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D-loop

A D-loop, or displacement loop, is a three-stranded DNA structure in which a single-stranded DNA molecule invades and base-pairs with a homologous double-stranded DNA, displacing one of the original strands to form a loop.^[1] This configuration arises during processes like strand invasion and serves as a critical intermediate in DNA metabolism.^[2] D-loops are observed across various biological contexts, including homologous recombination, mitochondrial DNA replication, and telomere protection, highlighting their versatility in maintaining genomic integrity.^[3] In homologous recombination (HR), D-loops form when a 3'-protruding single-stranded DNA, coated by recombinase proteins such as Rad51, invades a homologous duplex DNA template, enabling the repair of double-strand breaks (DSBs).^[1] This structure facilitates DNA strand exchange and subsequent synthesis to restore genetic information, with formation typically detectable within hours of DSB induction in model organisms like Saccharomyces cerevisiae.^[2] The stability and processing of D-loops are regulated by factors like Rad54, ensuring efficient progression to downstream repair outcomes such as gene conversion or crossover resolution.^[1] Within mitochondrial DNA (mtDNA), the D-loop refers to both a specific non-coding regulatory region and the associated triple-stranded structure formed during replication.^[4] Located in the major non-coding region (spanning nucleotides 16,024–576 in the human mitochondrial genome, wrapping around due to its circularity),^[5] it harbors origins of heavy-strand replication (O_H) and light-strand transcription, characterized by conserved sequence blocks (CSBs) and a high mutation rate linked to diseases like cancer.^[6] The structural D-loop emerges from premature termination of nascent heavy-strand synthesis at the termination-associated sequence (TAS), producing a short ~650-nucleotide 7S DNA fragment that displaces the parental heavy strand, potentially modulating replication fork progression via helicases like TWINKLE.^[3] At telomeres, D-loops contribute to end-protection by allowing the single-stranded 3' G-rich overhang to invade the adjacent double-stranded telomeric repeats, forming a displacement loop that may precede or integrate into the larger T-loop configuration.^[7] Stabilized by shelterin complex proteins such as TRF2, this invasion prevents recognition of chromosome ends as DSBs, thereby suppressing recombination and maintaining telomere length to avert genomic instability.^[8] Disruption of telomeric D-loops, often resolved by helicases like WRN or BLM, is implicated in aging and cancer when telomere maintenance fails.^[9]

Definition and Structure

Formation and Mechanism

A D-loop, also known as a displacement loop, is a three-stranded nucleic acid structure formed when a single-stranded DNA (ssDNA) invades a double-stranded DNA (dsDNA) molecule, base-pairing with its complementary strand and displacing the non-complementary strand, thereby creating a loop that visually resembles the letter "D".^[1] This structure serves as a key intermediate in processes such as homologous recombination and mitochondrial DNA replication. The D-loop was first observed in 1971, reported by Arnberg et al. in human HeLa cell mitochondrial DNA and independently by Kasamatsu et al. in mouse L-cell mitochondrial DNA, as a novel closed-circular form containing a replicated heavy-strand segment hydrogen-bonded to the light strand.^[10]^[11] The formation of a D-loop begins with the preparation of the invading ssDNA, which is coated by single-strand binding proteins such as SSB in bacteria or replication protein A (RPA) in eukaryotes; these proteins stabilize the ssDNA, remove secondary structures, and facilitate subsequent interactions.^[12] Recombinase proteins, including RecA in prokaryotes and RAD51 in eukaryotes, then polymerize along the coated ssDNA in an ATP-dependent manner to form a helical nucleoprotein filament; this filament enables an efficient search for homologous sequences within the target dsDNA.^[13] Upon homology recognition, the filament promotes strand invasion, where the invading ssDNA pairs with its complementary strand in the dsDNA, displacing the other strand and initiating D-loop formation.^[14] The D-loop is extended through branch migration, a process where the heteroduplex region grows as the invading strand progressively pairs further, driven by the recombinase filament's ATP hydrolysis activity, which provides the energy for filament dynamics, homology probing, and strand exchange while preventing stable binding to non-homologous DNA.^[15] ATP hydrolysis by RecA or RAD51 is essential for both presynaptic filament assembly on ssDNA and the disassembly of post-synaptic products, ensuring the reaction's directionality and efficiency.^[16] This mechanism is conserved across organisms and underlies the D-loop's role in DNA transactions, though specific contexts like mitochondrial replication may involve additional factors such as RNA primers.

Key Structural Features

The D-loop, or displacement loop, constitutes a triple-stranded DNA structure in which a single-stranded DNA molecule invades a double-stranded DNA duplex, pairing with one of the strands via Watson-Crick base pairing while displacing the non-complementary strand to form a looped-out single-stranded region. This configuration results in a branched molecule where the paired region maintains standard B-form double helix geometry, and the displaced strand extends as an unpaired loop, creating an asymmetric three-way junction. Although sometimes referred to as involving Hoogsteen-like interactions in specialized contexts such as certain triplex-forming systems, the primary pairing in canonical D-loops relies on Watson-Crick hydrogen bonds for stability in the invaded duplex segment.^[17]^[18]^[1] The length of the D-loop varies significantly based on the extent of sequence homology between the invading strand and the duplex, typically ranging from 100 to 2000 base pairs, with shorter segments (as few as 8-11 base pairs) sufficient for initial formation in minimal systems and longer extensions observed in recombination assays. This variability allows the structure to accommodate different biological contexts, such as short persistent loops in mitochondrial DNA or extended intermediates in repair pathways.^[18]^[1] Visualization of D-loops has historically relied on electron microscopy, which reveals the characteristic "D"-shaped morphology due to the looped displaced strand emanating from the duplex arms, often confirming structures in recombination intermediates. Complementary techniques include gel electrophoresis, where the branched architecture causes anomalous migration patterns compared to linear or circular DNA, enabling detection and quantification without high-resolution imaging.^[19] Stability of the D-loop is governed by several factors, including the degree of sequence homology that promotes extensive base pairing, ionic conditions such as elevated Mg²⁺ concentrations (typically 5-12 mM) that facilitate nucleoprotein filament formation and strand invasion, and accessory proteins like single-strand binding protein (SSB), which coats the displaced loop to prevent reannealing or degradation. These elements collectively enhance the persistence of the structure, with optimal conditions varying by system—e.g., higher Mg²⁺ favoring RecA-mediated formation in bacteria.^[20]^[21] Unlike Holliday junctions, which feature a symmetric four-stranded configuration often stabilized by covalent linkages and capable of branch migration, the D-loop is an asymmetric, initially non-covalent three-stranded intermediate lacking a continuous fourth strand, making it more transient and prone to dissociation without further processing. This distinction underscores the D-loop's role as an early invasion product rather than a mature crossover structure.^[17]^[18]^[22]

Role in Mitochondrial DNA

Replication Processes

In mammalian mitochondrial DNA (mtDNA), the D-loop forms at the heavy-strand origin of replication (OriH) within the control region, where synthesis of the nascent heavy (H)-strand displaces the parental H-strand, creating a triple-stranded structure.^[23] This initiation occurs through transcription from the light-strand promoter (LSP) by mitochondrial RNA polymerase (POLRMT), which generates an RNA primer that anneals near OriH and enables primer extension by DNA polymerase γ (POLG).^[24] The process was first evidenced in the 1970s through electron microscopy studies of circular mtDNA replicative intermediates in mouse L cells at Caltech, revealing D-loops as short three-stranded regions approximately 500-600 nucleotides in length, indicative of strand displacement during early replication.^[25] Two primary modes characterize mtDNA replication involving the D-loop: the strand-displacement model and coupled synthesis. In the displacement model, the predominant mechanism, H-strand synthesis proceeds continuously from the RNA primer at OriH, displacing the parental H-strand for about two-thirds of the genome circumference before light (L)-strand synthesis initiates at the origin of L-strand replication (OriL).^[26] Coupled synthesis, observed less frequently, involves simultaneous replication of both strands from OriH, potentially serving as an alternative pathway when displacement is stalled.^[27] Key proteins facilitate these processes: POLRMT synthesizes primers of 25-75 nucleotides for H-strand initiation; TWINKLE helicase unwinds the double-stranded DNA in a 5' to 3' direction to allow strand displacement and progression; and the heterotrimeric POLG complex (comprising the catalytic POLGα subunit and accessory POLGβ subunits) extends the primers with high processivity and proofreading fidelity.^[28]^[29] D-loop replication typically terminates prematurely after extension of approximately 600-700 nucleotides at conserved sequence blocks (CSB1, CSB2, and CSB3) near the termination-associated sequence (TAS), resulting in the release of a short 7S DNA fragment that remains hybridized to the parental L-strand.^[30] This abortive termination, occurring in over 95% of initiation events, is regulated by TWINKLE unloading at coreTAS and G-quadruplex structures at CSB2, which halt POLRMT transcription and prevent excessive displacement.^[27] The 7S DNA fragment, spanning from OriH to TAS, stabilizes the D-loop and fine-tunes mtDNA copy number by balancing initiation with full-length replication progression.^[23]

Control Region and Variation

The control region of human mitochondrial DNA (mtDNA), commonly referred to as the D-loop, comprises a non-coding segment approximately 1.1 kb in length that harbors critical regulatory elements for both transcription and replication. This region includes the heavy-strand promoter (HSP) for transcription of most mtDNA genes, the light-strand promoter (LSP) for the complementary strand, the origin of heavy-strand replication (O_H), and the origin of light-strand replication (O_L). A portion of this region, spanning about 650 bp, forms the characteristic three-stranded displacement loop structure stabilized by a short RNA or DNA segment known as 7S DNA.^[31]^[3] Within the D-loop, two hypervariable regions—HV1 (nucleotides 16,024–16,365) and HV2 (nucleotides 73–340)—exhibit elevated mutation rates, up to 10–100 times higher than nuclear DNA, primarily due to the absence of protective histones, limited repair mechanisms, and exposure to reactive oxygen species from the nearby electron transport chain. These regions accumulate polymorphisms rapidly, contributing to inter-individual variability while maintaining functional integrity through selective constraints.^[32]^[33]^[34] Polymorphisms in the D-loop define major mtDNA haplogroups, such as H (prevalent in ~40% of European maternal lineages) and U (common in Western Eurasian populations), which serve as markers for tracing maternal ancestry owing to mtDNA's uniparental, non-recombining inheritance. These haplogroups reflect ancient population migrations and bottlenecks, with H originating around 20,000–25,000 years ago in Southwest Asia.^[35] Recent studies between 2020 and 2025 have utilized D-loop variants for species identification and population genetics, particularly in conservation contexts. In gibbons (Hylobatidae), the D-loop's high evolutionary rate enables robust maternal-species delineation, outperforming coding genes like cox1 in phylogenetic analyses of over 200 samples across genera.^[36] Similarly, D-loop sequencing in Ethiopian goats revealed 231 haplotypes with high diversity (haplotype diversity = 0.9967 ± 0.001) across 13 populations, informing breed management.^[37] Key functional elements in the D-loop include binding sites for mitochondrial transcription factor A (TFAM), which interacts with promoter regions to initiate transcription and compact mtDNA into nucleoids via HMG-box domains that bend DNA up to 180 degrees. TFAM binding is enriched near O_H and the D-loop, supporting up to 445 dimer sites across the mtDNA genome. Additionally, three conserved sequence blocks (CSB1, CSB2, CSB3) within the central domain facilitate primer processing and replication termination; for instance, CSB1 serves as the termination site for 7S RNA transcripts, while CSB2's guanine tract can form G-quadruplexes to halt progression.^[38]^[30]^[39] Emerging research from 2020–2025 underscores the D-loop's role in mtDNA copy number regulation through its structural stability. In cancer contexts like glioblastoma, D-loop variants like m.16126T>C are associated with poorer prognosis (shorter median survival).^[40]

Role in Telomere Maintenance

T-loop Formation

In mammalian telomeres, the single-stranded 3' G-rich overhang invades the duplex region of the telomeric DNA, displacing one strand to form a D-loop and thereby creating a lariat-like T-loop structure that protects chromosome ends.^[41] This configuration was first visualized using electron microscopy on purified telomeric DNA from human and mouse cells, revealing loops with tails ranging from 0 to 12 kb and overall structures averaging 22 kb.^[41] The D-loop portion of the T-loop typically spans approximately 100-200 base pairs, corresponding to the length of the invading overhang.^[41] The strand invasion exhibits sequence specificity, particularly in humans where it involves the TTAGGG telomeric repeats; the 3' overhang anneals to the complementary C-rich strand in the duplex, typically occurring at the proximal (centromeric-proximal) end of the duplex region to initiate loop formation.^[42] This process relies on the shelterin protein complex, with TRF2 playing a central role in promoting the invasion and stabilizing the D-loop by binding near the 3' end and facilitating Holliday junction-like intermediates.^[43] TRF1 contributes by inducing bends and loops in the duplex DNA, aiding the overall architecture, while the broader shelterin components (including POT1, TIN2, TPP1, and hRAP1) support end protection.^[42] Studies spanning 1999 to the 2020s have confirmed that this TRF2-dependent mechanism hides the 3' telomere end from DNA damage response and repair pathways, preventing recognition as a double-strand break.^[43] Recent advances have illuminated T-loop dynamics using in vitro models demonstrating TRF2's ability to generate T-loops on telomeric substrates, underscoring the dynamic regulation of D-loop invasion during aging.^[43]

Stabilization and Protection

The stability of T-loops at telomeres is primarily maintained by the shelterin complex, particularly through the binding of the protection of telomeres 1 (POT1) protein to the single-stranded 3' G-rich overhang, which sequesters it within the duplex telomeric DNA and prevents its displacement or degradation by nucleases.^[44] This POT1-mediated stabilization ensures the integrity of the invasion site in the T-loop structure, where the overhang anneals to the telomeric repeats to form a displacement loop (D-loop). Complementing POT1, the telomeric repeat-binding factor 2 (TRF2) directly binds and inhibits the ATM kinase, suppressing its autophosphorylation and thereby preventing activation of the DNA damage response at chromosome ends.^[45] These mechanisms confer protective functions to T-loops by masking the linear chromosome ends, which would otherwise be recognized as double-strand breaks, and by compacting telomeric chromatin into tight structures that limit access to DNA repair factors.^[46] Consequently, T-loops reduce the incidence of end-to-end chromosomal fusions, which can lead to genomic instability such as dicentric chromosomes and breakage-fusion-bridge cycles. Unlike simple D-loops formed during general recombination, T-loops create closed, lasso-like configurations stabilized by telomeric repeats and shelterin proteins, providing specialized end protection.^[41] Disruption of T-loop stabilization, such as through POT1 or TRF2 deficiency, results in telomere deprotection, accelerated telomere attrition due to unregulated overhang resection, and induction of replicative senescence via persistent DNA damage signaling.^[44] Such disruptions are implicated in telomere biology disorders like dyskeratosis congenita, where germline mutations in shelterin components (e.g., TINF2) impair T-loop maintenance, leading to critically short telomeres below the first percentile for age and multisystem failure including bone marrow attrition.^[47] Experimental evidence for T-loop stabilization and protection includes electron microscopy visualizations from human cell lines, such as HeLa cells, where t-loops were observed in 15-40% of telomere-enriched molecules, with loop sizes matching average telomere lengths of 8-22 kb.^[41] More recent studies (2020-2025) have shown that loss of T-loop stabilizers like TELS1 in pluripotent cells reduces t-loop frequency to 5-8% (from 25% in wild-type), yet partial protection persists via alternative pathways; however, in cancer contexts, T-loop disassembly enhances telomerase access and telomere elongation (500-700 bp/day), promoting replicative immortality in telomerase-positive tumors.^[48]

Role in DNA Recombination and Repair

Homologous Recombination

In the repair of double-strand breaks (DSBs) in nuclear DNA via homologous recombination (HR), the D-loop serves as a pivotal intermediate. Following DSB induction and 5' to 3' end resection, the exposed 3' single-stranded DNA (ssDNA) tails are coated by RecA in prokaryotes or RAD51 in eukaryotes, forming right-handed helical nucleoprotein filaments capable of searching for homologous sequences. These presynaptic filaments invade a homologous duplex DNA donor, where the 3' ssDNA displaces one strand of the duplex to generate the D-loop, enabling templated DNA repair synthesis.^[49]^[22] Once formed, the invading 3' end within the D-loop is extended by a DNA polymerase, copying genetic information from the homologous template. This extension can proceed via two primary HR subpathways: synthesis-dependent strand annealing (SDSA), in which the extended strand dissociates from the donor and anneals to the other resected DSB end, yielding non-crossover products; or the double-strand break repair (DSBR) pathway, where capture of the second DSB end leads to double Holliday junction (dHJ) formation, as outlined in the seminal Szostak model.^[50] In the DSBR pathway, the dHJs are subsequently resolved by structure-specific endonucleases (resolvases) such as GEN1 or MUS81-EME1, which introduce symmetric incisions to produce either crossover or non-crossover outcomes.^[51] Biochemical in vitro assays in the 2020s have elucidated the dynamics of RAD51-mediated D-loop extension and displacement in eukaryotes. For instance, studies using purified human RAD51 and supercoiled plasmid substrates demonstrated that accessory factors like RDH54 stabilize RAD51 at nascent D-loops to promote efficient extension while limiting premature displacement, ensuring homology verification.^[52] Another 2020 investigation revealed that RDH54/TID1 inhibits excessive D-loop formation by RAD51-RAD54 complexes in an ATPase-independent manner, fine-tuning invasion to prevent aberrant repair.^[53] A key distinction from prokaryotic systems lies in the regulation of eukaryotic RAD51, which, unlike the autonomous RecA, requires mediators such as BRCA2 to load onto ssDNA and facilitate stable D-loop invasion under physiological conditions.^[54] BRCA2 interacts directly with RAD51 via BRC repeats, promoting filament nucleation and counteracting inhibitory factors to enable efficient HR.^[55] Recent structural studies as of 2025 have provided high-resolution insights into the D-loop intermediate using cryogenic electron microscopy (cryo-EM), revealing the detailed architecture of human RAD51-mediated D-loops and confirming conserved mechanisms across eukaryotes.^[18] Additionally, donor transcription by RNA polymerase II has been shown to suppress D-loop formation in cis in an orientation-dependent manner, promoting accurate homology-directed repair and preventing off-target events.^[56]

Meiotic Recombination Specifics

In meiosis, programmed double-strand breaks (DSBs) induced by the Spo11 protein initiate recombination, with resected DSB ends coated by the meiosis-specific recombinase Dmc1 in cooperation with Rad51 to facilitate strand invasion and D-loop formation.^[57] This process promotes interhomolog recombination essential for genetic diversity, where Dmc1 preferentially forms stable nucleoprotein filaments on single-stranded DNA to search for and invade homologous sequences, displacing the non-template strand to create the D-loop intermediate.^[58] Unlike somatic homologous recombination, which relies primarily on Rad51, the concerted action of Dmc1 and Rad51 in meiosis ensures efficient D-loop establishment at Spo11-generated DSBs, with Dmc1's strand exchange activity being critical for progression.^[59] D-loops in meiosis are preferentially stabilized to promote crossovers, a key outcome for proper chromosome segregation. The mismatch repair factors MLH1 and MLH3 are recruited to these intermediates, where they resolve double Holliday junctions (dHJs) formed from captured second ends, biasing resolution toward crossover products.^[60] Approximately 90% of meiotic crossovers in mammals, classified as class I events, depend on this MLH1-MLH3 pathway and involve D-loop stabilization leading to dHJs.^[61] This stabilization prevents dissolution into non-crossovers, ensuring chiasmata formation that physically links homologs during metaphase I. Mechanisms of D-loop regulation vary across species, reflecting adaptations in meiotic progression. In budding yeast (Saccharomyces cerevisiae), ZMM proteins such as Zip1 and Zip3 capture and stabilize D-loops, facilitating second-end capture and dHJ formation within the synaptonemal complex framework.^[62] In mammals, the synaptonemal complex similarly coordinates D-loop dynamics through analogous proteins like those in the RMM (required for meiotic divisions) group, integrating recombination with chromosome synapsis to enforce crossover interference and distribution.^[63] Recent studies have elucidated roles for structure-specific endonucleases in processing D-loops during meiosis. In 2024 research, concurrent cleavage of D-loops by Mus81 and Yen1 (the yeast ortholog of human GEN1) was shown to generate half-crossover precursors in vitro, providing a pathway for crossover maturation independent of full dHJ resolution and contributing to the diversity of meiotic outcomes.^[64] As of 2025, investigations into recombination-coupled DNA synthesis have highlighted its role in facilitating post-invasion progression of D-loops, ensuring efficient genetic exchange without genomic instability.^[65] Furthermore, homologous recombination counteracts mismatch repair to promote meiotic crossovers, refining the interplay at D-loop stages.^[66] Defects in D-loop formation or stabilization, such as mutations in Dmc1 or MLH3, disrupt crossover assurance, leading to univalents at metaphase I, improper chromosome segregation, and infertility in both males and females.^[67] These failures highlight the D-loop's central role in ensuring meiotic fidelity and genetic diversity across eukaryotes.

Applications in Research

Evolutionary and Population Genetics

The analysis of mitochondrial DNA (mtDNA) D-loop sequences has been instrumental in evolutionary and population genetics since the 1980s, when pioneering studies established the human mtDNA molecular clock and demonstrated its utility for tracing maternal ancestry.^[68] Early sequencing efforts, such as the 1987 work by Cann, Stoneking, and Wilson, revealed high variability in the D-loop region, enabling the reconstruction of ancient human migrations through phylogenetic analysis. This hypervariability, particularly in the non-coding control region, arises from a mutation rate approximately 10 times higher than the rest of the mtDNA genome, making it a sensitive marker for recent evolutionary events.^[69] The D-loop's hypervariability allows tracking of maternal lineages via haplogroups, which are clusters of related mtDNA variants defined by specific polymorphisms in the hypervariable (HV) regions I and II.^[70] These haplogroups have been used to support the Out-of-Africa model of human dispersal, where macrohaplogroup L3 derivatives (M and N) represent the primary lineages that exited Africa around 60,000–70,000 years ago, while African-specific L0–L6 lineages highlight deep-rooted continental diversity.^[71] For instance, phylogenetic trees constructed from D-loop sequences show that non-African populations derive from a subset of African haplogroups, illustrating serial founder effects during migrations.^[72] Methods for D-loop analysis typically involve PCR amplification and Sanger sequencing of the HV regions (approximately 400–600 bp), followed by alignment using tools like CLUSTALW and construction of phylogenetic trees via neighbor-joining or maximum-likelihood approaches to infer haplotype diversity and population structure.^[70] Nucleotide diversity (π) estimates from these sequences, often ranging from 0.02–0.05 in human populations, quantify variability and support coalescent models for lineage divergence.^[73] In population genetics applications, D-loop sequencing facilitates forensic identification by providing maternally inherited markers that are robust in degraded samples, such as skeletal remains, due to the high copy number of mtDNA.^[74] Beyond humans, phylogeographic studies in animals leverage D-loop polymorphisms; a 2025 analysis of gibbon (Hylobatidae) mtDNA used D-loop sequences to delineate species boundaries, revealing robust maternal lineages that outperformed cox1 in resolving recent divergences among 16 taxa.^[36] For non-mtDNA contexts, telomeric T-loop stability—formed by invasion of the 3' overhang into duplex telomeric DNA—has been linked to evolutionary adaptations to physiological stress, where enhanced loop formation in response to oxidative damage promotes genome stability in long-lived species.^[75]

Disease Associations and Biomarkers

Mutations in the mitochondrial DNA (mtDNA) D-loop region have been implicated in various human diseases, particularly cancers such as glioblastoma. A 2024 pilot study identified the m.16126T>C variant in the D-loop as a prognostic marker in glioblastoma patients, occurring in 18% of tumor samples and associated with reduced median survival of 9.5 months compared to wild-type cases.^[40] Similarly, a 2025 analysis of primary and recurrent gliomas highlighted the D-loop as the primary hotspot for somatic mtDNA mutations, especially in the polycytosine tract (D310), where slippage during replication promotes instability and contributes to tumor progression.^[76] Beyond cancer, D-loop variants are linked to primary open-angle glaucoma (POAG) and age-related changes. A 2023 next-generation sequencing (NGS) study of buffy coat DNA from POAG patients revealed that specific D-loop variants correlate with disease risk in a subgroup, potentially by disrupting mtDNA replication and leading to optic nerve degeneration.^[77] In aging, a 2025 Science Advances report demonstrated allele frequency shifts in mtDNA variants across somatic tissues, with higher mutation frequencies in the D-loop (2.7-fold increase over coding regions), but no age-related accumulation of mutations in oocytes, suggesting selective mechanisms preserve germline integrity.^[78] These variants often impair D-loop functions, affecting mtDNA replication and transcription, which can lead to reactive oxygen species (ROS) imbalance and oxidative stress. For instance, D-loop mutations may elevate ROS production, exacerbating cellular damage in disease contexts.^[79] Due to maternal inheritance of mtDNA, D-loop variants serve as biomarkers for tracing lineage-specific risks in mitochondrial disorders.^[80] Recent advances from 2020 to 2025 have positioned D-loop alterations in personalized medicine, with D-loop sequencing aiding diagnosis of mtDNA-related cancers and glaucoma. CRISPR-based editing has emerged as a therapeutic strategy for mtDNA disorders, including targeted correction of pathogenic variants.^[81]

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Nov 3, 2025 · This study aimed to investigate D-loop methylation and mtDNA copy number in DS. Peripheral blood DNA samples were collected from 59 individuals ...
[39]
D-loop mutations in mitochondrial DNA are a risk factor for ... - Nature
Dec 30, 2024 · Our analysis revealed a rise in mtDNA mutations following chemotherapy, particularly within the D-loop region. Moreover, mutations in a specific ...
[40]
D-Loop Mutations as Prognostic Markers in Glioblastoma—A Pilot ...
Apr 14, 2024 · This prospective case-control study aimed to assess the prognostic significance of the mtDNA D-loop m.16126T>C variant in glioblastoma patients.
[41]
the protein complex that shapes and safeguards human telomeres
TRF1 has the ability to bend, loop, and pair telomeric DNA in vitro and could potentially fold the telomere. The shelterin component TRF2 can mediate t-loop ...
[42]
Characterization of t-loop formation by TRF2 - PMC - NIH
T-loops are thought to hide telomeres from DNA damage signaling and DSB repair pathways. T-loop formation requires the shelterin component TRF2, ...
[43]
Telomere Checkpoint in Development and Aging - MDPI
Nov 5, 2023 · Telomere checkpoint ensures genome stability in multicellular organisms but aggravates the aging process, promoting the accumulation of damaged and senescent ...Telomere Checkpoint In... · 2. A Telomere Is A Dynamic... · 4. Telomeres In Aging...
[44]
https://www.cell.com/fulltext/S0092-8674(06)00763-X
[45]
The Telomeric Protein TRF2 Binds the ATM Kinase and Can Inhibit ...
Aug 17, 2004 · The telomeric protein TRF2 is required to prevent mammalian telomeres from activating DNA damage checkpoints.
[46]
https://www.cell.com/cell/fulltext/S0092-8674(16)30050-2
[47]
Mammalian Telomeres End in a Large Duplex Loop - ScienceDirect
Electron microscopy reported here demonstrated that TRF2 can remodel linear telomeric DNA into large duplex loops (t loops) in vitro.
[48]
Dyskeratosis congenita and telomere biology disorders - PMC
Dec 9, 2022 · Dyskeratosis congenita (DC) and related telomere biology disorders (TBDs) comprise a heterogeneous group of illnesses caused by germline mutations resulting in ...Missing: attrition | Show results with:attrition
[49]
https://www.nature.com/articles/cr20081
[50]
Homologous recombination in DNA repair and DNA damage tolerance
Jan 1, 2008 · These generate the D-loop intermediate, where the 3′-end of the invading strand primes DNA synthesis off the template duplex DNA (Figure 1). The ...
[51]
Homologous Recombination via Synthesis-Dependent Strand ...
Synthesis-dependent strand-annealing (SDSA)-mediated homologous recombination replaces the sequence around a DNA double-strand break (DSB) with a copy of a ...
[52]
Mechanism of Holliday junction resolution by the human GEN1 protein
Prokaryotes encode a specialized nuclease called RuvC that promotes the resolution of HJs that arise during recombinational DNA repair (West 1997). RuvC is a ...
[53]
Rdh54 stabilizes Rad51 at displacement loop intermediates to ...
Our data indicate that RDH54 regulates DNA strand exchange by stabilizing Rad51 at an early HR intermediate called the displacement loop (D-loop).
[54]
Rdh54/Tid1 inhibits Rad51-Rad54-mediated D-loop formation and ...
Nov 13, 2020 · Here, we show that Rdh54/Tid1 inhibits D-loop formation by Rad51 and Rad54 in an ATPase-independent manner.
[55]
Purified human BRCA2 stimulates RAD51-mediated recombination
Here we report purification of full length BRCA2 and show that it both binds RAD51 and potentiates recombinational DNA repair.
[56]
Unraveling the mechanism of BRCA2 in homologous recombination
The function of BRCA2 in recombination is to control RAD51, a protein that catalyzes homologous pairing and DNA strand exchange.
[57]
Mechanism and Regulation of Meiotic Recombination Initiation - PMC
Meiotic recombination involves the formation and repair of programmed DNA double-strand breaks (DSBs) catalyzed by the conserved Spo11 protein.
[58]
Meiotic Crossover Control by Concerted Action of Rad51-Dmc1 in ...
Two DNA strand-exchange proteins, Rad51 and Dmc1, are required for meiotic recombination in many organisms. Studies in budding yeast imply that Rad51 acts to ...
[59]
Rad51 facilitates filament assembly of meiosis-specific Dmc1 ... - NIH
May 13, 2020 · Our results show that Dmc1 recombinases possess evolutionarily conserved nucleation preference that allows 5′-to-3′ filament formation.
[60]
Mlh1-Mlh3, a Meiotic Crossover and DNA Mismatch Repair Factor ...
Background: Meiotic crossing over requires resolution of Holliday junctions through actions of the DNA mismatch repair factor Mlh1-Mlh3.
[61]
Mechanistic insight into crossing over during mouse meiosis - PMC
Many crossover products yielded no heteroduplex DNA, suggesting dismantling by D-loop migration. ... Unlike in mouse, in which ~90% of meiotic crossovers are MLH1 ...<|control11|><|separator|>
[62]
Biochemical characterisation of Mer3 helicase interactions and the ...
Either the D-loop is disassembled by the Sgs1 helicase (in the Sgs1/Top3/Rmi1–STR – complex) or the D-loop is captured and stabilised by members of the ZMM ...
[63]
Coupling crossover and synaptonemal complex in meiosis - PMC
(Left panel) The ZMM proteins (Zip4, Zip2, Spo16, Msh4, Msh5, Zip3, Zip1, and Mer3) channel DSB repair toward the homolog and stabilize the D-loop intermediate.
[64]
Concurrent D-loop cleavage by Mus81 and Yen1 yields half ...
The simultaneous action of Mus81 and Yen1, followed by ligation, is sufficient to recreate the formation of a half-crossover precursor in vitro.
[65]
Meiotic recombination and male infertility: from basic science ... - NIH
Therefore, reduced or absent meiotic recombination may lead to increased sperm aneuploidy frequencies, or even spermatogenic arrest, resulting in infertility.
[66]
"Mitochondrial DNA and Human Evolution" (1987), by Rebecca ...
Oct 10, 2014 · In 1981, Fred Sanger's group in Cambridge, England, published the entire sequence and organization of the human mtDNA genome. Cann, Stoneking, ...
[67]
Mitochondrial DNA in Human Diversity and Health - PubMed Central
Jul 27, 2023 · The present review explores the productive field of human mitochondrial genetics throughout 40 years of active research.
[68]
Mitochondrial DNA D‐loop hyper‐variable region ... - PubMed Central
Sequence alignment was performed using CLUSTALW package. Haplotype and nucleotide diversity were estimated using DNASP5.10 and phylogenetic tree was constructed ...
[69]
Whole-mtDNA Genome Sequence Analysis of Ancient African ...
Only 2 mtDNA macrohaplogroups (M and N) and their derivatives persisted in non-Africans after the migration of modern humans out of Africa. Macrohaplogroup L is ...
[70]
Maternal ancestry and population history from whole mitochondrial ...
Mar 10, 2015 · Outside Africa, haplogroup L0-L6 lineages are extremely rare and restricted to geographic areas that have received historic gene flow from ...
[71]
Investigation of mitochondrial DNA genetic diversity and phylogeny ...
Results showed that 2 409 haplotypes and 301 polymorphic sites were present within the 401-bp length D_loop region, the nucleotide diversity (Pi) was 0.03471, ...
[72]
Mitochondrial DNA in forensic use - PMC - NIH
Aug 10, 2021 · The D-loop consists of three strands of DNA, one complementary to one of the strands, holding it apart forming the displacement (D) loop [6].
[73]
The Power of Stress: The Telo-Hormesis Hypothesis - PMC - NIH
May 11, 2021 · We explore here the putative beneficial effects of changing the ends of eukaryotic chromosomes, the telomeres, in response to stress.
[74]
Mitochondrial DNA copy number alterations - Spandidos Publications
Jan 24, 2025 · The D-loop region acts as the primary hotspot for somatic mtDNA mutations, particularly within the polycytosine tract (D310), a reiterated ...
[75]
Mitochondrial DNA D-loop variants correlate with a primary open ...
The patients and controls in this study are part of the subjects (141/175) analyzed for mtDNA copy number and 4977 base pair deletion in a previous study in our ...
[76]
Allele frequency selection and no age-related increase in human ...
Aug 6, 2025 · Pedigree studies have suggested an increased mtDNA mutation frequency in children born to older mothers [e.g., (16–18)]; however, post– ...
[77]
Investigating the role of mitochondrial DNA D-loop variants ...
Mutations in this region may lead to an increase in the formation of cellular ROS and subsequent oxidative stress. This, in turn, can have an effect on the ...
[78]
Mitochondrial DNA variants in the pathogenesis and metabolic ...
This variant, which is found in the mtDNA D-loop region, may have an impact on transcription and replication of mtDNA, which could impair glucose metabolism ...Mitochondrial Dna Variants... · 3. Macrovascular... · 3.1. Animal Studies Related...
[79]
Lipid nanoparticle delivery of the CRISPR/Cas9 system directly into ...
Jun 19, 2025 · Here, we targeted a point mutation in mitochondrial DNA (mtDNA) that can cause mitochondrial diseases via delivery of the clustered, regularly ...Missing: loop disorders