scholarly journals CRISPR System: From Adaptive Immunity to Genome Editing

2017 ◽  
Vol 01 (02) ◽  
pp. 76-91
Author(s):  
Jennifer Doudna

CRISPR-Cas9 is a revolutionary genome-editing tool. Understanding how Cas9 recognizes DNA and how to control its function will be critical in improving the system. We used single-molecule FRET to elucidate a key validation step during DNA target recognition. We also used X-ray crystallography to show how a Cas9 inhibitor is able to permit DNA binding but prevent cleavage. Finally, CRISPR research is notable not just for the exciting applications, but also for its profound ethical implications.

2017 ◽  
Author(s):  
Yavuz S. Dagdas ◽  
Janice S. Chen ◽  
Samuel H. Sternberg ◽  
Jennifer A. Doudna ◽  
Ahmet Yildiz

AbstractThe Cas9 endonuclease is widely utilized for genome engineering applications by programming its single-guide RNA and ongoing work is aimed at improving the accuracy and efficiency of DNA targeting. DNA cleavage of Cas9 is controlled by the conformational state of the HNH nuclease domain, but the mechanism that governs HNH activation at on-target DNA while reducing cleavage activity at off-target sites remains poorly understood. Using single-molecule FRET, we identified an intermediate state of S. pyogenes Cas9, representing a conformational checkpoint between DNA binding and cleavage. Upon DNA binding, the HNH domain transitions between multiple conformations before docking into its active state. HNH docking requires divalent cations, but not strand scission, and this docked conformation persists following DNA cleavage. Sequence mismatches between the DNA target and guide RNA prevent transitions from the checkpoint intermediate to the active conformation, providing selective avoidance of DNA cleavage at stably bound off-target sites.


Author(s):  
Eaton E. Lattman ◽  
Thomas D. Grant ◽  
Edward H. Snell

This chapter provides an introduction to small angle solution scattering with particular reference to the complementary technique of X-ray crystallography and the relationship between the two. It describes at its most basic level the theoretical underpinnings of solution scattering starting from a single molecule and how this information is sampled in crystals versus in solution. A brief introduction is given to some of the primary types of structural information that can be obtained from experiments. The chapter concludes discussing some of the most common applications of the technique in structural biology, and where the future is likely headed.


2017 ◽  
Vol 114 (9) ◽  
pp. 2247-2252 ◽  
Author(s):  
Cornelius Gati ◽  
Dominik Oberthuer ◽  
Oleksandr Yefanov ◽  
Richard D. Bunker ◽  
Francesco Stellato ◽  
...  

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.


2012 ◽  
Vol 444 (3) ◽  
pp. 395-404 ◽  
Author(s):  
Ditte H. Welner ◽  
Søren Lindemose ◽  
J. Günter Grossmann ◽  
Niels Erik Møllegaard ◽  
Addie N. Olsen ◽  
...  

NAC (NAM/ATAF/CUC) plant transcription factors regulate essential processes in development, stress responses and nutrient distribution in important crop and model plants (rice, Populus, Arabidopsis), which makes them highly relevant in the context of crop optimization and bioenergy production. The structure of the DNA-binding NAC domain of ANAC019 has previously been determined by X-ray crystallography, revealing a dimeric and predominantly β-fold structure, but the mode of binding to cognate DNA has remained elusive. In the present study, information from low resolution X-ray structures and small angle X-ray scattering on complexes with oligonucleotides, mutagenesis and (DNase I and uranyl photo-) footprinting, is combined to form a structural view of DNA-binding, and for the first time provide experimental evidence for the speculated relationship between plant-specific NAC proteins, WRKY transcription factors and the mammalian GCM (Glial cell missing) transcription factors, which all use a β-strand motif for DNA-binding. The structure shows that the NAC domain inserts the edge of its core β-sheet into the major groove, while leaving the DNA largely undistorted. The structure of the NAC–DNA complex and a new crystal form of the unbound NAC also indicate limited flexibility of the NAC dimer arrangement, which could be important in recognizing suboptimal binding sites.


2018 ◽  
Vol 207 ◽  
pp. 251-265
Author(s):  
Subhas C. Bera ◽  
Tapas Paul ◽  
A. N. Sekar Iyengar ◽  
Padmaja P. Mishra

We have investigated the isomerization dynamics and plausible energy landscape of 4-way Holliday junctions (4WHJs) bound to integration host factor (IHF, a DNA binding protein), considering the effect of applied external force, by single-molecule FRET methods.


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