks a portion of the exposed non-target strand, activating its helicase activity. With the helicase activated, Cas3 unwinds the DNA and degrades the non-target strand in a 3’ to 5’ direction. This activity results destruction of the DNA target, blocking the phage infection and providing immunity. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596052039148-4C6BDF384IZOB9HIOC0S/type-ii-target-search CRISPR Primer - Type I Interference Cascade has to sort through the sea of double-stranded DNA in a cell to find a very specific, and rare, DNA target – a sequence that matches its crRNA. Unwinding all that DNA to check for regions complementary to the crRNA spacer would not be efficient. Instead, Cascade scans double-stranded DNA and binds to locations with a protospacer adjacent motif (PAM) sequence. In the original foreign DNA fragment used to generate the CRISPR array, and the PAM is found next to the protospacer, the sequence that is added as a CRISPR array spacer. Cascade “looks” for the PAM sequence in double-stranded DNA without having to unwind it. Though the PAM sequence is not unique to the phage DNA target, only searching near a PAM significantly reduces the number of locations to unwind. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596034712877-38EJV7NXF1BF43DOXCLC/Cascade-and-Cas9-structure CRISPR Primer - Type I Interference Type I systems are the most wide-spread CRISPR systems in nature. Like the more-well known Type II systems, Type I systems provide immunity by specifically degrading phage DNA. Type I systems use a CRISPR complex known as Cascade (CRISPR-associated complex for antiviral defense), that contains multiple proteins assembled on the crRNA. Unlike the Type II Cas9 protein, which both recognizes and cleaves the double-stranded DNA targets, Cascade doesn’t have DNA nuclease activity. The DNA cleavage is done by Cas3, a nuclease that, in most cases, is not part of Cascade but is recruited after target binding by Cascade. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1594932494280-YCU8W97SIB350LUAVEYC/type-i-unwinding CRISPR Primer - Type I Interference Binding to the PAM causes Cascade to begin unwinding the double-stranded DNA, exposing the target strand. As complementary target strand bases bind to crRNA, the DNA strands continue to separate, and a portion of the now single-stranded non-target strand is spooled out of Cascade. The PAM binding step also helps reduce the that the CRISPR system would cause autoimmunity by targeting and cleaving the copy of the spacer sequence in the CRISPR array. Though the PAM is part of the original foreign DNA sequence, it is removed when the spacer is inserted into the CRISPR array. This means only the foreign DNA will have a PAM next to the target sequence. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1621450897314-LKZ2SPUW50YDXKCVDDYB/Cas9+cleaving+DNA+thumbnail.png CRISPR Primer - Type I Interference - Type II Interference https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1605908721677-0AYYRKJ91BEUSBHVJQWM/bitmap.jpg CRISPR Primer - Type I Interference - Type III Interference https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596553410443-VH0LBFU16VVZHC57XGP3/What+is+CRISPR.png CRISPR Primer - Type I Interference - What is CRISPR? https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1605908777229-ACJA3WOUK8XZ676XKKEE/Cascade%2Bmodule%2Badditions.jpg CRISPR Primer - Type I Interference - Type I Tools https://www.thebaileylab.org/crispr-primer/type-iii-interference monthly 0.5 2022-10-14 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596155015227-NZ1RVGF9217F07X0PODN/type-iii-targeting CRISPR Primer - Type III Interference Type III CRISPR complexes target RNA transcripts and use their crRNA to specifically bind complementary sequences through base pairing. This binding triggers several activities within the complex. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596204905103-EQK963Q25VI0IM0MQQLA/type-iii-complex CRISPR Primer - Type III Interference Type III CRISPR systems are unique in that they only cleave phage DNA that is actively being transcribed. They are also capable of triggering cell death if an infection can’t be stopped, a strategy that would kill the host cell but prevent the infection from spreading to nearby cells. Type III CRISPR complexes are made up of multiple proteins assembled on the crRNA and can cleave RNA and DNA. They can also trigger RNA cleavage activity of Csm6 family proteins, which are not part of the complex. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1646952050920-LM9ZU1TI5HJR8MS6USJO/PFS.png CRISPR Primer - Type III Interference - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596156377602-8CWKRB7WH23CO06J9O0H/type-iii-ssDNA-and-Csm6 CRISPR Primer - Type III Interference After binding, the complex quickly cleaves single-stranded DNA (ssDNA) within the phage genome, and, at the same time, the complex starts converting ATP into cyclic oligoadenylates (cOAs). cOAs, which act as second messengers, bind to Csm6 proteins and trigger their RNA cleavage activity. Active Csm6 cleavage is not limited to phage RNA, but also cleaves host RNA. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596160239924-H1FKN3FKV4HQADIQ8RJI/type-iii-deactivation CRISPR Primer - Type III Interference Transcript binding also triggers slow cleavage of the transcript, at multiple sites within the region complementary to the crRNA. Once cleaved, the resulting RNA fragments are released and the Type III complex is deactivated. The slow rate of cleavage prior to RNA release acts as a timer, constraining how long the DNA cleavage and cOA production activities proceed. The complexity of Type III interference allows for different outcomes depending on the conditions of an infection. If the infection is cleared early, deactivation of DNA cleavage and cOA production activities can limit the potential collateral damage to the host’s own DNA and RNA. If it takes longer to clear the infection, the cumulative amount of active Csm6 may cause cleavage of enough host RNA to lead to cell dormancy, which provides more time to destroy the invading phage. In situations when the phage cannot be destroyed, Csm6 activity could lead to cell death, preventing the infection from spreading to nearby cells. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1621451002900-MF7TJKA1SJ7A9P5KJKFD/Cas9+cleaving+DNA+thumbnail.png CRISPR Primer - Type III Interference - Type II Interference https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1595273382179-VSPU8EAZNJQN98R33JHE/Cascade.png CRISPR Primer - Type III Interference - Type I Interference https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596553488534-F33WLNAVGMHWPXD3H1P0/What+is+CRISPR.png CRISPR Primer - Type III Interference - What is CRISPR? https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596492067620-AZH6KCXU8NCQXIP8ZNSS/Type+III+fragment+release.png CRISPR Primer - Type III Interference - Type III Tools https://www.thebaileylab.org/crispr-primer/type-ii-tools monthly 0.5 2022-10-14 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1620750133175-KGPXL1Q4WZA3J4AB6B2A/Cas9-simplicity CRISPR Primer - Type II Tools - Simplicity and Flexibility CRISPR-Cas9 system interference only requires three components: the Cas9 protein, a crRNA containing the spacer sequence for targeting, and a trans-activating crRNA (tracrRNA), making it relatively easy to deliver into many cell types, from bacteria to archaea to eukaryotes. Only he the crRNA sequence needs to be changed to redirect the complex to a new sequence, and the crRNA can be fused to tracrRNA, forming a single guide RNA (sgRNA), further simplifying the system. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1620748856767-YZ69LCL34C7PEWY8Q2NE/cas9-precision CRISPR Primer - Type II Tools - Precision CRISPR-Cas9 systems cleave both the target and non-target DNA strand at a single location, generating a blunt cut at a specific distance from the PAM. This provides a predictable cut location, providing researchers have taken advantage of for a range of genetic engineering tools. At their most basic, Cas9 tools act as a precise pair of scissors, introducing cuts that allow for targeted deletions or insertions, often by taking advantage of DNA repair capabilities of cells, particularly non-homology end joining (NHEJ) and homology-directed repair (HDR). https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1620749457782-23K7NPBIMX5SIFO0XS96/Cas9-tools-targeting CRISPR Primer - Type II Tools - Targeting Researchers can use the programable targeting of the Cas9 complex to guide effector domains with a variety of activities beyond DNA cleavage. A Cas9 complex with the cleavage activity inactivated can still target and bind to a specific DNA sequence and will carry any fused domains along with it. For example, a Cas9 fusion to a transcriptional activator can be targeted to a region just upstream of a gene to induce transcription. Fusions with a fluorescent protein can be used to visualize the location of specific genetic sequences in a cell. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1605909578524-O85326CJXY6NDNHFRGY9/Cascade%252Bmodule%252Badditions.jpg CRISPR Primer - Type II Tools - Type I Tools https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1601414950912-G6P18TSUWMCCLLQLIRUQ/Type+III+fragment+release.png CRISPR Primer - Type II Tools - Type III Tools https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596553583710-JP19MOCN4R6KXZS5RMU2/What+is+CRISPR.png CRISPR Primer - Type II Tools - What is CRISPR? https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1621452127810-CJDHBIE59IT6T5EM837P/Cas9+cleaving+DNA+thumbnail.png CRISPR Primer - Type II Tools - Type II Interference https://www.thebaileylab.org/crispr-primer/type-ii-interference monthly 0.5 2022-10-14 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1620926578848-H67YZWA9WJMUTNWYPSIK/Type+II+target+serach CRISPR Primer - Type II Interference Cas9 complexes target DNA sequences that match their crRNAs, but cells are filled with double-stranded DNA, and sequences that match the crRNA are rare – if they are even present. Unwinding all that DNA to check for regions complementary to the crRNA spacer would not be efficient. Instead, the Cas9 complex searches for protospacer adjacent motif (PAM) sequences in double-stranded DNA. In the original foreign DNA fragment used to generate the CRISPR array, and the PAM is found next to the protospacer, the sequence that is added as a CRISPR array spacer. The Cas9 complex identities the PAM without needing to first unwind the DNA. Though the PAM sequence is not unique to the phage DNA target, only searching near a PAM significantly reduces the number of locations to unwind. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1618881172441-GP7LHG9MI5PXVYCOZ3OC/cas9 CRISPR Primer - Type II Interference Type II systems, also known as CRISPR-Cas9 systems, are widely-known because of their use as genetic engineering tools, which was the subject of the recent Nobel Prize in Chemistry, awarded to awarded to Emmanuelle Charpentier and Jennifer Doudna. Type II systems identify and cleave double-stranded DNA from phages, and use a CRISPR complex containing a single protein, Cas9, and two RNAs. In addition to the crRNA found in all CRISPR complexes, Type II complexes have a tracrRNA (trans-activating crRNA), a small RNA that plays a role in the assembly and activation of the Cas9 complex and includes a region that complements a portion of the crRNA. The Cas9 complex both recognizes and cleaves the double-stranded DNA targets. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1619053036517-VCFAUAL6S6V2MEZ35NUT/DNA-cleavage-by-cas9 CRISPR Primer - Type II Interference In Type II systems, the pairing of the target strand to the crRNA activates two nucleases domains, which each cleave one strand of the DNA in the same location, resulting in a blunt cut. This activity results in destruction of the DNA target, blocking the phage infection and providing immunity. CRISPR interference could cause autoimmunity if the complex was to target and cleave the spacer sequence in the host’s CRISPR array. In Type II systems, the PAM binding requirement reduces the chances of this, because the PAM is not part of the spacer sequence found in the CRISPR array, so the Cas9 complex will not bind to the array. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1620927237527-EBB8CGWTSU5PLJZ8LN8G/Cas9-binding.png CRISPR Primer - Type II Interference - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596553410443-VH0LBFU16VVZHC57XGP3/What+is+CRISPR.png CRISPR Primer - Type II Interference - What is CRISPR? https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1601905053147-P5COIRWX0HKKN2Q2IN0M/Cascade.png CRISPR Primer - Type II Interference - Type I Interference https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1605908721677-0AYYRKJ91BEUSBHVJQWM/bitmap.jpg CRISPR Primer - Type II Interference - Type III Interference https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1621452082107-ELAMWLDC5CLBFNIUZNRJ/Cas9+with+fusion+thumbnail.jpg CRISPR Primer - Type II Interference - Type II Tools https://www.thebaileylab.org/crispr-primer/crispr-comparisons monthly 0.5 2022-08-16 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1646851616393-IEX0QOUPH0QW8MDFPAV6/3.png CRISPR Primer - CRISPR Comparisons - Type III systems have complexes contain multiple protein subunits and a crRNA. The complex forms a worm-like structure, with two curved lines of protein subunits generally arranged into two curved lines, including a backbone of subunit repeats. Type III systems have multiple cleavage activities. In the complex itself, each backbone repeat makes a cut in the target RNA, and another subunit has non-specific DNA cleavage activity. That subunit also produces secondary messengers that activate Csm6-family proteins with RNA cleavage activity. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1650389826009-NK04QHFJFXZ937VXPGV5/type+I+cleavage.png CRISPR Primer - CRISPR Comparisons - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1650389606248-6DHQWVWZR67V5VX4V9BR/abundance.png CRISPR Primer - CRISPR Comparisons - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1646851562783-0U3S94RHMR2SVORT4QM4/2.png CRISPR Primer - CRISPR Comparisons - Type II systems have complexes made of a single protein (Cas9), a crRNA and a tracrRNA (trans-activating crRNA). The protein forms a bilobed structure, with the target DNA sitting in between the “jaws” of the nuclease and recognition lobes. The tracrRNA is complementary to a portion of the crRNA and binds to it in the complex; in many gene editing tools these two RNAs are combined into a single guide RNA. Two domains in the nuclease lobe each make a single cut, one in target strand and the other in the non-target strand, resulting in the target DNA being cleaved with blunt ends. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1650389859388-R2RRAMVVPB2JHL4IYV8L/type+III++cleavage.png CRISPR Primer - CRISPR Comparisons - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1650389141158-5XEFPNN0X8P4GCT61YFI/PAmcrispr.png CRISPR Primer - CRISPR Comparisons - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1646952050920-LM9ZU1TI5HJR8MS6USJO/PFS.png CRISPR Primer - CRISPR Comparisons - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1650389269992-6PM2BF64OKACAUEQJSSZ/PAMsearch.png CRISPR Primer - CRISPR Comparisons - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1646851582426-D9H43258PFMVTYRPKLZ9/1.png CRISPR Primer - CRISPR Comparisons - Type I systems use complexes known as Cascade (CRISPR-associated complex for antiviral defense), which contain multiple protein subunits and a crRNA. Cascade has a “seahorse” structure, with the protein subunits generally arranged into two twisted filaments. It has a backbone of repeating subunits spanning the head and body of the seahorse shape, with other subunit proteins flanking and making up the seahorse shape’s belly and tail. Cascade does not have DNA cleavage activity and recruits a separate protein, Cas3, to cleave target DNA that matches the crRNA. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1650389843186-QCD1UR039I0TIRNFOPIR/type+II+cleavage.png CRISPR Primer - CRISPR Comparisons - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.thebaileylab.org/crispr-primer/category/Interference monthly 0.5 https://www.thebaileylab.org/crispr-primer/category/Type+I monthly 0.5 https://www.thebaileylab.org/crispr-primer/category/Basic+Bio+to+Tools monthly 0.5 https://www.thebaileylab.org/crispr-primer/tag/Type+I+Tools monthly 0.5 https://www.thebaileylab.org/crispr-primer/tag/Type+III monthly 0.5 https://www.thebaileylab.org/crispr-primer/tag/Type+I monthly 0.5 https://www.thebaileylab.org/crispr-primer/tag/Interference monthly 0.5 https://www.thebaileylab.org/crispr-primer/tag/Tools monthly 0.5 https://www.thebaileylab.org/crispr-primer/tag/Type+II monthly 0.5 https://www.thebaileylab.org/crispr-primer/tag/System+tools monthly 0.5 https://www.thebaileylab.org/team daily 0.75 2023-01-30 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1570828579693-3O6ZB1FHA86XID8Z8KFI/BrianLearn.jpg Team https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1570828405910-VPJ9VY8HCX2I6K8ZFRWA/MorganBeckett.jpg Team https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1626267674093-4K4W71RPOQX68Q4ET9IS/Elvar+Bjarkason.jpg Team - Make it stand out Elvar Bjarkason https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1570637282348-Q0WYOZTEZ9RIUU8SVWHL/Scott%2Bsmallfile.jpg Team Scott Bailey smiling. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1594652514622-0DUG71IL825WU5M13I14/Charlie+Lenihan.jpg Team Charlie Lenihan https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/6a6613de-17cd-42b7-b303-de131b75b7a0/Brynn+Durecki.jpg Team - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/7a06e874-0d37-44f5-9e47-2bf990675c44/Zoe-Hutchinson.jpg Team - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.thebaileylab.org/join-us daily 0.75 2020-11-11 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1572385029750-RSIE74LFU5L2LPAK4L87/bottles+darkened.jpg Join Us https://www.thebaileylab.org/research daily 0.75 2022-01-11 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1572384740299-XJE3NBY38VUQKZMHFQYL/akta+darkened.jpg Research https://www.thebaileylab.org/publications daily 0.75 2022-08-31 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1572385729354-O0EPD5QV33L7ZI9IYFGF/bookshelf+darkened.jpg Publications https://www.thebaileylab.org/contact daily 0.75 2022-07-20 https://www.thebaileylab.org/crispr-primer-landing daily 0.75 2022-04-25 https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596641322175-PNCMLKHSMYBZUKET24OQ/system+components CRISPR Primer CRISPR systems are diverse and several different types have been identified, but they have a number of common components. The “library” of CRISPR systems is a DNA array that alternates between short repeat regions and “spacer” sequences that come from past invaders. The name CRISPR comes from an early description of these arrays: Clustered Regularly Interspaced Short Palindromic Repeats. Genes that code for the proteins involved in CRISPR are called cas (CRISPR associated) genes, usually located near the CRISPR array. The spacers in the CRISPR arrays are transcribed and processed into crRNAs that are each used to match a single spacer. Invading genetic sequences are targeted and destroyed by CRISPR complexes. These complexes all contain at least one protein and a crRNA but are highly diverse, and different CRISPR systems are often distinguished by their complexes. In some systems the CRISPR complex has multiple protein subunits, while others have a single protein. Some also have additional components, such as the Type II CRISPR/Cas9 system’s tracrRNA. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1595272921728-CSIFV24TFT4Q96SF8RQ4/Cascade+module+additions.png CRISPR Primer - Type I Tools https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1621450560678-M44TCI8I8SW1STUIJYBB/Cas9+with+fusion+thumbnail.jpg CRISPR Primer - Type II Tools https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596465185894-NDBLBUIJXLHTUZ8GBHQ3/Type+III+fragment+release.png CRISPR Primer - Type III Tools https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596641716558-JEF8TUK0Z73BMR08VEP9/Cells+with+and+without+crispr CRISPR Primer CRISPR is most commonly known as a set of gene editing tools - even showing up in TV shows and movies, recognized by the general public. While CRISPR is relatively new to researchers, to bacteria and archaea, it is an ancient adaptive immune system. Though we often think of microbes as the targets of immune systems, they themselves face a number of threats, including viruses and other sources of foreign genetic material that could hijack their cells. CRISPR is just one of the defenses that bacteria and archaea use to fend off these attacks, but is of particular interest because it adapts to target new threats. Phages, which are viruses that infect bacteria and archaea, are a common target of CRISPR systems. Bacteria and archaea with CRISPR systems build libraries of short genetic sequences from past invaders, and use CRISPR complexes to identify those invaders if they show up again. Matching genetic sequences are destroyed, preventing an infection. https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1650917603115-JOP6AGYTEBIPBPNYZC4W/distribution+thumbnail+16x9.png CRISPR Primer - CRISPR Comparisons CRISPR Comparisons https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1594830097651-3MVLOVWKPCA1NASXB5MX/interference-thumb.jpg CRISPR Primer - Type I Interference https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1621449836447-UCFESU6OTDLBNFYCI9JN/Cas9+cleaving+DNA+thumbnail.png CRISPR Primer - Type II Interference https://images.squarespace-cdn.com/content/v1/5d960e694de3d96d190eb8c7/1596478060873-G6VRXAL80KS5LQ94MLTE/Type%2BIII%2Binterference.jpg CRISPR Primer - Type III Interference https://www.thebaileylab.org/privacy-and-cookie-policy daily 0.75 2021-11-29