Open research questions in CRISPR and Genetic Engineering
788 gap statements mined from CRISPR and Genetic Engineering papers in our 7.9M-paper local library, which holds 4,648 papers on the topic — drawn mostly from each paper's own stated research gap, future-work, challenge and limitation notes, and its abstract. The ones listed below are a selection still marked open; each names the study that raised it, with a DOI link where the paper has one.
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What the literature leaves open
Requires prior sequence information for guide RNA design. The RNA switch needs to be activated by a specific DNA regulator. The detection sensitivity needs to approach a single genome copy per microliter.
Programmable Genome Sensing with Visual, Fluorescence, and Glucometer Readings: Cell-Free In Vitro Translation Approach Using RNA Switch-CRISPR · 2026 · DOIConventional detection methods require long incubation periods. CRISPR/Cas12a-based detection technologies have limitations, such as requiring additional exonuclease enzymes or having strict requirements for canonical PAM sequences.
PAM-free dsDNA substrates enable Cas12a trans-cleavage activation for sensitive detection of Vibrio harveyi · 2026 · DOIThe distribution of CRISPR-Cas systems across the Leptospira genus is unknown. The lack of knowledge about CRISPR-Cas systems in the Leptospira genus hinders the development of gene-editing systems for this genus. The study aims to fill this knowledge gap by identifying CRISPR-Cas systems in the Leptospira genus.
Bioinformatic Identification of CRISPR–Cas Systems in Leptospira Genus: An Update on Their Distribution Across 77 Species · 2025 · DOIThe study highlights the need for a rapid and streamlined diagnostic method. The challenge of reducing processing time while maintaining detection limits is also mentioned.
A Novel Diagnostic Tool for West Nile Virus Lineage 1a and 2 Using a CRISPR-Cas12a System · 2025 · DOIThe lack of treatments and vaccinations for WNV makes early diagnosis crucial. Existing diagnostic techniques may not be rapid or sensitive enough. The paper identifies the need for a more streamlined and efficient diagnostic method.
A Novel Diagnostic Tool for West Nile Virus Lineage 1a and 2 Using a CRISPR-Cas12a System · 2025 · DOIThe inherent limitations of traditional sensor systems, which lack specificity and sensitivity. The need for innovative approaches to enhance the functionality of biosensors. The challenge of detecting non-nucleic acid targets using split CRISPR/Cas12a systems.
Advancements and Applications of Split Technology in CRISPR/Cas12a: Transforming Molecular Diagnostics and Biosensing · 2025 · DOIAvoiding the need for commercial oligo pools or large-scale synthesis. Developing a cost-effective strategy for generating starting libraries. Overcoming the limitations of conventional PCR, which is optimized for fidelity.
The Power of Old Hats: Rediscovering Inosine-EpPCR to Create Starting Libraries for Whole-Cell-SELEX · 2025 · DOIThe need for large, commercially available libraries of synthetic oligonucleotides with randomized sequences. The lack of a cost-effective strategy for generating starting libraries. The potential for revisiting established techniques to address current challenges in aptamer development.
The Power of Old Hats: Rediscovering Inosine-EpPCR to Create Starting Libraries for Whole-Cell-SELEX · 2025 · DOITraditional microbial genome-editing techniques are restricted by their limited scalability and technical complexity. The lack of precise genome editing technologies hinders the full utilization of microbial potential in synthetic biology, environmental remediation, and biotechnology.
Microbial Genome Editing with CRISPR–Cas9: Recent Advances and Emerging Applications Across Sectors · 2025 · DOILimited efficiency of the CRISPR-dCas9 system for gene expression activation. Complexity of the Ehrlich pathway and the need for precise regulation of key genes.
CRISPRa-Mediated Triple-Gene Activation of ARO10, ARO80, and ADH2 for Enhancing 2-Phenylethanol Biosynthesis via the Ehrlich Pathway in Saccharomyces cerevisiae · 2025 · DOIRandom mutagenesis lacks target specificity and reproducibility and produces off-target mutations. Homologous recombination exhibits low efficiency and limited scalability and requires selectable markers and long homology arms. A fundamental bottleneck is the delivery of CRISPR components across the robust glycoproteinaceous cell wall characteristic of many strains.
CRISPR-Cas Technology Turns Chlamydomonas reinhardtii into a Flagship for Algal Biotechnology · 2025 · DOITraditional detection methods are laborious and time-consuming. Molecular technologies, including conventional PCR and qPCR, have limitations. There is a need for rapid and efficient field detection methods.
Comparative Evaluation of PCR-Based, LAMP and RPA-CRISPR/Cas12a Assays for the Rapid Detection of Diaporthe aspalathi · 2024 · DOIThe paper highlights the need for efficient and cost-effective methods for delivering the CRISPR/Cas system to plant cells.
Further research is needed to improve the efficiency and host range of Agrobacterium spp.
The gene mutation rate in the hydrodynamic tail-vein injection procedure is limited, - The pressure on the liver might lead to heart failure, - Viral vectors have raised mutagenicity and safety concerns, - Oncogenicity and immunogenicity…
From scissors to editors: how the evolution of precision is redefining therapeutic genome editing · 2026 · DOIFurther study on the treatment of Cystic Fibrosis, - Exploration of non-viral vectors, - Investigation of the applications of gene editing in various…
From scissors to editors: how the evolution of precision is redefining therapeutic genome editing · 2026 · DOIAI-guided gRNA libraries, - mechano-responsive scaffolds, - long-term tracking of epigenetic…
Further studies are needed to explore the functionality of the CRISPR-Cas system in Leptospira species, - The use of CRISPR-Cas systems for gene editing in Leptospira species should be investigated, - The study of CRISPR-Cas systems in other bacterial species can provide insights into their evolution…
Bioinformatic Identification of CRISPR–Cas Systems in Leptospira Genus: An Update on Their Distribution Across 77 Species · 2025 · DOIThe technology is limited by the PAM sequence, - The technology is completed in two steps, which may interfere with the detection results owing to aerosol contamination, - The detection of a single bacterium using CRISPR/Cas12a-based biosensors…
CRISPR/Cas12a-Based Biosensing: Advances in Mechanisms and Applications for Nucleic Acid Detection · 2025 · DOISimplifying the reaction process. Enhancing precision. Broadening the scope of disease detection. Facilitating the translation of research findings into clinical practice.
CRISPR/Cas12a-Based Biosensing: Advances in Mechanisms and Applications for Nucleic Acid Detection · 2025 · DOISensitivity limitations without pre-amplification. Specificity issues. Complex sample preparation.
CRISPR-Cas-Based Diagnostics in Biomedicine: Principles, Applications, and Future Trajectories · 2025 · DOIInnovative solutions are needed to accelerate the translation of CRISPR/Cas system-based biosensors into practical applications, - Further research is needed to improve the specificity and sensitivity of CRISPR/Cas system-based biosensors, - The development of integrated biosensing systems, such as microfluidic devices and portable biosensors, is a promising area…
Recent Advances in Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated Proteins System-Based Biosensors · 2025 · DOIFurther development of molecular diagnostic tests, - Exploration of other applications of CRISPR-Cas proteins in disease…
Engineering split crRNA-Cas12a platforms that incorporate aptamer or allosteric ribozyme modules, - Expanding the detection repertoire to non-nucleic acid targets, - Advancement of split crRNA designs and delivery methodologies for live-cell imaging and real-time…
Advancements and Applications of Split Technology in CRISPR/Cas12a: Transforming Molecular Diagnostics and Biosensing · 2025 · DOIEfforts in the future should be oriented toward integrating multi-omics for enhanced accuracy predictions, - Building tools that can cope with novel emerging genomic contexts across various microorganisms, - Ongoing optimization of prediction models…
Microbial Genome Editing with CRISPR–Cas9: Recent Advances and Emerging Applications Across Sectors · 2025 · DOI
Most-cited papers in CRISPR and Genetic Engineering
- A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity · Science · 2012 · 15,745 citations
- Multiplex Genome Engineering Using CRISPR/Cas Systems · Science · 2013 · 14,247 citations
- RNA-Guided Human Genome Engineering via Cas9 · Science · 2013 · 8,551 citations
- The new frontier of genome engineering with CRISPR-Cas9 · Science · 2014 · 6,261 citations
- Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage · Nature · 2016 · 5,215 citations
- Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells · Science · 2013 · 4,984 citations
- Search-and-replace genome editing without double-strand breaks or donor DNA · Nature · 2019 · 4,538 citations
- CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity · Science · 2018 · 4,329 citations
- Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage · Nature · 2017 · 4,034 citations
- Nucleic acid detection with CRISPR-Cas13a/C2c2 · Science · 2017 · 3,740 citations
Most recent work
- CRISPR-on-Chip for Point-of-Care Diagnostics · ACS Nano · 2026
- Engineered TnpB genome editors for plants and human cells identified by ribonucleoprotein mutational scanning · Nature Biotechnology · 2026
- High-efficiency, transgene-free plant genome editing by viral delivery of an engineered TnpB · Nature Plants · 2026
- Non-Viral CRISPR carriers: transient delivery with lasting effects · Drug Delivery · 2026
- Frequent, context-dependent effects of human genetic variation on Cas9 activity revealed by population-scale GUIDE-seq-2 and deep combinatorial CHANCE-seq profiling · bioRxiv · 2026
- Programmable genome editing in human cells using RNA-guided bridge recombinases · Science · 2026
- Customizing CRISPR–Cas PAM specificity with protein language models · Nature Biotechnology · 2026
- Engineering delivery platforms for CRISPR-Cas and their applications in healthcare, agriculture and beyond · Nanoscale Advances · 2026
- Targeted delivery of genome editors in vivo · Nature Biotechnology · 2026
- Structural modeling reveals phage proteins that manipulate bacterial immune signaling · Science · 2026
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