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DNA fragmentation
DNA fragmentation
DNA fragmentation
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DNA fragmentation is the separation or breaking of DNA strands into pieces. It can be done intentionally by laboratory personnel or by cells, or can occur spontaneously. Spontaneous or accidental DNA fragmentation is fragmentation that gradually accumulates in a cell. It can be measured by e.g. the comet assay or by the TUNEL assay.

Its main units of measurement is the DNA Fragmentation Index (DFI).[1] A DFI of 20% or more significantly reduces the success rates after ICSI.[1]

DNA fragmentation was first documented by Williamson in 1970 when he observed discrete oligomeric fragments occurring during cell death in primary neonatal liver cultures. He described the cytoplasmic DNA isolated from mouse liver cells after culture as characterized by DNA fragments with a molecular weight consisting of multiples of 135 kDa. This finding was consistent with the hypothesis that these DNA fragments were a specific degradation product of nuclear DNA.[2]

Intentional

[edit]

DNA fragmentation is often necessary prior to library construction or subcloning for DNA sequences. A variety of methods involving the mechanical breakage of DNA have been employed where DNA is fragmented by laboratory personnel. Such methods include sonication, needle shear, nebulisation, point-sink shearing and passage through a pressure cell.[3]

  • Restriction digest is the intentional laboratory breaking of DNA strands. It is an enzyme-based treatment used in biotechnology to cut DNA into smaller strands in order to study fragment length differences among individuals or for gene cloning.[4] This method fragments DNA either by the simultaneous cleavage of both strands, or by generation of nicks on each strand of dsDNA to produce dsDNA breaks.[5]
  • Acoustic shearing of the transmission of high-frequency acoustic energy waves delivered to a DNA library. The transducer is bowl shaped so that the waves converge at the target of interest.[5]
  • Nebulization forces DNA through a small hole in a nebulizer unit, which results in the formation of a fine mist that is collected. Fragment size is determined by the pressure of the gas used to push the DNA through the nebulizer, the speed at which the DNA solution passes through the hole, the viscosity of the solution, and the temperature.[5][6]
  • Sonication, a type of hydrodynamic shearing, subjects DNA to acoustic cavitation and hydrodynamic shearing by exposure to brief periods of sonication, usually resulting in 700bp fragments. For DNA fragmentation, sonication is commonly applied at burst cycles using a probe-type sonicator.[7]
  • Point-sink shearing, a type of hydrodynamic shearing, uses a syringe pump to create hydrodynamic shear forces by pushing a DNA library through a small abrupt contraction. About 90% of fragment lengths fall within a two-fold range.[5]
  • Needle shearing creates shearing forces by passing DNA libraries through small gauge needle.[5] The DNA pass through a gauge needle several times to physically tear the DNA into fine pieces.
  • French pressure cells pass DNA through a narrow valve under high pressure to create high shearing forces.[5] With a French press, the shear force can be carefully modulated by adjusting the piston pressure. The Press provides a single pass through the point of maximum shear force, limiting damage to delicate biological structures due to repeated shear, as occurs in other disruption methods.
  • In transposome mediated fragmentation (tagmentation) transposomes are prepared with DNA that is afterwards cut so that the transposition events result in fragmented DNA with adapters (instead of an insertion). The relative concentration of transposomes and DNA must be appropriate.

Spontaneous

[edit]

Apoptotic DNA fragmentation is a natural fragmentation that cells perform in apoptosis (programmed cell death). DNA fragmentation is a biochemical hallmark of apoptosis. In dying cells, DNA is cleaved by an endonuclease that fragments the chromatin into nucleosomal units, which are multiples of about 180-bp oligomers and appear as a DNA ladder when run on an agarose gel.[8] The enzyme responsible for apoptotic DNA fragmentation is the Caspase-activated DNase. CAD is normally inhibited by another protein, the Inhibitor of Caspase Activated DNase (ICAD). During apoptosis, the apoptotic effector caspase, caspase 3, cleaves ICAD and thus causes CAD to become activated.[9]

A DNA double strand wrapped around a core of histone proteins
A nucleosome, consisting of DNA (grey) wrapped around a histone tetramer (coloured). In apoptotic DNA fragmentation, the DNA is cleaved in the internucleosomal linker region, which is the part of the DNA not wrapped around the histones.

CAD cleaves the DNA at the internucleosomal linker sites between the nucleosomes, protein-containing structures that occur in chromatin at ~180-bp intervals. This is because the DNA is normally tightly wrapped around histones, the core proteins of the nucleosomes. The linker sites are the only parts of the DNA strand that are exposed and thus accessible to CAD.

Men with sperm motility defects often have high levels of sperm DNA fragmentation.[10] The degree of DNA fragmentation in sperm cells can predict outcomes for in vitro fertilization[11] (IVF) and its expansion intracytoplasmic sperm injection[1] (ICSI). The sperm chromatin dispersion test (SCD) and TUNEL assay are both effective in detecting sperm DNA damage.[12][13] Using bright-field microscopy, the SCD test appears to be more sensitive than the TUNEL assay.[13]

Uses

[edit]

DNA Fragmentation plays an important part in forensics, especially that of DNA profiling.

  • Restriction Fragment Length Polymorphism (RFLP) is a technique for analyzing the variable lengths of DNA fragments that result from digesting a DNA sample with a restriction endonuclease. The restriction endonuclease cuts DNA at a specific sequence pattern known as a restriction endonuclease recognition site. The presence or absence of certain recognition sites in a DNA sample generates variable lengths of DNA fragments, which are separated using gel electrophoresis. They are then hybridized with DNA probes that bind to a complementary DNA sequence in the sample.[14]
  • In polymerase chain reaction (PCR) analysis, millions of exact copies of DNA from a biological sample are made. It used to amplify a specific region of a DNA strand (the DNA target). Most PCR methods typically amplify DNA fragments of between 0.1 and 10 kilo base pairs (kb), although some techniques allow amplification of fragments up to 40 kb in size.[14] PCR also uses heat to separate the DNA strands.
  • DNA fragmented during apoptosis, of a size from 1 to 20 nucleosomes, can be selectively isolated from the cells fixed in the denaturing fixative ethanol [15]

References

[edit]
Revisions and contributorsEdit on WikipediaRead on Wikipedia

DNA fragmentation

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from Grokipedia
DNA fragmentation is the endonuclease-mediated cleavage of genomic DNA into smaller fragments, a process that occurs naturally during cellular events such as and can also be induced intentionally in laboratory techniques for applications. In , , this fragmentation is a biochemical hallmark characterized by the degradation of chromosomal DNA into a ladder-like pattern of oligonucleosomal units, typically 180–200 base pairs in length, which facilitates the orderly dismantling of the cell and prevents inflammatory responses. The primary executor of this cleavage is caspase-activated DNase (CAD), which is released from its inhibitor (ICAD) upon caspase-3 activation, allowing it to hydrolyze DNA at internucleosomal linker regions. Apoptosis, the programmed cell death process featuring this DNA fragmentation, was first described morphologically in 1972, with the DNA laddering pattern identified as a hallmark in 1980. This process plays crucial roles in development, tissue , and immune regulation by ensuring efficient chromatin condensation and disposal by , thereby averting . In CAD-deficient models, particularly in lupus-prone backgrounds, apoptotic cells exhibit reduced DNA laddering and increased susceptibility to systemic erythematosus-like autoimmune diseases due to incomplete DNA degradation and exposure of self-antigens. Beyond , DNA fragmentation manifests in other pathological contexts, including sperm DNA damage associated with , where single- or double-strand breaks exceeding 30% fragmentation index correlate with reduced pregnancy success and higher rates. In circulating cell-free DNA (cfDNA), fragmentation patterns—peaking at around 167 base pairs—serve as noninvasive biomarkers for cancer detection and , reflecting nucleosome-protected genomic segments released from dying cells. Laboratory methods exploit DNA fragmentation for research and diagnostics, such as or enzymatic shearing to prepare DNA libraries for next-generation sequencing, and assays like TUNEL ( dUTP nick end labeling) or assays to quantify fragmentation in apoptotic or damaged cells. While random DNA breaks can arise from , , or replication errors in non-apoptotic scenarios like , the controlled, internucleosomal cleavage in distinguishes it as a regulated event essential for multicellular organismal integrity.

Overview

Definition

DNA fragmentation refers to the physical breaking of the DNA double helix into smaller pieces, resulting in either single-strand breaks (SSBs), where one strand is severed, or double-strand breaks (DSBs), where both strands are disrupted at the same or nearby locations. These breaks compromise the structural integrity of the and are a fundamental aspect of cellular biology. In biological contexts, DNA fragmentation occurs naturally during essential processes such as , where it facilitates the orderly dismantling of the nucleus. It can also be induced artificially in environments through exposure to genotoxic agents like or chemicals, enabling studies of DNA damage responses. Enzymatically, fragmentation proceeds via endonucleolytic pathways, in which endonucleases cleave phosphodiester bonds internally at specific or random sites to generate discrete fragments, or exonucleolytic pathways, where exonucleases progressively remove nucleotides from the free ends of DNA strands. The primary molecular consequences of DNA fragmentation include the exposure of reactive DNA ends, which serve as signals for cellular machinery to initiate repair via pathways like for SSBs or for DSBs. If these breaks remain unrepaired, they can propagate genomic instability, leading to , chromosomal aberrations, or activation of programs to prevent propagation of damaged cells.

Historical Background

The discovery of fragmentation as a cellular traces back to 1970, when Robert Williamson first observed discrete oligomeric DNA fragments in the cytoplasmic fraction of primary cultures of embryonic liver cells. These fragments, approximately 135 in size, were identified through pulse-labeling experiments and , revealing a pattern suggestive of nucleosomal units. This finding, published in the Journal of Molecular Biology, represented the initial documentation of what would later be recognized as the "nucleosomal ladder" characteristic of DNA degradation during processes. In the 1970s and 1980s, research on advanced significantly, establishing a clear link between DNA fragmentation and . The term "" was coined in 1972 by John Kerr, Andrew Wyllie, and Alastair Currie to describe a distinct mode of involving orderly nuclear changes, including condensation. By 1980, Wyllie further demonstrated that glucocorticoid-induced in thymocytes involved endogenous endonuclease activation, leading to internucleosomal DNA cleavage and the formation of a 180-200 ladder pattern upon . These studies solidified DNA fragmentation as a biochemical hallmark of , shifting focus from morphological observations to molecular mechanisms. The measurement of DNA fragmentation evolved from rudimentary techniques in the early decades to more sophisticated assays by the 1990s and 2000s. Initial detection relied on agarose gel electrophoresis to visualize the nucleosomal ladder, a method popularized in the 1980s following Wyllie's work. In the 1990s, the TUNEL assay, introduced by Gavrieli et al. in 1992, enabled in situ labeling of DNA strand breaks using terminal deoxynucleotidyl transferase, improving sensitivity for apoptotic detection in tissues. By the 2000s, quantitative methods such as flow cytometry-based TUNEL and ELISA kits for cytoplasmic histone-associated DNA fragments became widely adopted, allowing for high-throughput analysis while building on the foundational electrophoretic approaches.

Mechanisms

Intentional Mechanisms

Intentional mechanisms of DNA fragmentation involve deliberate biochemical or physical interventions to cleave DNA at specific or random sites, enabling precise manipulation for experimental purposes. These methods are essential in , where controlled fragmentation generates DNA pieces of defined lengths suitable for downstream applications such as vector insertion or high-throughput . Unlike natural processes, these techniques are engineered for reproducibility and specificity, often leveraging enzymes or external forces to produce either targeted cuts or a distribution of fragment sizes. Enzymatic mechanisms primarily utilize restriction endonucleases, which are bacterial enzymes that recognize and hydrolyze DNA at short, palindromic nucleotide sequences, typically 4 to 8 base pairs long. For instance, EcoRI, isolated from Escherichia coli, specifically cleaves the sequence 5'-GAATTC-3', generating sticky ends with 5' overhangs of four nucleotides, which facilitate ligation into compatible vectors. This site-specific cleavage allows for the predictable production of fragments, a cornerstone of recombinant DNA technology since its discovery in the 1970s. Other type II restriction endonucleases, such as HindIII or BamHI, operate similarly by binding as dimers to symmetric recognition sites in the presence of magnesium ions, ensuring high fidelity in double-strand breaks. A notable enzymatic example for random fragmentation is DNase I, a that introduces double-strand breaks at non-specific phosphodiester bonds, producing a of fragments with a of sizes. This randomness is particularly useful for creating diverse DNA libraries, as demonstrated in early approaches where DNase I-generated fragments were cloned into vectors for whole-genome analysis. The enzyme's activity can be tuned by adjusting incubation time and concentration to achieve average fragment lengths of 300–500 base pairs, ideal for next-generation sequencing platforms. Modern methods include tagmentation, which uses hyperactive transposases (e.g., Tn5) to simultaneously fragment DNA and attach sequences, streamlining library preparation for NGS as of 2025. Non-enzymatic methods rely on physical forces to shear DNA strands without sequence specificity. Mechanical shearing via hydrodynamic forces, for example, employs high-velocity fluid flow through narrow channels or orifices to generate tensile stresses that break the DNA backbone, yielding fragments typically in the 100–1000 range. This approach, often implemented using devices like nebulizers or focused ultrasonication, avoids enzymatic biases and is isothermal, preserving DNA integrity during fragmentation. These intentional mechanisms serve to prepare DNA for cloning, where restriction fragments are inserted into plasmids for propagation; sequencing, by generating uniform libraries for assembly; and analysis, such as gel electrophoresis or PCR amplification of specific loci. By producing predictable or adjustable fragment sizes, they underpin advancements in genomics and biotechnology, enabling scalable manipulation of genetic material.

Spontaneous Mechanisms

Spontaneous DNA fragmentation occurs through endogenous cellular processes and environmental exposures that compromise DNA integrity without deliberate external intervention. These mechanisms include oxidative damage from (ROS), enzymatic cleavage during , and lesions induced by radiation or chemicals that propagate breaks during attempted repair. Such fragmentation can lead to pathways or genomic instability if unrepaired. One primary spontaneous mechanism involves oxidative stress, where ROS such as the hydroxyl radical (•OH) directly attack the deoxyribose sugar in the DNA backbone. This abstraction of hydrogen atoms from the sugar moiety generates carbon-centered radicals, which react with oxygen to form peroxyl radicals and ultimately cause strand breaks through cleavage of phosphodiester bonds. The reactivity is highest at the 5' position of deoxyribose, followed by the 4' and 3' positions, leading to single- or double-strand breaks that vary in size depending on the extent of radical propagation. In apoptosis, a physiological process, DNA fragmentation is mediated enzymatically by multiple endonucleases. The primary executor is caspase-activated DNase (CAD), also known as DNA fragmentation factor subunit beta (DFF40). Upon activation of initiator , effector cleaves the inhibitor of CAD (ICAD), releasing active CAD, which preferentially targets internucleosomal linker regions between nucleosomes. This results in double-strand breaks spaced at approximately 180 base pairs (bp), producing a characteristic "nucleosomal ladder" pattern of oligonucleosomal fragments upon . Other nucleases, such as endonuclease G (EndoG) from mitochondria and DNase II from lysosomes, contribute to the process, particularly for initial high-molecular-weight fragmentation or in specific cell types. CAD's activity is essential for the internucleosomal cleavage observed in apoptotic cells across various tissues. Radiation and chemical exposures, such as ultraviolet (UV) light, induce spontaneous fragmentation through the formation of DNA lesions that trigger repair-associated breaks. UV-B radiation primarily generates cyclobutane pyrimidine dimers (CPDs), including thymine dimers, which distort the DNA helix and stall replication forks or transcription. During (NER), endonucleases incise the damaged strand 24–32 nucleotides from the , excising the containing the dimer; however, if repair is incomplete or overwhelmed, these incisions can convert to double-strand breaks, especially in replicating cells where fork collapse occurs. This process is exacerbated in NER-deficient conditions, leading to persistent lesions and fragmentation. Fragment sizes in spontaneous fragmentation differ markedly by mechanism. In apoptosis driven by CAD, breaks occur at regular 180–200 bp intervals corresponding to spacing, yielding discrete multiples that form ladders. In contrast, or UV-induced damage produces variable fragment sizes, often including high-molecular-weight pieces (50–300 kilobase pairs or larger) and random single-strand breaks without uniform laddering, reflecting non-specific radical attacks or repair errors. These distinctions aid in distinguishing apoptotic from necrotic or damage-induced .

Techniques

Induction Methods

Mechanical methods for inducing DNA fragmentation rely on physical forces to break DNA strands randomly, producing fragments suitable for downstream applications like next-generation sequencing (NGS) library preparation. Sonication employs high-frequency waves to generate bubbles that shear DNA, typically yielding fragments of approximately 200-1000 base pairs (), with average sizes around 400-700 depending on duration and intensity. Nebulization forces DNA solution through a narrow aperture under high-pressure nitrogen gas (e.g., 10-20 psi), creating a fine mist that results in random double-stranded breaks, commonly producing fragments in the 700-1500 range. The applies high hydraulic pressure (up to 30,000 psi) to pass DNA through a small orifice, generating shear forces that fragment DNA into smaller pieces, with number-average sizes around 230 under standard conditions. Enzymatic protocols offer precise control over fragmentation by leveraging enzymes to cleave DNA at specific or semi-random sites. Restriction digestion uses Type II endonucleases, such as EcoRI or HindIII, which recognize and cut at defined palindromic sequences, enabling site-specific fragmentation for applications requiring targeted cuts; reaction conditions typically involve incubation at 37°C in appropriate buffers with 1-10 units of enzyme per microgram of DNA. Tagmentation, developed for NGS workflows, utilizes hyperactive Tn5 transposase bound to adapters to simultaneously fragment DNA and append sequencing motifs, producing library-ready fragments of 200-1000 bp in a single step; this method is performed in a magnesium-containing buffer at 55°C for 5-10 minutes with enzyme concentrations optimized at 1-5 nM transposome per reaction. Emerging techniques enhance reproducibility and scalability for NGS library preparation by refining mechanical shearing principles. Acoustic shearing, often via instruments like the Covaris system, directs focused ultrasonic energy to DNA in a controlled acoustic field, achieving uniform fragments from 100-5000 bp without significant sequence bias, ideal for high-molecular-weight input DNA. Point-sink shearing employs hydrodynamic forces in a recirculating flow system, where DNA is pumped through a narrow constriction (e.g., via syringe or HPLC pump at 0.5-2 mL/min), generating unbiased fragments of 1-10 kilobase pairs (kbp) with high yield (75-92%) and minimal equipment needs. These methods are particularly valued in NGS prep for their ability to handle low-input samples while maintaining fragment end integrity. Optimization of induction methods is crucial for achieving desired fragment sizes, especially 200-500 for Illumina sequencing platforms, to ensure even coverage and library efficiency. For mechanical approaches, parameters like cycles (e.g., 30-60 seconds at 20 kHz) or nebulization pressure must be titrated to avoid over- or under-fragmentation, often verified by gel or Bioanalyzer. Enzymatic protocols require balancing buffer (e.g., 10-50 mM Tris-HCl, pH 7.5-8.0), divalent cations (1-10 mM Mg²⁺), and enzyme concentrations (0.1-1 unit/μg DNA) to control cut frequency and prevent bias toward AT-rich regions; for tagmentation, input DNA amounts (1-100 ng) and reaction times are adjusted to yield peak fragment sizes around 300 post-amplification. Such tuning minimizes artifacts like chimeric ends in mechanical methods or insertion biases in enzymatic ones, enhancing overall NGS performance.

Detection Methods

One of the classical methods for detecting DNA fragmentation, particularly in apoptotic cells, is agarose gel electrophoresis, which visualizes the characteristic nucleosomal ladder pattern resulting from internucleosomal cleavage. In this technique, genomic DNA is extracted from cells, separated by size on an agarose gel, and stained with ethidium bromide or similar dyes; apoptotic DNA appears as a series of bands at multiples of approximately 180 base pairs, corresponding to the length wrapped around nucleosomes, distinguishing it from the high-molecular-weight smear seen in necrosis. This method provides qualitative evidence of fragmentation but lacks quantitative precision for low-level damage. The terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay is a widely used technique for detecting and quantifying DNA double-strand breaks by labeling the 3'-hydroxyl ends of fragmented DNA. In the TUNEL procedure, terminal deoxynucleotidyl transferase (TdT) enzyme incorporates fluorescently or biotin-labeled dUTP nucleotides onto the free ends of DNA breaks, which can then be visualized via microscopy, flow cytometry, or immunohistochemistry; this assay is particularly sensitive for identifying apoptotic cells in tissues or cell suspensions. For fertility assessment, the sperm chromatin dispersion (SCD) test evaluates DNA integrity by treating sperm with acid to denature chromatin, followed by lysis, where intact DNA forms a large halo of dispersed loops around the sperm head upon staining and microscopy, while fragmented DNA results in small or absent halos. The SCD method is simple, cost-effective, and correlates well with other fragmentation assays for semen analysis. Quantitative assessment of DNA fragmentation often employs metrics like the DNA Fragmentation Index (DFI), which measures the percentage of sperm with damaged DNA using assays such as the sperm chromatin structure assay (SCSA); a DFI exceeding 30% indicates significant damage associated with reduced fertility success, including lower implantation rates in assisted reproduction. In reproductive contexts, elevated DFI values are associated with lower fertility success, as detailed in studies on assisted reproduction. The , also known as , detects DNA strand breaks (single- and double-strand) in individual cells by embedding them in on a slide, subjecting them to , and to visualize DNA migration forming a "; the tail length and intensity quantify fragmentation levels, making it useful for assessing and . Advanced techniques enable single-cell resolution and detailed size profiling. Flow cytometry combined with propidium iodide (PI) staining assesses DNA content by measuring fluorescence intensity, identifying sub-G1 peaks indicative of fragmented DNA in apoptotic or damaged cells, allowing high-throughput analysis of heterogeneous populations. For fragment size distribution, quantitative PCR (qPCR)-based methods amplify specific DNA regions with primers targeting varying lengths; shorter amplicons amplify more efficiently in fragmented samples, enabling estimation of average fragment sizes through comparative cycle threshold (ΔCt) values without electrophoresis. These qPCR approaches are particularly useful for analyzing cell-free DNA in liquid biopsies or post-treatment samples.

Biological Significance

Role in Programmed Cell Death

DNA fragmentation serves as a key biochemical hallmark and executor in , the predominant form of , where it facilitates the orderly dismantling of the to prevent inflammatory responses. During , endonucleases cleave chromosomal DNA specifically at internucleosomal linker regions, producing a characteristic ladder of fragments approximately 180–200 base pairs in length, which corresponds to the spacing between nucleosomes. This internucleosomal cleavage is primarily mediated by caspase-activated DNase (CAD), also known as DNA fragmentation factor 40 (DFF40), an endonuclease that generates these discrete fragments and contributes to morphological changes such as chromatin condensation and pyknotic nuclei. The activation of CAD is tightly linked to the caspase cascade central to . Apoptotic signals trigger the proteolytic activation of (and to a lesser extent ), which cleaves the inhibitory subunit ICAD (inhibitor of CAD), thereby releasing and activating CAD to translocate to the nucleus and execute fragmentation. This caspase-dependent mechanism ensures that DNA degradation occurs downstream of commitment to , amplifying the apoptotic program while avoiding premature genomic damage. In contrast to , DNA fragmentation plays a more limited or absent role in other pathways. Necroptosis, a regulated necrotic process triggered by death receptor signaling in the absence of , exhibits minimal internucleosomal DNA cleavage due to the lack of activation, resulting instead in random, high-molecular-weight DNA degradation and cell lysis. , an iron-dependent form of cell death driven by , similarly lacks significant DNA fragmentation or involvement in its core execution phase, though emerging 2020s research indicates that certain (such as ) may modulate sensitivity by regulating antioxidant responses rather than directly inducing fragmentation. Biologically, DNA fragmentation in programmed cell death ensures the non-inflammatory clearance of compromised cells by packaging genomic material into apoptotic bodies, thereby preventing the propagation of damaged DNA and maintaining tissue homeostasis. This process is indispensable for embryonic development, immune regulation, and the elimination of potentially oncogenic or virally infected cells, underscoring its evolutionary conservation across metazoans.

Role in Reproduction and Fertility

DNA fragmentation in sperm, often quantified by the DNA fragmentation index (DFI), plays a critical role in male fertility by impairing gamete integrity and subsequent reproductive outcomes. Oxidative stress is a primary cause of sperm DNA fragmentation, arising from endogenous factors like varicocele and exogenous influences such as smoking or environmental pollutants, which generate reactive oxygen species that damage sperm chromatin. Elevated DFI levels, particularly above 20-30%, are associated with reduced success rates in assisted reproductive technologies (ART), including lower fertilization rates (e.g., 73.3% for low DFI <25% vs. 53.2% for high DFI ≥25% in IVF), implantation rates, and clinical pregnancy outcomes in both IVF and intracytoplasmic sperm injection (ICSI) cycles. In oocytes, DNA fragmentation increases with advanced maternal age due to accumulated oxidative damage and diminished repair mechanisms, directly compromising embryo viability and development. Age-related DNA breaks in oocytes lead to higher rates of chromosomal abnormalities and reduced capacity to repair paternal DNA damage, resulting in poorer embryo quality, lower blastocyst formation rates (e.g., 49.6% for low SDF vs. 30.2% for high SDF in women >40 years), and decreased fertility potential. Studies indicate that oocytes from women over 40 exhibit significantly elevated DNA fragmentation, contributing to embryonic arrest and lower ongoing pregnancy rates in ART. Paternal and maternal DNA fragmentation poses inheritance risks by transmitting genomic instability to offspring, increasing the likelihood of developmental abnormalities. High sperm DFI correlates with elevated chromosomal and fragmentation in embryos, leading to random distribution of paternal chromosomal fragments and higher rates of embryonic lethality or congenital defects. Similarly, unrepaired maternal DNA damage exacerbates these risks, with paternal exposure shown to induce transgenerational and embryonic lethality in animal models. Meta-analyses from 2010-2020 demonstrate that sperm DNA fragmentation significantly elevates rates in ART, with odds ratios ranging from 2.28 to 2.48 for high DFI cases compared to low DFI, independent of female factors. Emerging research as of 2025 highlights the potential of cell-free DNA (cfDNA) from seminal plasma as a non-invasive diagnostic tool for assessing DNA fragmentation in fertility evaluations. Fragmentomic analysis of seminal cfDNA reveals distinct profiles associated with male infertility conditions like varicocele or azoospermia, offering insights into fragmentation levels and predicting ART success without invasive sperm assays such as TUNEL or sperm chromatin dispersion (SCD). These advancements underscore cfDNA's role in early fertility diagnostics, correlating fragmentation patterns with miscarriage risks and embryonic viability.

Applications

In Research and Biotechnology

DNA fragmentation plays a pivotal role in next-generation sequencing (NGS) library preparation, where it generates DNA fragments suitable for short-read platforms such as Illumina, which typically require insert sizes of 200-500 base pairs to optimize sequencing efficiency and coverage uniformity. This step involves methods like enzymatic fragmentation or acoustic shearing to produce sheared DNA, followed by end repair, A-tailing, and adapter ligation to create a library ready for amplification and sequencing. Without controlled fragmentation, libraries would yield uneven fragment distributions, leading to biases in read mapping and reduced . In and (PCR)-based techniques, DNA fragmentation via restriction enzymes enables precise insertion of target DNA fragments into cloning vectors. Restriction nucleases cleave DNA at specific recognition sites, generating cohesive ends that facilitate ligation into plasmids or other vectors, allowing construction and propagation in host cells. Similarly, (RFLP) analysis exploits these enzyme-induced fragments to detect variations in DNA sequence length, serving as markers for genetic mapping by identifying polymorphic loci across genomes. In , followed by sequencing (ChIP-seq) relies on DNA fragmentation to isolate and sequence protein-bound DNA regions, elucidating protein-DNA interactions. or enzymatic shearing fragments crosslinked into sizes around 200-500 base pairs, enabling enrichment of specific interactions and high-resolution mapping of binding sites or modifications. Recent advances from 2020 to 2025 have integrated tagmentation—using Tn5 for simultaneous fragmentation and adapter addition—into workflows, enhancing throughput and reducing bias in profiling accessibility and multi-omics data from thousands of cells. Additionally, cell-free DNA (cfDNA) fragmentation patterns have emerged as a tool for epigenetic analysis, where positioning and status influence fragment end motifs, allowing non-invasive inference of tissue-specific profiles with high accuracy via models.

In Medicine and Forensics

In medicine, analysis of cell-free DNA (cfDNA) fragmentation patterns from liquid biopsies has emerged as a powerful tool for noninvasive cancer detection and monitoring. Fragmentomics, which examines cfDNA size distribution, end motifs, and nucleosome footprints, reveals tumor-specific signatures; for instance, shorter fragments (around 50 bp) are enriched in promoter regions of cancer cells, while longer fragments (>500 bp) correlate with euchromatic regions in hepatocellular carcinoma (HCC). Methods like DNA evaluation of fragments for early interception (DELFI) use genome-wide size ratios to achieve high sensitivity (84%) and specificity (53%) for lung cancer screening, enabling tissue-of-origin prediction with area under the curve (AUC) values up to 0.94. Recent advances, including AI-driven models such as EMIT (AUC 0.962), integrate multimodal data for improved early detection, as validated in clinical trials like NCT04825834. In , DNA fragmentation index (DFI) assessment guides fertility treatments, particularly (ICSI), by identifying cases where high fragmentation impairs outcomes. Elevated DFI (>30%) is associated with reduced fertilization rates, poorer quality, and higher risk in assisted reproductive technologies (), prompting the use of testicular extraction for ICSI in men with oligozoospermia and high ejaculated DFI. Antioxidants, such as , vitamins C and E, , and (DHA), mitigate —the primary cause of fragmentation—reducing DFI by up to 22.1% in clinical studies and improving parameters and rates. Testing is recommended for recurrent failures or unexplained infertility, with DFI thresholds like <27% linked to better IVF success. Forensic applications leverage DNA fragmentation analysis to profile samples from degraded sources, such as crime scenes or mass disasters. (PCR) amplification targets short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), enabling analysis of minute (0.4 ng) or fragmented DNA that earlier methods could not handle. Historically, (RFLP) was used in the 1980s–1990s for by digesting DNA with restriction enzymes to detect variable length fragments, offering high discrimination but requiring large, intact samples (micrograms). PCR-based STR multiplexing largely replaced RFLP by the mid-1990s due to its superior sensitivity for degraded material, faster processing, and compatibility with databases like CODIS. Emerging applications from 2020 to 2025 include non-invasive (NIPT) via fetal cfDNA fragments, which screens for aneuploidies like trisomy 21 with 98–99% from maternal blood after 10 weeks . Advances in genome-wide NIPT have expanded detection to rare aneuploidies, abnormalities, and microdeletions (e.g., 22q11.2), improving positive predictive values through size selection of shorter fetal fragments. Additionally, inhibitors target excessive DNA fragmentation in apoptosis-related diseases; broad-spectrum inhibitors like Q-VD-OPh prevent activation and fragmentation in preclinical models of Alzheimer's and Huntington's diseases, while emricasan (IDN-6556) has been trialed for nonalcoholic (NASH) to preserve cell viability, though efficacy remains limited in clinical settings.

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