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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Targeted amplification for enhanced detection of biothreat agents by next-generation sequencing

Background: Historically, identification of causal agents of disease has relied heavily on the ability to culture the organism in the laboratory and/or the use of pathogen-specific antibodies or sequence-based probes. However, these methods can be limiting: Even highly sensitive PCR-based assays must be continually updated due to signature degradation as new target strains and near neighbors are sequenced. Thus, there has been a need for assays that do not suffer as greatly from these limitations and/or biases. Recent advances in library preparation technologies for Next-Generation Sequencing (NGS) are focusing on the use of targeted amplification and targeted enrichment/ capture to ensure that the most highly discriminating regions of the genomes of known targets (organism-unique regions and/or regions containing functionally important genes or phylogenetically-discriminating SNPs) will be sequenced, regardless of the complex sample background. Results: In the present study, we have assessed the feasibility of targeted sequence enhancement via amplification to facilitate detection of a bacterial pathogen present in low copy numbers in a background of human genomic material. Our results indicate that the targeted amplification of signature regions can effectively identify pathogen genomic material present in as little as 10 copies per ml in a complex sample. Importantly, the correct species and strain calls could be made in amplified samples, while this was not possible in unamplified samples. Conclusions: The results presented here demonstrate the efficacy of a targeted amplification approach to biothreat detection, using multiple highly-discriminative amplicons per biothreat organism that provide redundancy in case of variation in some primer regions. Importantly, strain level discrimination was possible at levels of 10 genome equivalents. Similar results could be obtained through use of panels focused on the identification of amplicons targeted for specific genes or SNPs instead of, or in addition to, those targeted for specific organisms (ongoing gene-targeting work to be reported later). Note that without some form of targeted enhancement, the enormous background present in complex clinical and environmental samples makes it highly unlikely that sufficient coverage of key pathogen(s) present in the sample will be achieved with current NGS technology to guarantee that the most highly discriminating regions will be sequenced.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Sequencing Intractable DNA to Close Microbial Genomes

Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled intractable resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such difficult regions in the non-contiguous finished Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. These developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing

Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa–a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3–V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Comparative Sequence Analysis of Multidrug-Resistant IncA/C Plasmids from Salmonella enterica

Determinants of multidrug resistance (MDR) are often encoded on mobile elements, such as plasmids, transposons, and integrons, which have the potential to transfer among foodborne pathogens, as well as to other virulent pathogens, increasing the threats these traits pose to human and veterinary health. Our understanding of MDR among Salmonella has been limited by the lack of closed plasmid genomes for comparisons across resistance phenotypes, due to difficulties in effectively separating the DNA of these high-molecular weight, low-copy-number plasmids from chromosomal DNA. To resolve this problem, we demonstrate an efficient protocol for isolating, sequencing and closing IncA/C plasmids from Salmonella sp. using single molecule real-time sequencing on a Pacific Biosciences (Pacbio) RS II Sequencer. We obtained six Salmonella enterica isolates from poultry, representing six different serovars, each exhibiting the MDR-Ampc resistance profile. Salmonella plasmids were obtained using a modified mini preparation and transformed with Escherichia coli DH10Br. A Qiagen Large-Construct kitTM was used to recover highly concentrated and purified plasmid DNA that was sequenced using PacBio technology. These six closed IncA/C plasmids ranged in size from 104 to 191 kb and shared a stable, conserved backbone containing 98 core genes, with only six differences among those core genes. The plasmids encoded a number of antimicrobial resistance genes, including those for quaternary ammonium compounds and mercury. We then compared our six IncA/C plasmid sequences: first with 14 IncA/C plasmids derived from S. enterica available at the National Center for Biotechnology Information (NCBI), and then with an additional 38 IncA/C plasmids derived from different taxa. These comparisons allowed us to build an evolutionary picture of how antimicrobial resistance may be mediated by this common plasmid backbone. Our project provides detailed genetic information about resistance genes in plasmids, advances in plasmid sequencing, and phylogenetic analyses, and important insights about how MDR evolution occurs across diverse serotypes from different animal sources, particularly in agricultural settings where antimicrobial drug use practices vary.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Role of the site of synaptic competition and the balance of learning forces for Hebbian encoding of probabilistic Markov sequences

The majority of distinct sensory and motor events occur as temporally ordered sequences with rich probabilistic structure. Sequences can be characterized by the probability of transitioning from the current state to upcoming states (forward probability), as well as the probability of having transitioned to the current state from previous states (backward probability). Despite the prevalence of probabilistic sequencing of both sensory and motor events, the Hebbian mechanisms that mold synapses to reflect the statistics of experienced probabilistic sequences are not well understood. Here, we show through analytic calculations and numerical simulations that Hebbian plasticity (correlation, covariance, and STDP) with pre-synaptic competition can develop synaptic weights equal to the conditional forward transition probabilities present in the input sequence. In contrast, post-synaptic competition can develop synaptic weights proportional to the conditional backward probabilities of the same input sequence. We demonstrate that to stably reflect the conditional probability of a neuron’s inputs and outputs, local Hebbian plasticity requires balance between competitive learning forces that promote synaptic differentiation and homogenizing learning forces that promote synaptic stabilization. The balance between these forces dictates a prior over the distribution of learned synaptic weights, strongly influencing both the rate at which structure emerges and the entropy of the final distribution of synaptic weights. Together, these results demonstrate a simple correspondence between the biophysical organization of neurons, the site of synaptic competition, and the temporal flow of information encoded in synaptic weights by Hebbian plasticity while highlighting the utility of balancing learning forces to accurately encode probability distributions, and prior expectations over such probability distributions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Achieving Health Security and Threat Reduction through Sharing Sequence Data

With the rapid development and broad applications of next-generation sequencing platforms and bioinformatic analytical tools, genomics has become a popular area for biosurveillance and international scientific collaboration. Governments from countries including the United States (US), Canada, Germany, and the United Kingdom have leveraged these advancements to support international cooperative programs that aim to reduce biological threats and build scientific capacity worldwide. A recent conference panel addressed the impacts of the enhancement of genomic sequencing capabilities through three major US bioengagement programs on international scientific engagement and biosecurity risk reduction. Here, the panel contrasted the risks and benefits of supporting the enhancement of genomic sequencing capabilities through international scientific engagement to achieve biological threat reduction and global health security. The lower costs and new bioinformatic tools available have led to the greater application of sequencing to biosurveillance. Strengthening sequencing capabilities globally for the diagnosis and detection of infectious diseases through mutual collaborations has a high return on investment for increasing global health security. International collaborations based on genomics and shared sequence data can build and leverage scientific networks and improve the timeliness and accuracy of disease surveillance reporting needed to identify and mitigate infectious disease outbreaks and comply with international norms. Further efforts to promote scientific transparency within international collaboration will improve trust, reduce threats, and promote global health security.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Fine Structures in the Main Sequence Revealed by Gaia Data Release 2

The Hertzsprung–Russell diagram (HRD) is fully examined using the Fourier analysis. This work shows more stars are above the gap in the lower main sequence than below it, and this implies that stars spend more time above the gap while they undergo variability associated with the {sup 3}He instability. The enhanced HRD also shows the width of the gap is not linear and depends on the G{sub BP}−G{sub RP} color up until G{sub BP}−G{sub RP}=2.7. Beyond this color limit, the gap is hardly seen. Besides, a new low density region is revealed for the first time centered at M {sub G} ≈ 10.7 and G {sub BP} − G {sub RP} ≈ 2.8, which is below the lower right corner of the gap. This work also shows that the main sequence appears to have fine stripes where stellar densities are relatively low or high compared to their adjacent regions on the main sequence. These stripes can be seen throughout the main sequence of stars redder than G {sub BP} − G {sub RP} = 0.8 and are not limited to any specific color or spectral type. Slopes of these features are different from the main sequence, but are pretty consistent throughout the main sequence, with a few exceptions. We are perplexed by these new features, but the complexities of stellar atmospheric features and opacities of dwarfs may have caused these patterns.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2015

Sequencing to Station in 12 Months (Targeting Orbital 5 Launch, March 30th)

The Biomolecule Sequencer is a Commercial Off-The-Shelf device developed by Oxford Nanopore Technologies and implements a method of DNA sequencing unlike any other current sequencers. The device measures changes in electrical current through a nanopore depending on the sequence of the DNA strand that is passing through it. Since the technology is built on nanometer-scale ion pores, the hardware itself is exceptionally small (3 x 1 x 58 inches), lightweight (less than 120 grams with USB cable), and powered only by a USB connection. The sequencing device is permanent, while the flow cells, to which the samples are added, are periodically replaced. The goal of our upcoming technology demonstration on ISS is to provide evidence that DNA sequencing in space is possible, which holds the exciting potential to enable the identification of microorganisms, monitor changes in microbes and humans in response to spaceflight, and possibly aid in the detection of DNA-based life elsewhere in the universe.

microorganisms↗
NASA NTRS1992

Protein sequences and redox titrations indicate that the electron acceptors in reaction centers from heliobacteria are similar to Photosystem I

Photosynthetic reaction centers isolated from Heliobacillus mobilis exhibit a single major protein on SDS-PAGE of 47 000 Mr. Attempts to sequence the reaction center polypeptide indicated that the N-terminus is blocked. After enzymatic and chemical cleavage, four peptide fragments were sequenced from the Heliobacillus mobilis apoprotein. Only one of these sequences showed significant specific similarity to any of the protein and deduced protein sequences in the GenBank data base. This fragment is identical with 56% of the residues, including both cysteines, found in highly conserved region that is proposed to bind iron-sulfur center Fx in the Photosystem I reaction center peptide that is the psaB gene product. The similarity to the psaA gene product in this region is 48%. Redox titrations of laser-flash-induced photobleaching with millisecond decay kinetics on isolated reaction centers from Heliobacterium gestii indicate a midpoint potential of -414 mV with n = 2 titration behavior. In membranes, the behavior is intermediate between n = 1 and n = 2, and the apparent midpoint potential is -444 mV. This is compared to the behavior in Photosystem I, where the intermediate electron acceptor A1, thought to be a phylloquinone molecule, has been proposed to undergo a double reduction at low redox potentials in the presence of viologen redox mediators. These results strongly suggest that the acceptor side electron transfer system in reaction centers from heliobacteria is indeed analogous to that found in Photosystem I. The sequence similarities indicate that the divergence of the heliobacteria from the Photosystem I line occurred before the gene duplication and subsequent divergence that lead to the heterodimeric protein core of the Photosystem I reaction center.

NASA Discipline Number 52-30↗
DOE OSTI2024

Long- and short-read sequencing methods discover distinct circular RNA pools in Lotus japonicus

Circular RNAs (circRNAs) are covalently closed single-stranded RNAs, generated through a back-splicing process that links a downstream 5′ site to an upstream 3′ end. The only distinction in the sequence between circRNA and their linear cognate RNA is the back splice junction. Their low abundance and sequence similarity with their linear origin RNA have made the discovery and identification of circRNA challenging. We have identified almost 6000 novel circRNAs from Lotus japonicus leaf tissue using different enrichment, amplification, and sequencing methods as well as alternative bioinformatics pipelines. The different methodologies identified different pools of circRNA with little overlap. We validated circRNA identified by the different methods using reverse transcription polymerase chain reaction and characterized sequence variations using nanopore sequencing. We compared validated circRNA identified in L. japonicus to other plant species and showed conservation of high-confidence circRNA-expressing genes. This is the first identification of L. japonicus circRNA and provides a resource for further characterization of their function in gene regulation. CircRNAs identified in this study originated from genes involved in all biological functions of eukaryotic cells. The comparison of methodologies and technologies to sequence, identify, analyze, and validate circRNA from plant tissues will enable further research to characterize the function and biogenesis of circRNA in L. japonicus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

An evaluation of point-insertion sequences for incremental Delaunay tessellations

Currently, incremental algorithms may be seen as the lowest-cost computational methods to generate Delaunay tessellations in several point distributions. In this work, eight point-insertion sequences in incremental algorithms for generating Delaunay tessellations are evaluated. More specifically, four point-insertion sequences in incremental algorithms for generating Delaunay tessellations are proposed: with orders given by the red–black tree with in-order and level-order traversals, spiral ordering, and H-indexing. These four incremental algorithms with such sequences are compared with four incremental algorithms with point-insertion orders given by the following sequences: the Hilbert and Lebesgue curves, cut-longest-edge kd-tree, and random order. Six 2-D and seven 3-D point distributions are tested, with sets ranging from 25,000 to 8,000,000 points. The results of computational and storage costs of these eight algorithms are analyzed. It follows that the incremental algorithm with a point-insertion sequence in the order given by the cut-longest-edge kd-tree shows the lowest computational and storage costs of the sequences tested.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

The relation between lignin sequence and its 3D structure

Background: Lignin, the second most abundant biopolymer on earth, plays a major structural role in plants, conferring mechanical strength and regulating water conduction. Understanding the three-dimensional structure of lignin is important for fundamental reasons as well as engineering plants towards lignin valorization. Lignin lacks a specific primary sequence, making its average chemical composition the focus of most recent studies. However, it remains unclear whether the 3D structure of lignin molecules depends on their sequence. Methods: In this work, we performed all-atom molecular dynamics simulation of three S/G-lignin molecules with the same average composition but different sequence. Results: A detailed statistical analysis of the radius of gyration and relative shape anisotropy reveals that the lignin sequence has no statistically significant effect on the global three-dimensional structure. We found however, that homopolymers of C-lignin with the same molecular weight have smaller radii of gyration than S/G-lignin. We attribute this to lower hydroxyl content of C-lignin, which makes it more compact and rigid. Conclusions: The 3D structure of lignin is influenced by the overall content of monomeric units and interunit linkages and not by its precise primary sequence. General Significance: Lignin is assumed to not have a well-defined primary structure. The results presented here demonstrate there are no significant differences in the global 3D structure of lignin molecules with the same average composition but different primary sequence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Sequence conservation of protein binding segments in intrinsically disordered regions

Highlights: • Sequence conservation in protein-binding segments in IDRs is analyzed. • Functionally constraint residues in protein-binding segments in IDRs are conserved. • Evolutionary distance should be considered in the comparison of IDRs. • Cryptic binding regions may influence sequence conservation of IDRs. Intrinsically disordered proteins are proteins with intrinsically disordered regions (IDRs) that do not adopt a globular structure in their free state. IDRs have unique regions having protein-binding segments of which play pivotal roles in many biological processes. The binding sites in IDRs are heterogeneous in terms of their sequence conservation: some are conserved and others are not. We have been running a database of intrinsically disordered proteins, IDEAL, and collecting such binding segments, which are called protean segments (ProSs), within it. In this study, we compared the sequence conservation of ProSs, structural domains (SDs), and IDRs other than ProSs (non-ProSs) and found that i) functionally constrained residues in ProSs tend to be conserved, ii) the distribution of conservation scores of ProSs is similar to those of SDs but not non-ProSs, and iii) ProSs found in human proteins are mostly conserved only in vertebrates. These results indicate that the conservation patterns in ProSs principally follow the general rules found in SDs. However, we need to consider evolutionary distance when comparing IDR sequences because ProSs can readily emerge and disappear over the course of protein evolution. Moreover, many ProSs may remain to be identified, which may account for the heterogeneity of the sequence conservation of IDRs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Focusing ions at atmospheric pressure using nonlinear DC voltage sequences applied to a stacked ring ion guide

Many modern ion mobility (IM) and mass spectrometers (MS) operate under low pressure (= 10 Torr) and employ high voltage radiofrequencies (RF) to provide ion confinement. Unfortunately, RF effectiveness drastically decreases as pressure increases, and few techniques for focusing ions at elevated pressures exist. Here we demonstrate a new approach for focusing ions at atmospheric pressure (AP) by applying nonlinear DC voltage sequences following quadratic and power (exponential) functions to a stacked ring ion guide. In this work, we used ion trajectory simulations to rigorously explore how ions react to nonlinear electric fields and validate the simulations with a set of ion current measurements performed at AP. Ion trajectory simulations show that ions initially defocus near the entrance of the device but then become intensely focused as they travel through the device. Contour plots for both nonlinear voltage sequences show electric field lines that increasingly curve inwards as a function of distance, resulting in spatial ion focusing. Experimental ion current and spot size measurements were performed at AP using a 10-cm stacked ring ion guide and a segmented Faraday cup detector. Quadratic sequences produced ~5% smaller spot sizes (~22.8 mm) and ~25% higher ion current compared to a linear voltage sequence (~24.0 mm). Alternatively, power sequences produced ~64% smaller spot sizes (~8.7 mm), albeit with ~10x lower ion current. However, both nonlinear voltage sequences produced similar ion currents at the center of the Faraday cup detector, indicating that higher ion densities are achieved when using nonlinear voltage gradients. These results demonstrate a new way to focus ions at AP, and the capabilities demonstrated here provide fundamental insights on how to keep ions inside analytical devices at elevated pressures without RF.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

An extended methodology for automated calculations of non-Boltzmann kinetic sequences: H + C 2 H 2 + X and combustion impact

It is generally assumed in phenomenological kinetic models that bimolecular reactions only occur between species whose rovibrational energy follows a Boltzmann (thermal) distribution. That is, any complexes initially formed in non-Boltzmann distributions are assumed to be thermalized by energy-transferring collisions prior to bimolecular reactions. Given the high mole fractions of reactive species, X, in combustion environments, reactive collisions of the complexes with X often occur on the same timescale as energy-transferring collisions – yielding sequences proceeding through non-Boltzmann intermediates across multiple potential energy surfaces. Recent studies have shown that such non-Boltzmann kinetic sequences can have substantial impact on the global reactivity in combustion systems. Simulations of these non-Boltzmann reaction sequences, which can be described in phenomenological kinetic models via chemically termolecular reactions, require that rovibrational excitation from one potential energy surface be carried over to the next. Here this paper presents an extended theoretical and computational methodology that couples multiple master equations and derives rate constants for phenomenological reactions describing the conversion of thermal reactants to thermal products for use in phenomenological kinetic schemes. The methodology is then implemented using in-house scripts for non-Boltzmann sequences involving C2H$^*_3$ + X (with X = O 2 , H, and OH) where C 2 H$^*_3$ is formed via H + C 2 H 2 association – which were identified as having strong potential for influencing combustion predictions in a recent study. The results reveal that non-Boltzmann reaction sequences for X = O 2 (the primary focus of this paper) significantly alters the total conversion rate from H + C 2 H 2 to products and product branching fractions from those of thermal sequential pathways. Furthermore, the present results demonstrate that non-Boltzmann reaction sequences have significant impact – as high as an order of magnitude – on predicted ignition delay times. Similarly, they yield significantly different dependence of ignition delay times with temperature and O 2 mole fraction – yielding signatures that are likely observable experimentally.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Effects of Charge Sequence Pattern and Lysine-to-Arginine Substitution on the Structural Stability of Bioinspired Polyampholytes

A comprehensive study focusing on the combined influence of the charge sequence pattern and the type of positively charged amino acids on the formation of secondary structures in sequence-specific polyampholytes is presented. The sequences of interest consisting exclusively of ionizable amino acids (lysine, K; arginine, R; and glutamic acid, E) are (EKEK) 5 , (EKKE) 5 , (ERER) 5 , (ERRE) 5 , and (EKER) 5 . The stability of the secondary structure was examined at three pH values in the presence of urea and NaCl. The results presented here underscore the combined prominent effects of the charge sequence pattern and the type of positively charged monomers on secondary structure formation. Additionally, (ERRE) 5 readily aggregated across a wide range of pH. In contrast, sequences with the same charge pattern, (EKKE) 5 , as well as the sequences with the equivalent amino acid content, (ERER) 5 , exhibited no aggregate formation under equivalent pH and concentration conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Local Chain Dynamics in Sequence-Controlled Polymers as a Tunable Handle for Rare Earth Sequestration

Chain dynamics govern the intricate behaviors of proteins, underpinning functions such as catalysis, recognition, and stimulus response, and are an increasingly appreciated aspect of structure–function relationships. Analogously, manipulating chain dynamics and structure in abiotic polymers via sequence control is an exciting, yet underexplored, strategy for improving material functions. In this work, we report a systematic study relating the sequence of polymeric sequestrants to their structure and dynamics, as well as to their binding affinity and selectivity for model substrates, rare earth elements (REEs). A series of sequence-controlled polymers with metal chelating, solubilizing, and structure forming monomers was synthesized via multiblock polymerization, yielding compositionally identical polymers with spectroscopically resolved domains and distinct morphologies. Using a combination of small-angle X-ray scattering and 19 F NMR relaxometry measurements, we connected differences in polymer structure and dynamics to polymer sequence variables such as the patchiness (density) of the structure forming monomer and the location of the chelating monomer. Furthermore, we found that, relative to calcium, all polymers in the series collapse more and have slower dynamics when binding REEs (lanthanum and lutetium) , though the extent of these effects were sequence-dependent and localized to specific domains within the polymer. Notably, sequence-controlled polymers that exhibited the largest conformational and dynamic changes upon binding REEs also bound REEs with the greatest affinity and modest selectivity. Collectively, these results correlate monomer patterning with dynamics, morphology, and REE binding performance en route to the development of efficient and selective macromolecular chelators.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Genome dependent Cas9/gRNA search time underlies sequence dependent gRNA activity

Abstract CRISPR-Cas9 is a powerful DNA editing tool. A gRNA directs Cas9 to cleave any DNA sequence with a PAM. However, some gRNA sequences mediate cleavage at higher efficiencies than others. To understand this, numerous studies have screened large gRNA libraries and developed algorithms to predict gRNA sequence dependent activity. These algorithms do not predict other datasets as well as their training dataset and do not predict well between species. Here, to better understand these discrepancies, we retrospectively examine sequence features that impact gRNA activity in 44 published data sets. We find strong evidence that gRNA sequence dependent activity is largely influenced by the ability of the Cas9/gRNA complex to find the target site rather than activity at the target site and that this drives sequence dependent differences in gRNA activity between different species. This understanding will help guide future work to understand Cas9 activity as well as efforts to identify optimal gRNAs and improve Cas9 variants.

59 BASIC BIOLOGICAL SCIENCES↗