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Nuclear localization sequence

A nuclear localization sequence (NLS), also referred to as a nuclear localization signal, is a short amino acid motif within a protein that functions as a targeting signal to mediate the active transport of the protein from the cytoplasm into the nucleus through the nuclear pore complex (NPC).^[1] These sequences are essential for the nuclear import of many proteins involved in cellular processes such as gene regulation, DNA repair, and signal transduction, ensuring that nuclear-specific functions occur in the appropriate compartment.^[2] The classical NLS, which is the most well-characterized type, consists of either a single cluster of basic amino acids (monopartite NLS, e.g., PKKKRKV from the SV40 large T antigen) or two such clusters separated by a 10–12 amino acid linker (bipartite NLS, e.g., KRPAATKKAGQAKKKK from nucleoplasmin).^[1] In contrast, non-classical NLSs exhibit greater diversity, lacking strict basic residue patterns and often including motifs like the PY-NLS (e.g., R/K/H(X)₂₋₅PY at the C-terminus), which are recognized by different transport receptors.^[2] First identified in the 1980s through studies on viral proteins like the SV40 large T antigen, NLSs have since been found in approximately 45% of yeast proteins and play critical roles in both normal physiology and pathologies, including cancer and viral infections.^[1]^[2] The mechanism of NLS-dependent nuclear import relies on the Ran GTPase cycle and karyopherin receptors (importins). For classical NLSs, the sequence binds to the importin α subunit in the cytoplasm, forming a complex with importin β that docks to the NPC and translocates the cargo; upon reaching the nucleus, RanGTP binding to importin β dissociates the complex, releasing the protein for nuclear function.^[1] Non-classical pathways may bypass importin α, directly engaging importin β family members or alternative mechanisms like nucleoporin interactions, with transport regulated by post-translational modifications such as phosphorylation.^[2] This selective trafficking maintains nuclear-cytoplasmic compartmentalization, underscoring the NLS's role as a fundamental determinant of protein localization in eukaryotic cells.^[1]

Fundamentals

Definition and Function

A nuclear localization sequence (NLS) is a short peptide sequence composed of specific amino acids that functions as a targeting signal, directing cargo proteins from the cytoplasm into the nucleus via active transport pathways.^[3] This sequence was first identified as an autonomous motif capable of specifying nuclear localization in studies of viral proteins.^[4] The primary function of an NLS is to mediate nuclear import by enabling interaction with the nuclear transport machinery, which ensures efficient delivery of proteins required for nuclear activities.^[1] In doing so, it counterbalances nuclear export signals (NES) to regulate the overall localization and shuttling of proteins, thereby maintaining cellular homeostasis and responding to physiological cues.^[3] Unlike passive diffusion, which restricts entry through nuclear pore complexes (NPCs) to molecules smaller than approximately 40-60 kDa, NLS-directed active transport allows larger proteins to traverse these selective barriers, overcoming size limitations that would otherwise prevent nuclear accumulation.^[1]^[3] NLS motifs exhibit evolutionary conservation across eukaryotic species, reflecting their critical role in compartmentalizing essential nuclear processes such as transcription and DNA replication.^[3] This widespread presence underscores the NLS's indispensability for the spatial organization of eukaryotic genomes and proteomes.^[1]

Sequence Composition and Structure

Nuclear localization sequences (NLSs) are typically composed of short stretches of amino acids enriched in positively charged residues, particularly lysine (K) and arginine (R), which form clusters that impart a net positive charge essential for their recognition in nuclear import processes.^[2] These basic residues contribute to electrostatic interactions through their positively charged side chains. The high density of these residues results in a net positive charge that distinguishes NLSs from other protein motifs and underscores their role in targeting.^[5] NLSs exhibit considerable length variability, generally spanning 4 to 20 amino acids, allowing for diverse architectures within proteins. Monopartite NLSs consist of a single cluster of 4–8 basic residues, while bipartite NLSs feature two such clusters separated by a flexible linker of 10–12 residues, enabling modular recognition patterns.^[2] This variability accommodates evolutionary adaptations across species, yet maintains functional conservation in nuclear targeting.^[6] Structurally, NLSs often reside in intrinsically disordered regions of proteins, characterized by high flexibility and low conformational stability, as evidenced by elevated B-factors and reduced structure determination rates in crystallographic analyses.^[7] Upon interaction with transport factors, these disordered segments can adopt alpha-helical or extended conformations, facilitating specific engagements without rigid tertiary structures.^[7] Consensus patterns for NLSs emphasize charge clustering, with monopartite motifs commonly following the sequence K(K/R)X(K/R)—where X is any amino acid—and bipartite motifs adhering to (K/R)X_{10-12}(K/R)_3, prioritizing basic residue density over strict sequence identity.^[8] These patterns, derived from early mutational studies, highlight the tolerance for minor variations while requiring sufficient positive charge for efficacy.^[5]

Types and Classification

Classical NLS

The classical nuclear localization sequence (cNLS) refers to a family of well-characterized motifs that mediate nuclear import through specific interaction with importin α, consisting of either monopartite or bipartite variants defined by clusters of basic amino acids. Monopartite cNLSs feature a single stretch of 4-6 basic residues, typically following a consensus pattern of K(K/R)X(K/R) where X is any amino acid, and are exemplified by the sequence PKKKRKV from the SV40 large T-antigen. This motif was first identified as sufficient for directing nuclear accumulation when fused to reporter proteins, with mutations disrupting the basic cluster abolishing localization. Bipartite cNLSs, in contrast, comprise two basic clusters separated by a 9-12 residue linker of non-basic amino acids, as seen in the nucleoplasmin sequence KRPAATKKAGQAKKKK. This structure allows cooperative binding, enhancing import efficiency compared to monopartite forms. Recognition of cNLSs occurs primarily through the armadillo (ARM) repeat domain of importin α, a concave surface groove formed by 10 tandem ARM repeats that accommodates the basic residues via electrostatic interactions. Monopartite sequences bind to the major site (ARM repeats 2-4), while bipartite motifs engage both the major site with the C-terminal cluster and the minor site (ARM repeats 7-8) with the N-terminal cluster, forming a high-affinity complex with dissociation constants around 10 nM. Structural studies confirm that conserved residues like tryptophans in the ARM pockets stabilize these interactions through hydrogen bonding and van der Waals contacts with the NLS lysines and arginines. Classical NLSs are prevalent in numerous nuclear proteins, including transcription factors such as c-Myc and p53, as well as core histones like H2B, facilitating their essential roles in gene regulation and chromatin assembly. Experimental validation through site-directed mutagenesis, such as alanine substitutions in the basic clusters of SV40 or nucleoplasmin NLSs, consistently demonstrates loss of nuclear localization and reduced import rates, underscoring the functional necessity of these motifs for cargo recognition by the importin α/β heterodimer.

Non-classical NLS

Non-classical nuclear localization sequences (ncNLS) are peptide motifs that facilitate nuclear import of proteins but lack the characteristic clusters of basic arginine and lysine residues found in classical NLS. Instead, they often incorporate hydrophobic, proline-tyrosine, or glycine-rich elements and are typically recognized directly by importin-β family members, such as transportin (importin-β2) or importin-8, without requiring the adaptor importin-α. These signals exhibit greater sequence and structural variability, frequently adopting disordered conformations or integrating with functional domains like RNA-binding regions, enabling diverse recognition mechanisms distinct from the canonical import pathway.^[3] A well-characterized example is the M9 domain in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), a glycine-rich sequence (residues 263–289: FGNYNNQSSNFGPMKGGNFGGRSSGPY) that functions as both an import and export signal by binding transportin. This motif, located near the C-terminus, is essential for the shuttling of hnRNP A1 and exemplifies how RNA-binding domains can serve as ncNLS. Another key variant is the PY-NLS, defined by a consensus pattern of an N-terminal hydrophobic or basic stretch followed by [R/H/K]-(X)_2–5-PY, which also engages transportin; subtypes include the hydrophobic PY-NLS (hPY-NLS) in hnRNP A1 and the basic PY-NLS (bPY-NLS) in yeast Hrp1 protein. In yeast, the KIPIK motif within the Matα2 homeodomain acts as a ncNLS, directing nuclear localization independently of basic clusters through direct interaction with import factors.^[9]^[3]^[10] ncNLS display considerable structural diversity, encompassing disordered peptides, coiled-coil regions, and multifunctional domains that couple localization with other cellular processes. For U snRNPs, nuclear import relies on a composite ncNLS involving the 2,2,7-trimethylguanosine (m³G) cap and Sm core domain, which recruit adaptor proteins like snurportin1 to bridge interaction with importin-β. Recent identifications, such as the motif RRKLPVGRS binding importin-8, underscore the expanding repertoire of ncNLS and their roles in specialized transport, as demonstrated in post-2020 bioinformatics and biochemical analyses.^[11]^[12]^[13]

Discovery and History

Initial Identification

The initial observations of selective nuclear accumulation of proteins emerged in the 1970s through microinjection experiments in Xenopus laevis frog oocytes, pioneered by John Gurdon, which demonstrated that certain cytoplasmic proteins could migrate into and accumulate within the nucleus, while others remained excluded. These studies, using radioactively labeled proteins injected into oocytes, revealed that nuclear import was highly selective and dependent on intrinsic properties of the proteins, laying the groundwork for identifying specific targeting mechanisms.^[14] A pivotal advancement came in 1982 with experiments by Colin Dingwall and Ronald Laskey, who investigated nucleoplasmin, a abundant nuclear protein in Xenopus oocytes. By creating fusion proteins that combined fragments of nucleoplasmin with a non-nuclear protein (pyruvate kinase), they identified a specific 14-amino-acid polypeptide domain in the C-terminal tail of nucleoplasmin that was sufficient to direct the fusion protein to the nucleus upon microinjection into oocytes.90242-2) This demonstrated that a discrete sequence within the protein acted as a portable signal for nuclear import, independent of the protein's overall structure. In 1984, David Kalderon, William D. Richardson, and colleagues further refined this concept using deletion mapping on the simian virus 40 (SV40) large T-antigen, a viral protein known to localize to the nucleus. Through systematic deletions and point mutations expressed in mammalian cells, they pinpointed a short basic sequence, PKKKRKV (residues 126-132), as essential for nuclear accumulation, showing that its removal caused cytoplasmic retention while its addition to a non-nuclear protein conferred nuclear targeting.90457-4) These early findings established a paradigm shift in understanding nuclear import, proving it to be an active, signal-mediated process rather than a passive diffusion driven solely by protein size or net charge.90242-2)90457-4)

Subsequent Developments

In the 1990s, significant progress in NLS research included the identification of cytosolic proteins that bind NLS sequences, serving as receptors for nuclear import. These receptors, later characterized as importin α and β, were first described by Adam and Gerace in 1991 through experiments demonstrating their specific interaction with NLS-bearing substrates in permeabilized cell assays.90197-W) Concurrently, the characterization of bipartite NLS motifs advanced, with Robbins et al. in 1991 delineating the nucleoplasmin NLS as consisting of two basic clusters separated by a flexible linker, establishing a key subclass of classical signals through mutagenesis and import assays.90198-X) The 2000s saw the expansion to non-classical NLS types, exemplified by the discovery of the PY-NLS in 2009, a proline-tyrosine motif recognized by karyopherin β2 (transportin), which facilitates import of RNA-binding proteins like hnRNP A1 without relying on importin α. Structural insights from X-ray crystallography further elucidated binding interfaces, as Conti et al. in 2000 resolved the importin α armadillo repeat domain interacting with both monopartite and bipartite NLS peptides, revealing hydrophobic and electrostatic contacts that confer specificity.00107-6) Post-2015 developments incorporated computational advances, with a 2025 deep learning study by Li et al. introducing a neural network model trained on diverse protein sequences to predict NLS motifs, uncovering hidden patterns such as subtle secondary structure influences on localization efficiency. In parallel, engineering innovations emerged, including hairpin internal NLS (hiNLS) sequences integrated into CRISPR-Cas9 in 2025, which form stable stem-loop structures to boost nuclear accumulation and editing efficiency in primary human T cells by up to twofold compared to traditional terminal NLS fusions. Experimental methodologies for NLS validation evolved from early microinjection assays in Xenopus oocytes, which directly assessed import kinetics, to yeast two-hybrid systems in the 1990s for high-throughput receptor-cargo interaction screening, as demonstrated in studies mapping importin α binding partners. By the 2000s and beyond, live-cell imaging techniques, utilizing fluorescently tagged NLS reporters and confocal microscopy, enabled real-time observation of translocation dynamics in mammalian cells, providing quantitative data on import rates and pathway dependencies.

Mechanism of Action

Binding to Transport Receptors

The binding of nuclear localization sequences (NLSs) to transport receptors initiates the nuclear import process in eukaryotic cells. For classical NLSs, which include monopartite and bipartite motifs rich in basic amino acids such as lysine and arginine, the primary receptors are the importin α/β heterodimer. Importin α serves as an adaptor that directly recognizes the classical NLS through electrostatic interactions between the positively charged residues of the NLS and negatively charged pockets within the armadillo (ARM) repeats of importin α's C-terminal domain.^[3]^[15] These interactions occur primarily at the major binding site (ARM repeats 2-4) for monopartite NLSs and both major and minor sites (ARM repeats 6-8) for bipartite NLSs, resulting in high-affinity binding with dissociation constants (Kd) typically in the range of 1-10 nM.^[16]^[17] In this complex, importin α acts as an adaptor by linking the NLS-bearing cargo to importin β, which provides the interface for subsequent transport steps. The N-terminal importin β-binding (IBB) domain of importin α mediates this heterodimerization, ensuring specific recognition of classical NLSs while excluding non-classical variants.^[3]^[18] Non-classical NLSs, such as the PY-type motifs found in proteins like heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), bypass importin α and bind directly to members of the importin β family, notably transportin (also known as importin β2). This direct interaction involves hydrophobic and electrostatic contacts between the PY motif (characterized by a proline-tyrosine dipeptide near the C-terminus) and a concave surface on transportin, enabling selective import of these cargoes without an adaptor.^[19]^[3] Specificity in these binding events is enhanced by conformational changes in the receptors upon NLS engagement; for instance, NLS binding to importin α induces subtle shifts in the ARM repeats that optimize cargo affinity and prevent non-specific interactions. Additionally, competitors such as calreticulin can inhibit binding by associating with the NLS region of certain cargoes, like steroid hormone receptors, thereby masking the signal and blocking importin α recruitment.^[15]

Translocation Through Nuclear Pores

The nuclear pore complex (NPC) is a large macromolecular assembly with a molecular mass of approximately 120 MDa in vertebrate cells, composed of multiple copies of around 30 distinct nucleoporins arranged in an eightfold symmetric structure that spans the double membrane of the nuclear envelope. The central transport channel of the NPC has an inner diameter of about 40 nm, providing a conduit for molecular exchange between the cytoplasm and nucleus. Within this channel, the selective permeability barrier is formed by flexible, intrinsically disordered domains of FG-nucleoporins (FG-Nups), which contain numerous phenylalanine-glycine (FG) repeats; these domains create a dense, hydrogel-like meshwork through hydrophobic interactions that allows passive diffusion of molecules smaller than 40-60 kDa while impeding larger entities.31127-3)^[20]^[21] Translocation of the preformed NLS-cargo complex with importins through the NPC proceeds via a facilitated diffusion mechanism, where importin β mediates passage by transiently binding to the FG repeats lining the channel. These interactions occur through hydrophobic patches on the concave surface of importin β, enabling the complex to dissolve into the FG meshwork and advance via repeated association-dissociation cycles without a fixed track, thus supporting bidirectional transit. This model, supported by structural and biophysical studies, explains the high selectivity and speed of transport, as the low-affinity bindings (dissociation constants in the micromolar range) allow rapid equilibration across the barrier.^[22]^[23]00791-X) The translocation process itself is energetically passive, requiring no direct ATP consumption for movement through the pore, and is instead powered by the steep Ran-GTP concentration gradient across the nuclear envelope. This asymmetry, with Ran-GTP levels ~100- to 1000-fold higher in the nucleus due to localized guanine nucleotide exchange factor RCC1 and cytoplasmic GTPase-activating protein RanGAP1, provides the thermodynamic driving force for net import without fueling the diffusion step.^[24]^[25] NPCs exhibit high transport capacity, with single pores supporting translocation rates of up to ~1000 events per second for importin β-cargo complexes and a mass flux approaching 100 MDa per second under saturating conditions. For complexes up to 1 MDa, the transit time through the channel is typically less than 10 ms, though throughput saturates at elevated cargo concentrations due to competition for FG-binding sites, limiting concurrent passages to a few large complexes per pore.^[26]^[27]

Release and Recycling

Once the import complex has traversed the nuclear pore complex and entered the nucleus, the high concentration of Ran-GTP—generated by the chromatin-bound guanine nucleotide exchange factor RCC1—binds to importin β. This interaction induces a conformational change in importin β, shifting its dissociation constant (K_d) for importin α and the associated NLS-cargo from the nanomolar (nM) to micromolar (μM) range, thereby promoting rapid dissociation of the entire complex.^[28]^[29] Dissociation results in the release of the NLS-containing cargo protein into the nucleoplasm, freeing it to engage in nuclear-specific functions; for instance, transcription factors such as STAT1 can then bind DNA and initiate gene activation.^[1] Following cargo release, the importin β-Ran-GTP complex is exported back to the cytoplasm via the nuclear pore complex, while importin α is separately recycled by forming a ternary complex with the export receptor CAS and Ran-GTP. In the cytoplasm, RanGAP stimulates GTP hydrolysis on Ran, converting it to Ran-GDP and releasing importin β (and importin α from its complex), thereby regenerating free receptors for subsequent rounds of nuclear import.^[30]81773-6/fulltext) The nuclear Ran-GTP gradient is maintained by chromatin-associated RCC1, which preferentially exchanges GDP for GTP on Ran in the nucleus, ensuring directional transport; perturbations to this gradient, such as RCC1 depletion or RanGAP overexpression, significantly reduce nuclear import efficiency by slowing complex dissociation and recycling.^[31]^[32]

Significance and Applications

Roles in Cellular Biology

The nuclear localization sequence (NLS) plays a pivotal role in protein targeting by directing essential nuclear proteins from the cytoplasm to the nucleus, ensuring they reach their site of action for proper cellular function. For instance, DNA polymerase β contains a functional NLS in its N-terminal lyase domain, which facilitates its active transport into the nucleus independent of DNA binding, allowing it to participate in DNA repair and replication processes.^[33] Similarly, splicing factors such as SR proteins rely on NLS-like motifs, including arginine/serine-rich domains recognized by transportin-SR, to localize within the nucleus and assemble into speckles for pre-mRNA splicing.^[34] This targeted import maintains the nuclear proteome's integrity, preventing mislocalization that could disrupt genomic stability and RNA processing.^[7] In gene regulation, NLS motifs in transcription factors enable precise control of gene expression by facilitating their signal-dependent nuclear entry. The STAT family of transcription factors, such as STAT1 and STAT3, possess NLS sequences that become exposed upon tyrosine phosphorylation and dimerization, allowing binding to importin-α5 and subsequent nuclear translocation to activate target genes in response to cytokines or growth factors.^[35] For example, phosphorylated STAT1 interacts directly with importin-α, promoting its nuclear import and binding to specific DNA sequences to regulate interferon-stimulated genes.^[35] This mechanism ensures that transcriptional responses are tightly coupled to extracellular signals, modulating processes like immune activation and cell proliferation.^[36] NLS-mediated nuclear import is crucial for coordinating the cell cycle, particularly through the transport of cyclins and cyclin-dependent kinases (CDKs) that drive progression through mitotic phases. Cyclin A- and cyclin E-CDK complexes shuttle between the cytoplasm and nucleus via distinct NLS motifs on the cyclin subunit, enabling them to phosphorylate nuclear substrates and regulate DNA replication and mitosis.^[37] In yeast, cell cycle-dependent nuclear localization of transcription factors like SBF is governed by CDK phosphorylation adjacent to an NLS, which unmasks the signal for import during G1/S transition.^[38] This dynamic import ensures timely activation of cell cycle genes, synchronizing nuclear events with cytoplasmic checkpoints.^[39] Viruses exploit host NLS machinery to hijack the nucleus for replication, using viral proteins with embedded NLS to facilitate nuclear entry. The HIV-1 Rev protein contains an arginine-rich NLS that directly binds importin-β, enabling its nuclear import and subsequent export of unspliced viral RNAs via the Rev response element.^[40] This NLS-mediated trafficking allows Rev to accumulate in the nucleolus, where it coordinates viral gene expression and assembly, subverting host nuclear transport for efficient virion production.^[41] Such viral strategies highlight the NLS's vulnerability as a target for cellular invasion while underscoring its central role in nuclear homeostasis.^[42]

Associations with Diseases

Dysfunction or mutations in nuclear localization sequences (NLS) have been implicated in various human diseases, particularly through aberrant protein localization that disrupts normal cellular regulation. In cancer, mutations affecting the NLS of the tumor suppressor p53 can lead to its cytoplasmic retention, impairing its nuclear functions in DNA repair and apoptosis, thereby promoting oncogenesis. For instance, certain cancer-associated p53 point mutations, such as R273H and Y220C, enhance cytoplasmic localization, contributing to tumor progression in breast and colorectal cancers. Similarly, in BRCA1, mutations like M1775K and V1809F alter subcellular localization, leading to cytoplasmic sequestration and loss of its nuclear roles in DNA damage response, which is observed in sporadic breast tumors and increases susceptibility to oncogenesis. Aberrant cytoplasmic localization of wild-type p53 has also been noted in subsets of primary tumors, including breast cancer, colon cancer, and neuroblastoma, further linking NLS defects to malignant transformation. In neurodegenerative disorders, NLS defects in TARDBP (encoding TDP-43) are associated with amyotrophic lateral sclerosis (ALS), where mutations drive cytoplasmic mislocalization, resulting in nuclear clearance and the formation of toxic aggregates. These aggregates, a hallmark in over 90% of sporadic and familial ALS cases, deplete nuclear TDP-43, disrupting RNA processing and contributing to motor neuron degeneration. Although direct mutations in the TDP-43 NLS are infrequent, C-terminal mutations promote cytoplasmic accumulation and aggregation, exacerbating nuclear loss of function in ALS and frontotemporal dementia (FTD). Recent studies highlight TDP-43 seeding as a mechanism amplifying cytoplasmic aggregation while depleting nuclear pools, underscoring the pathological impact of NLS-related dysfunction. Viral pathogens exploit host NLS machinery for replication, with dysfunction or targeting of viral NLS offering therapeutic avenues. In SARS-CoV-2, the nucleocapsid (N) protein contains two critical NLS sequences essential for its nuclear import, which facilitates viral genome replication and evasion of host defenses by modulating nucleocytoplasmic trafficking. Disruption of these NLS prevents nuclear localization of the N protein, inhibiting viral replication. Similarly, inhibitors targeting importin-mediated nuclear import, such as ivermectin, block SARS-CoV-2 N protein shuttling and reduce viral propagation. Therapeutic strategies leveraging NLS mimicry have emerged to disrupt pathogen nuclear import. For example, in Toxoplasma gondii, the SV40 T-antigen NLS peptide targets importin α, impairing parasite viability and suggesting potential for NLS-based inhibitors against intracellular protozoan infections. Such approaches highlight the promise of NLS-targeted interventions to restore cellular homeostasis in infectious diseases.

Engineering and Prediction Methods

Prediction of nuclear localization sequences (NLSs) relies on computational tools that analyze protein sequences to identify motifs directing nuclear import. NLStradamus, a Hidden Markov Model-based predictor, identifies both classical and non-classical NLSs by modeling sequence patterns, achieving consistent detection of around 37% of known NLSs with low false positives. Recent advances incorporate machine learning, such as NLSExplorer, a 2025 deep learning model that uncovers hidden NLS patterns across diverse proteins, enabling interpretable predictions of nuclear localization probability through attention mechanisms on sequence features.00110-2) Similarly, the pSAM model uses deep learning to prioritize mutations altering NLS function, accurately forecasting nuclear localization changes with high precision in cancer-related proteins.^[43] Engineering NLSs involves fusing synthetic motifs to proteins to enhance nuclear delivery, particularly in gene therapy applications. Attaching NLS peptides to plasmid DNA or therapeutic proteins facilitates recognition by importins, improving transfection efficiency in non-dividing cells like neurons.^[44] For instance, human-derived NLSs integrated into chitosan-based vectors boost gene transfer by promoting nuclear accumulation of polyplexes.^[45] In CRISPR-Cas9 systems, hairpin internal NLS (hiNLS) variants inserted within the Cas9 protein structure enhance editing efficiency in primary human T cells, outperforming traditional terminal NLS fusions by up to twofold in indel formation rates as of 2025.^[46] Synthetic design of NLS motifs optimizes specificity and potency for targeted applications, such as nuclear delivery of antibodies in cancer therapy. Engineering strategies refine basic or bipartite motifs by adjusting arginine/lysine content and spacing to maximize importin-β binding affinity, enabling conjugation to antibodies for precise nuclear targeting of tumor-associated antigens.^[47] For CRISPR-Cas12a, optimized NLS architectures, including multiple monopartite signals, increase genome editing rates by facilitating rapid nuclear import without compromising nuclease activity.^[48] These designs prioritize minimal sequence alterations to avoid immunogenicity while enhancing therapeutic payload delivery.^[49] Experimental validation of engineered NLSs employs fluorescence microscopy and import assays to confirm nuclear localization. In fluorescence-based methods, GFP-tagged proteins with candidate NLSs are imaged in live cells to quantify nuclear-to-cytoplasmic ratios, revealing import kinetics post-microinjection.^[50] Post-2020 advances include high-throughput screening via automated microscopy pipelines, such as pooled multicolour tagging combined with machine learning for analyzing subcellular dynamics in thousands of variants.^[51] Image-based sorting systems further enable isolation of micronucleated cells expressing functional NLSs, accelerating validation in diverse cell types.^[52]

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STATs get their move on - PMC - PubMed Central
For nuclear import, large proteins must possess sequences or structures that serve as nuclear localization signals (NLSs). These signals can either function ...
[38]
Cyclin A- and Cyclin E-Cdk Complexes Shuttle between the Nucleus ...
We found that cyclin A and cyclin E are able to regulate both nuclear and cytoplasmic events because they both shuttle between the nucleus and the cytoplasm.
[39]
Cyclin-dependent kinase site-regulated signal-dependent nuclear ...
Jul 21, 1995 · Cell cycle-dependent nuclear localization in yeast was both NLS and cdk site-dependent, whereby mutation of the cdk site serines (Ser646 and ...
[40]
Nuclear Import of Cdk/Cyclin Complexes: Identification of Distinct ...
We found that the nuclear import machinery recognizes these Cdk/cyclin complexes through direct interactions with the cyclin component.
[41]
Interactions between HIV Rev and nuclear import and export factors
Dec 19, 1997 · Rev binds directly via its arginine-rich NLS to the human nuclear import receptor, importin-beta. This interaction was highly specific and was abolished by ...
[42]
Nucleolar Localization of HIV-1 Rev Is Required, Yet Insufficient for ...
Unlike Tat, which accumulates in the nucleus and nucleolus, Rev has mainly nucleolar subcellular localization. Upon viral infection, HIV genomic reverse ...
[43]
Intermolecular masking of the HIV-1 Rev NLS by the cellular protein ...
Mar 14, 2011 · The basic arginine-rich Rev NLS mediates both Rev nuclear import and binding to the Rev Response Element (RRE), a cis-acting RNA element present ...
[44]
Deep learning prioritizes cancer mutations that alter protein ... - Nature
Mar 14, 2025 · The rigorous evaluation convincingly reveals that the pSAM model built in this study accurately predicts nuclear localization probability with ...
[45]
NLS bioconjugates for targeting therapeutic genes to the nucleus
Subramanian et al. studied another import system, the non-classical nuclear localization sequence of the heterogeneous nuclear ribonucleoproteins hnRNP A1, ...Nls Bioconjugates For... · 3. Nucleus And Nuclear... · 5. Nuclear Proteins And Nls...
[46]
Human-derived NLS enhance the gene transfer efficiency of chitosan
These results indicate that the integration of IGFBP-NLS-3 peptides into polyplexes has potential as a strategy to enhance the efficiency of non-viral vectors.
[47]
Hairpin Internal Nuclear Localization Signals in CRISPR-Cas9 ...
Apr 17, 2025 · (1) Positively charged NLS helps promote localization of RNP to the negatively charged cell surface, promoting efficiency of intracellular ...
[48]
Nuclear‐Targeting Peptides for Cancer Therapy - Yi - 2024
Aug 30, 2024 · This review summarizes the most recent applications of nuclear-targeting peptides in targeting tumor associated proteins, chemotherapy, photodynamic/ ...1 Introduction · 3.2 The Mechanism Of... · 5 Summary And Prospects
[49]
Optimization of Nuclear Localization Signal Composition Improves ...
Jun 14, 2022 · Here we describe optimization to the nuclear localization signal (NLS) composition and architecture of Cas12a to facilitate highly efficient targeted ...
[50]
Nuclear Localization Signal-Tagged Systems - PubMed Central - NIH
We offer a roadmap for understanding the basic mechanisms of nuclear import in the context of actionable therapeutic design for developing NLS-therapeutics.
[51]
Nuclear Localization Signals for Optimization of Genetically ...
Jul 19, 2022 · We used this tool for comparative analysis of nuclear transport dynamics mediated by nuclear localization signals (NLSs) with different importin specificities.Figure 1 · Nuclear Transport Dynamics... · Optimization Of Nir Ot For...
[52]
Pooled multicolour tagging for visualizing subcellular protein dynamics
Apr 19, 2024 · We describe a strategy that combines high-throughput microscopy, computer vision and machine learning to detect perturbation-induced changes in multicolour ...
[53]
Image-based identification and isolation of micronucleated cells to ...
Jun 2, 2025 · This valuable paper reports machine learning-based image analysis pipelines for the automated segmentation of micronuclei and the detection and sorting of ...