No abstract

The RNA-guided CRISPR–Cas9 nuclease has revolutionized genome engineering, yet its mechanism for DNA target selection is not fully understood. A crucial step in Cas9 target recognition involves unwinding of the DNA duplex to form a three-stranded R-loop structure. Work reported here demonstrates direct detection of Cas9-mediated DNA unwinding by a combination of site-directed spin labeling and molecular dynamics simulations. The results support a model in which the unwound nontarget strand is stabilized by a positively charged patch located between the two nuclease domains of Cas9 and reveal uneven increases in flexibility along the unwound nontarget strand upon scissions of the DNA backbone. This work establishes the synergistic combination of spin-labeling and molecular dynamics to directly monitor Cas9-mediated DNA conformational changes and yields information on the target DNA in different stages of Cas9 function, thus advancing mechanistic understanding of CRISPR–Cas9 and aiding future technological development.

A thorough understanding of the oxidation chemistry of cycloalkanes is integral to the development of alternative fuels and improving current fuel performance. An important class of reactions essential to this chemistry is the hydrogen migration; however, they have largely been omitted from the literature for cycloalkanes. The present work investigates all of the hydrogen migration reactions available to methylcyclopentane, ethylcyclopentane, methylcyclohexane, and ethylcyclohexane. The kinetic and thermodynamic parameters have been studied by a combination of computational methods and compared to their corresponding n-alkyl and methylalkyl counterparts to determine the effect that the cycloalkane ring has on these reactions. In particular, although the alkylcycloalkyl activation energies for the dominant 1,4, 1,5, and 1,6 H-migration are higher than in n-alkyl and methylalkyl radicals, because several of the rotors needed to form the transition state are locked into place as part of the cycloalkane ring, the A-factors are higher for the alkylcycloalkyl reactions, making the rates closer to the noncyclic systems, at higher temperatures. The results presented here suggest that the relative importance of each H-migration pathway differs from the trends predicted by either the n-alkyl or methylalkyl radical systems. Of particular interest is the observation that since the barrier height of the 1,4 H-migration is only 3-5 kcal mol(-1) higher than the 1,5 H-migration in the methyl and ethylcycloalkyl radicals, compared to a difference of roughly 7 kcal mol(-1) in similar reactions for both the n-alkyl and methylalkyl radicals, the 1,4 H-migrations in alkylcycloalkyl radicals will be more important in the overall mechanism than would be predicted based on the n-alkyl and methylalkyl radicals. These results have important combustion model implications, particularly for fuels with high cycloalkane content.

No abstract

In a type II Clustered-Regularly-Interspersed-Short-Palindromic-Repeats (CRISPR) system, RNAs derived from the CRISPR locus complex with the CRISPR-associated (Cas) protein Cas9 to form an RNA-guided nuclease that cleaves double-stranded DNAs at specific sites. In recent years, the CRISPR-Cas9 system has been successfully adapted for genome engineering in a wide range of organisms. Studies have indicated that a series of conformational changes in Cas9, coordinated by the RNA and the target DNA, direct the protein into its active conformation, yet, details on these conformational changes, as well as their roles in the mechanism of function of Cas9, remain to be elucidated. Here, nucleic-acid dependent conformational changes in Streptococcus pyogenes Cas9 (SpyCas9) were investigated using the method of site-directed spin labeling (SDSL). Single nitroxide spin labels were attached, one at a time, at one of the two native cysteine residues (Cys80 and Cys574) of SpyCas9, and the spin-labeled proteins were shown to maintain its function. X-band continuous-wave electron paramagnetic resonance spectra of the nitroxide attached at Cys80 revealed conformational changes of SpyCas9 that are consistent with a large scale domain re-arrangement upon binding to its RNA partner. The results demonstrate the use of SDSL to monitor conformational changes in CRISPR-Cas9, which will provide key information for understanding the mechanism of CRISPR function.