Clustered regularly interspaced palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins, particularly Cas9, have provided unprecedented control on targeting and editing specific DNA sequences. If the target sequences are prone to folding into noncanonical secondary structures, such as G-quadruplex (GQ), the conformational states and activity of the CRISPR-Cas9 complex may be influenced, but the impact has not been assessed. Using single molecule FRET, we investigated structural characteristics of the complex formed by CRISPR-Cas9 and target DNA, which contains a potentially GQ forming sequence (PQS) in either the target or the nontarget strand (TS or NTS). We observed different conformational states and dynamics depending on the stability of the GQ and the position of PQS. When PQS was in NTS, we observed evidence for GQ formation for both weak and stable GQs. This is consistent with R-loop formation between TS and crRNA releasing NTS from Watson-Crick pairing and facilitating secondary structure formation in it. When PQS was in TS, R-loop formation was adequate to maintain a weak GQ in the unfolded state but not a GQ with moderate or high stability. The observed structural heterogeneity within the target dsDNA and the R-loop strongly depended on whether the PQS was in TS or NTS. We propose these variations in the complex structures to have functional implications for Cas9 activity.

The most commonly known relationship between the macromolecules of life – DNA, RNA and protein – is the central dogma which states that information flows from DNA to RNA through transcription and from RNA to protein through translation. The discovery of non-coding RNAs has altered and expanded this picture by revealing many more functions of RNA as well as different ways nucleic acids and proteins interact. For example, tRNAs act as a link between mRNA and ribosomes in translation, ribosomal RNA together with proteins make up the main translation machinery, riboswitches enable mRNA to regulate its own activity, miRNA and siRNA regulate gene expression through RNA interference. A notable recent addition to this list is the adaptive prokaryotic CRSIPR immune system where RNA molecules guide proteins to destroy the invading viral DNA. The CRISPR systems were made famous by the discovery of the Cas9 endonuclease, a single RNA-guided protein, which can perform target search, recognition and cleavage without other proteins involved. This has made Cas9 the golden tool for gene editing, making the latter cheaper, faster and easier than it has ever been before.

The Streptococcus pyogenes CRISPR/Cas9 (SpCas9) nuclease has been widely applied in genetic engineering. Despite its importance in genome editing, aspects of the precise molecular mechanism of Cas9 activity remain ambiguous. In particular, because of the lack of a method with high spatio-temporal resolution, transient interactions between Cas9 and DNA could not be reliably investigated. It therefore remains controversial how Cas9 searches for protospacer adjacent motif (PAM) sequences. We have developed single-molecule Förster resonance energy transfer (smFRET) assays to monitor transient interactions of Cas9 and DNA in real time. Our study shows that Cas9 interacts with the PAM sequence weakly, yet probing neighboring sequences via facilitated diffusion. This dynamic mode of interactions leads to translocation of Cas9 to another PAM nearby and consequently an on-target sequence. We propose a model in which lateral diffusion competes with three-dimensional diffusion and thus is involved in PAM finding and consequently on-target binding. Our results imply that the neighboring sequences can be very important when choosing a target in genetic engineering applications.

Since its discovery, the CRISPR–Cas9 system has been in the center of attention for its promising applications in genome editing. However, in order to apply this system successfully in genetic engineering, all aspects of its molecular mechanism have to be well understood. One of the best ways to investigate the intricacies of the molecular mechanism is single-molecule studies as they allow real-time observation of the kinetic processes and provide high spatiotemporal resolution. This chapter describes single-molecule fluorescence resonance energy transfer experiments carried out to investigate the Cas9 protein from Streptococcus pyogenes, providing information on the effects of target truncation, Cas9-induced double-stranded DNA dynamics, and target search.

Most everyday processes in life involve a necessity for an entity to locate its target. On a cellular level, many proteins have to find their target to perform their function. From gene-expression regulation to DNA repair to host defense, numerous nucleic acid-interacting proteins use distinct target search mechanisms. Several proteins achieve that with the help of short RNA strands known as guides. This review focuses on single-molecule advances studying the target search and recognition mechanism of Argonaute and CRISPR (clustered regularly interspaced short palindromic repeats) systems. We discuss different steps involved in search and recognition, from the initial complex prearrangement into the target-search competent state to the final proofreading steps. We focus on target search mechanisms that range from weak interactions, to one- and three-dimensional diffusion, to conformational proofreading. We compare the mechanisms of Argonaute and CRISPR with a well-studied target search system, RecA.