Beyond RNA/DNA: exploring the emerging role of Poly(ADP-ribose): structure, function, and condensate formation

Introduction

For decades, DNA and RNA have dominated nucleic acid research as the primary carriers of genetic information, with well-defined structural architectures, base-pairing rules, and regulatory roles that underpin molecular biology. Within this broader family, however, poly(ADP-ribose) (PAR) emerges as a distinct polymer that deviates from these conventions. PAR is a linear or branched homopolymer of adenosine diphosphate-ribose (ADPr) units (Figure 1a) synthesized as a post-translational modification to proteins in response to cellular stress, particularly DNA damage (Malanga and Althauss, 1994; Gupte et al., 2017). Recent studies have shown that ADP-ribosylation also occurs on DNA and RNA, broadening its functional roles in genome regulation and RNA biology (Jankevicius et al., 2016; Munnur et al., 2019; Musheev et al., 2022). Unlike nucleic acids, PAR does not encode genetic information; instead, it plays a central role in maintaining genomic integrity. Free PAR or poly(ADP-ribose) polymerase (PARP) enzymes function as a dynamic molecular signal involved in diverse processes, including DNA damage repair (Zong C. et al., 2022), chromatin remodeling (Chaudhuri and Nussenzweig, 2017; Hottiger, 2015), RNA biogenesis (Engbrecht and Mangerich, 2020; Boamah et al., 2012), spindle formation (Chang et al., 2004), stress response (Duan et al., 2019), bone calcification (Zecca et al., 2025; Mueller et al., 2019), inflammation and others (Gibson and Kraus, 2012; Schreiber et al., 2006; Rhine et al., 2023; Leung, 2014; Suskiewicz et al., 2023; Teloni and Altmeyer, 2016). Dysregulation of PAR is associated with multiple diseases, including cancer, neurodegenerative disorders such as Alzheimer’s and Parkinson’s, autoimmune conditions, and cell death (McGurk et al., 2018a; Lüscher et al., 2018; McGurk et al., 2018c; Kam et al., 2018; Park et al., 2020; Virag, 2005; Zhu et al., 2021), highlighting its critical yet underexplored role in cellular biology.

PAR is produced by the PARP family of enzymes, which control the timing, localization, branching frequency and extent of PAR chain formation (Schreiber et al., 2006; Alemasova and Lavrik, 2019). PARPs use nicotinamide adenine dinucleotide (NAD⁺) as a substrate to synthesize ADP-ribose units that are covalently attached as post-translational modifications to specific amino acids, including aspartate, glutamate, lysine, arginine, histidine, and cysteine (Hendriks et al., 2021; Luo and Kraus, 2012) (Figure 1b, top). Transfer of a single ADP-ribose unit results in mono(ADP-ribosyl)ation (MARylation), whereas addition of polymeric chains leads to poly(ADP-ribosylation) (PARylation) (Vyas et al., 2014; Hottiger et al., 2010). The PARP family consists of 17 multidomain proteins sharing a conserved catalytic core (Li and Chen, 2014; Amé et al., 2004). Among them, PARP1 is the most abundant and accounts for ∼80% of cellular PAR synthesis during the DNA damage response, followed by PARP2 (∼10–15%), with the remainder produced by other PARP isoforms (PARP3 to 16) (Gibson and Kraus, 2012; Suskiewicz et al., 2023). Functionally, PARP1, PARP2, and PARP5a/b (or Tankyrases) catalyze PARylation, while many other family members mainly mediate MARylation. These enzymes are distributed across cellular compartments in the nucleus and cytosol (Suskiewicz et al., 2023), and respond to diverse stresses, including DNA damage, metabolic imbalance, oxidative stress, inflammation, and oncogenic signals. PARylation is reversible: PAR chains are degraded by enzymes such as poly(ADP-ribose) glycohydrolase (PARG) and ADP-ribosyl-acceptor hydrolase 3 (ARH3) following completion of repair processes (Rack et al., 2020) (Figure 1b, top).

PAR was first identified more than 6 decades ago by Chambon and colleagues (Chambon et al., 1963; Fujimura et al., 1967). Early studies mistook it for polyadenylic acid (poly(rA)) due to their chemical similarity, as both contain phosphate groups, ribose sugars, and adenine bases (Figure 1a). Despite this resemblance, PAR is typically present at nanomolar levels in cells (Yamashita et al., 2022), whereas RNA exists at micromolar concentrations (Milo et al., 2010). This raises an important question: how does a low-abundance polymer perform essential and highly specific cellular functions in an RNA-dominated environment? This apparent paradox underscores that PAR is not merely a chemical variant of RNA but a specialized polymer whose unique properties enable functions that cannot be readily substituted by RNA or DNA, revealing an additional layer of cellular regulation that is only beginning to be understood.

Although chemically related to nucleic acids, PAR differs in several fundamental ways. It is approximately twice as highly charged as single-stranded RNA or DNA, as each repeating unit contains two phosphate groups instead of one (Figure 1a). Moreover, the linear distribution of these charges differs: nucleic acids exhibit a relatively uniform charge distribution along their backbone, whereas PAR features closely spaced phosphate groups within each monomer, resulting in a heterogeneous, block-like charge pattern. This higher charge content and non-uniform charge organization contribute to increased mechanical stiffness relative to RNA and DNA (Badiee et al., 2023). In addition, while RNA and DNA are predominantly linear polymers, PAR can adopt both linear and branched architectures (Juarez-Salinas et al., 1982; Alemasova and Lavrik, 2022b; Reber and Mangerich, 2021; Aberle et al., 2020), introducing further structural and functional complexity. In this review, we examine the unique structural characteristics of PAR and how they shape its functional roles, pathological implications, and capacity to drive condensate formation.

Functional roles of PAR

Numerous studies have linked PAR to biomolecular condensates, suggesting that condensate formation may contribute to PAR-dependent cellular processes (Rhine et al., 2022; Altmeyer et al., 2015; Leung, 2014; 2020). Biomolecular condensates are micron-scale, membraneless assemblies that arise via liquid-liquid phase separation of biomolecules (Brangwynne et al., 2009; 2015; Banani et al., 2017; Alberti et al., 2019). A central driver of condensate formation is multivalency (Li et al., 2012), i.e., the presence of multiple interaction sites that enable cooperative molecular interaction. Owing to its high charge content and block-like charge distribution, PAR may act as an efficient multivalent scaffold that recruits diverse biomolecules, particularly intrinsically disordered proteins (IDPs), thereby promoting condensate nucleation (Rhine et al., 2022). We note that the studies discussed in this review encompass a wide array of experimental and computational techniques, each of which probes distinct aspects of PAR biology. Although these studies provide important insights into PAR-dependent processes, comparisons across studies require further validation when extrapolating findings between different systems.

DNA damage repair and chromatin remodeling

A prominent example occurs during DNA damage repair. Efficient repair requires swift and spatially precise organization of repair factors at sites of DNA lesions (Singatulina et al., 2019), where structural alterations or damages to the chemical structure of DNA occur (Figure 1b, top). Upon DNA damage, PARP enzymes are rapidly activated at break sites and synthesize PAR chains. The multivalent nature of PAR enables the efficient recruitment and concentration of DNA repair proteins such as THRAP3 and FET-family proteins (FUS, EWS, and TAF15) at damage foci, facilitating the assembly of repair complexes. Several experimental studies (Altmeyer et al., 2015; Chen, 2015; Patel et al., 2015) have suggested that PAR acts as a molecular seed that triggers the phase separation of FET-family proteins, with their recruitment and condensation at damage sites occurring in a PAR-dependent manner.

Importantly, live-cell imaging showed that PAR-mediated assemblies exhibit molecular selectivity (Altmeyer et al., 2015; Chen, 2015). PAR preferentially recruits these proteins while excluding others, such as those involved in later or independent pathways in DNA damage, including MDC1, 53BP1, Ku70, and NBS1, which are associated with nucleolar compartments. This selectivity indicates that PAR may function not only as a nucleating scaffold but also as a molecular sieve, potentially enriching specific repair proteins at DNA repair foci. A recent in vitro study (Rhine et al., 2022) has shown that PAR promotes FUS condensation through multivalent electrostatic interaction. Another (Levone et al., 2021) suggests that FUS-dependent phase separation contributes to the initiation of DNA repair and the assembly of repair complexes. In addition, Chappidi et al. (2024) demonstrated that PARP1–DNA co-condensates stabilize broken DNA ends, promote PAR synthesis, and recruit FUS into those condensates. Together, these studies provide mechanistic insights into the potential role of PAR–FUS interaction and condensate formation in DNA repair. However, the functional importance of these condensates remains a testable hypothesis, requiring further validation, particularly in cellular contexts.

Interestingly, many DNA repair factors and FET-family proteins are canonical DNA/RNA-binding proteins that contain structured nucleic acid-binding domains along with intrinsically disordered regions (IDRs). These features confer an inherent affinity for DNA and RNA. This raises a key mechanistic question: how does PAR compete with DNA or RNA for binding to proteins that are already associated with nucleic acids or exhibit strong nucleic acid affinity? Recent experimental and computational studies suggested that the distinct physicochemical properties of PAR may offer clues to answering this question (Badiee et al., 2023; Wang et al., 2024; Baidya et al., 2026). In particular, PAR has been observed to be more sensitive to multivalent ions than RNA or DNA and to undergo structural transitions at nearly an order of magnitude lower divalent ion concentrations (Baidya et al., 2026) (Figure 2a). IDRs, which are enriched in charged and multivalent residues, may function analogously to multivalent cations in mediating electrostatic interaction (Badiee et al., 2023). Based on this model, PAR may respond more strongly to IDR-containing proteins than nucleic acids. Accordingly, this enhanced sensitivity and multivalent electrostatic complementarity could enable PAR to compete with DNA and RNA for protein binding and thereby recruiting proteins that are either already bound to nucleic acids or possess intrinsic nucleic acid affinity.

Indeed, a recent study suggested that high PAR concentrations promote irreversible nucleosome unwrapping (decondensation) through interactions between PAR and histone tails (Yang et al., 2026). These observations raise the possibility that competitive interaction between PAR and nucleic acids might contribute to the early stages of the DNA damage response (dos Santos et al., 2021; Hauer and Gasser, 2017), underscoring PAR’s ability to transiently rewire nucleic acid-protein interactions to facilitate repair (Figure 1c). This competitive advantage may be particularly relevant in chromatin, where damaged DNA is tightly wrapped around positively charged histone proteins. For repair to proceed, the damaged region must become accessible. Histones are enriched in lysine- and arginine-rich domains, resulting in a high content of positive charges that drive strong electrostatic interactions with negatively charged polyanions. Due to the higher charge content and greater sensitivity to multivalent interactions, PAR can associate with histones more effectively than DNA (Panzeter et al., 1992). Such preferential binding has been proposed to promote the transient displacement of histones from DNA, the so-called histone shuttling, thereby inducing local chromatin decondensation and increasing accessibility of damaged DNA to repair factors (Realini and Althaus, 1992; Dinant et al., 2012; Belousova and Lavrik, 2023). However, alternative mechanisms have been proposed in which PARP-mediated PARylation of histones, rather than free PAR, promotes chromatin decondensation (Poirier et al., 1982). Thus, the relative contributions of free PAR (Yang et al., 2026) and histone PARylation (Poirier et al., 1982; Zong W. et al., 2022; Strickfaden et al., 2016) to chromatin remodeling during DNA repair remain an open question. Furthermore, Strickfaden et al. (2016) induced DNA damage in living cells and showed that PARP1 activity is required for rapid chromatin decondensation. However, their findings did not support the histone shuttling model, as histone H1 and other histones were depleted rather than accumulated at PAR-enriched sites. As a result, the contribution of histone shuttling to PAR-mediated chromatin remodeling remains to be further validated.

mRNA metabolism

Beyond DNA damage repair, PARP proteins and PARylation also regulate multiple steps of mRNA metabolism, including transcription initiation, elongation, splicing, mRNA processing and export to cytoplasm (Bock et al., 2015; Ke et al., 2019; Eleazer and Fondufe-Mittendorf, 2021). At the level of transcription initiation, chromatin must be opened so that DNA becomes accessible to the transcription machinery. PARylation helps to promote this by loosening chromatin structure (Figure 1c), thereby enabling transcription to begin (Krishnakumar and Kraus, 2010).

During transcription elongation, PARP1 helps release RNA polymerase II (RNAP II) from promoter-proximal pausing (Gibson et al., 2016). RNAP II is temporarily stalled by the negative elongation factor (NELF) complex, which acts as a checkpoint to ensure proper recruitment of transcription and RNA-processing factors, including splicing machinery, before elongation proceeds. PARylation of NELF components promotes their release from RNAP II and nascent mRNA, allowing productive elongation (Gibson et al., 2016).

PARP1 also regulates alternative splicing by binding at exon-intron junctions, bridging chromatin with nascent mRNA, and recruiting specific splicing factors to target sites (Matveeva et al., 2016). After transcription, PARP1 influences mRNA maturation by PARylating poly(A) polymerase (PAP), causing its release from pre-mRNA and reducing polyadenylation efficiency (Di Giammartino et al., 2013), particularly under stress. Since the poly(A) tail is important for mRNA stability, nuclear export, and translation, this leads to widespread effects on gene expression (Passmore and Coller, 2022).

Finally, PARP1 regulates mRNA export by interacting with and PARylating components of the THO/TREX complex that packages mature mRNAs into export-ready ribonucleoprotein particles, ensuring efficient transport from the nucleus to the cytoplasm (Ke et al., 2019; Isabelle et al., 2010; Miyazaki et al., 2014).

Nucleolar organization and ribosome biogenesis

A substantial fraction of PARP proteins (∼50%) localize to the nucleolus, a membraneless organelle that serves as the primary site of ribosome biogenesis (Boamah et al., 2012; Pederson, 2011; Lafontaine et al., 2021). The nucleolus is organized into three distinct subcompartments: the Fibrillar Center (FC), the Dense Fibrillar Component (DFC), and the outermost Granular Component (GC). These subcompartments behave as liquid-like immiscible phases and are functionally linked to different stages of ribosome biogenesis: rDNA transcription initiation in the FC, pre-rRNA processing in the DFC, and ribosomal subunit assembly in the GC (Feric et al., 2016).

Interestingly, in lower eukaryotes including budding yeast, the bipartite core structure consisting of the FC and DFC is absent and instead exists as a single core region (Thiry and Lafontaine, 2005; Engbrecht and Mangerich, 2020). Notably, these organisms also lack PAR within their nucleoli (Citarelli et al., 2010). This correlation suggests that PAR may contribute to establishing or maintaining the separation between the FC and DFC regions. Consistent with this idea, studies in Drosophila nucleoli have shown that the inhibition of PAR synthesis leads to nucleolar disintegration and impaired rRNA processing (Boamah et al., 2012). PAR is enriched in the DFC and therefore might facilitate the recruitment of key nucleolar proteins, including nucleophosmin, fibrillarin, and nucleolin, during different stages of ribosome biogenesis such as rRNA processing, maturation, and ribosomal assembly. In the absence of PAR, these proteins may become mislocalized, leading to defects in rRNA processing and ribosome assembly.

The preference for PAR over RNA or DNA in nucleolar organization may arise from the transient and dynamic nature of PAR-protein interaction. In vitro studies (Rhine et al., 2022; 2023) have shown that PAR-protein interactions are highly dynamic and promote the formation of liquid-like condensates, whereas RNA-protein interactions are comparatively less dynamic and tend to form more solid-like assemblies. This difference may contribute to the role of PAR in organizing liquid-like immiscible nucleolar subcompartments rather than relying on existing RNA or DNA molecules (Alemasova and Lavrik, 2022b; Buerkle and Virag, 2013; Alemasova and Lavrik, 2022a; Boamah et al., 2012; Guerrero and Maggert, 2011; Leung, 2014).

Stress granule assembly

PAR also plays an important role in the assembly of stress granules (SGs), transient membraneless organelles that form in the cytoplasm in response to cellular stress (Protter and Parker, 2016; Hofmann et al., 2021). They function as dynamic protective hubs that sequester untranslated mRNAs and RNA-binding proteins (RBPs), thereby preventing damage from stressors such as heat shock, oxidative stress, and viral infection. PARylation regulates both the assembly and disassembly of stress granules, as well as modulates their molecular composition (Singatulina et al., 2022; Jin et al., 2021; Leung et al., 2011; Duan et al., 2019; Isabelle et al., 2012). SGs form in a highly time- and location-specific manner, which requires the selective recruitment of particular RBPs.

Both PAR and RNA interact with RBPs often through electrostatic interactions (Singatulina et al., 2022). Recent simulations suggest that electrostatic interactions involving RNA persist over a longer length scale than those involving PAR in the presence of divalent ions (Baidya et al., 2026; Maity et al., 2025). This shorter interaction range of PAR may enable it to preferentially recruit nearby proteins that are directly involved in SG formation. Consistent with this idea, experiments have shown that PAR binds to the disordered arginine-glycine-rich region of the RNA-binding protein G3BP1 (Isabelle et al., 2012), promoting its localization to specific cytoplasmic sites where RNA-dependent phase separation and SG assembly occur (Yang et al., 2020; Guillen-Boixet et al., 2020). In vivo studies suggested that under normal conditions, when PAR levels are low, TDP-43 is mostly localized in the nucleus. Upon stress, TDP-43 translocates to the cytoplasm and forms PAR and TDP-43 foci (McGurk et al., 2018a; Marcus et al., 2021). In addition, reduced levels of PAR have been shown to disrupt the proper localization of the RBP hnRNPA1 and might lead to SG disintegration (Duan et al., 2019). The same study further suggested that higher PAR levels promote the co-condensation of TDP-43 and hnRNPA1, which has been associated with neuronal cytotoxicity. Together, these findings suggest that PAR may facilitate the recruitment and organization of specific RNA-binding proteins during SG assembly.

At the same time, PAR can also modulate the material properties of SGs. Excessive accumulation of PAR within SGs can reduce their internal dynamics and promote the formation of more stable, pathological aggregates, a phenomenon associated with several neurodegenerative diseases (Duan et al., 2019; McGurk et al., 2018b). Yeast SGs have viscous and more solid-like properties than mammalian counterparts (Kroschwald et al., 2015), which is presumably due to the lack of the PARylation machinery (Citarelli et al., 2010).

Many cellular condensates, including nucleoli and SGs, can exhibit multiphasic organization, where distinct immiscible phases coexist within a single condensate and display unique material properties to support specialized functions (Fare et al., 2021; Lafontaine et al., 2021; Kaur et al., 2021; Glauninger et al., 2022). Guo et al. (2025) has shown that mixtures of DNA and RNA with identical sequences, in the presence of proteins, can spontaneously organize into multiphasic condensates with DNA-rich and RNA-rich core–shell architectures. By tuning nucleic acid sequences, these multiphasic condensates can be engineered with distinct properties that are capable of selective recruitment of small molecules and regulation of RNA folding or cleavage. Similarly, mixtures of polyphosphate (poly(P)), DNA, and Mg 2 + can form multiphasic condensates whose properties can be modulated by DNA length and concentration (Chawla et al., 2024). These findings suggest that complex mixtures containing PAR and other biomolecules may also generate multiphasic condensates with distinct structures, dynamics, and material properties. Understanding and engineering such condensates could provide new insights into cellular organization and enable the development of synthetic biomaterials with potential applications in drug delivery and biotechnology.

Heterogeneous ensemble of PAR structure

Challenges

The function of a biomolecule is closely linked to its structure, making structural characterization essential for understanding its biological roles. Several studies on proteins (Dignon et al., 2018; Lin and Chan, 2017; Baidya and Reddy, 2022; Baidya et al., 2025a; b) and nucleic acids (Nguyen et al., 2022; Maity et al., 2023; Ramachandran and Potoyan, 2024; Maity et al., 2024) have highlighted the importance of single-chain properties as critical determinants of collective phase separation behavior. These studies suggest that understanding the conformational landscape of individual biomolecules at single molecule level, including the effects of chain length, ionic environment, and chain flexibility, can provide important insights into the molecular principles underlying their condensate formation. Accordingly, it is instructive to first examine the molecular structure and conformational properties of individual PAR molecules before considering their collective behavior in condensates. Although extensive biochemical studies have elucidated the mechanisms of PARP enzymes, PAR synthesis, and their involvement in diverse cellular processes, the biophysical characterization of PAR structure remains relatively limited. One of the major challenges in this area is the difficulty of synthesizing PAR with well-defined length and branching architecture, limiting detailed investigations into how PAR topology influences its physical properties and biological functions (Wu et al., 2025).

In addition, PAR exists as a heterogeneous ensemble of conformations due to its highly disordered nature. Although PAR was discovered more than 60 years ago, its structural heterogeneity has made it difficult to characterize PAR conformational ensemble, as traditional experimental tools are often inadequate for probing such disorder (Alvarez-Gonzalez and Jacobson, 1987; Demurcia et al., 1983; Hayashi et al., 1983). However, recent advances of several experimental approaches, including small-angle X-ray scattering (SAXS) (Wang et al., 2024), fluorescence resonance energy transfer (FRET) (Badiee et al., 2023), atomic force microscopy (AFM) (Sukhanova et al., 2016), and nuclear magnetic resonance (NMR) spectroscopy (Schultheisz et al., 2009), allow better characterization of PAR structures. Despite successful advances, these techniques are still limited in their spatiotemporal resolution and cannot fully resolve microscopic structural details.

A complementary approach for studying PAR structure is the use of computer simulations, which can provide detailed microscopic insights into its conformational ensemble. However, conventional atomistic simulations face significant challenges, including the lack of well-parameterized force fields for the unusual topology of PAR and the difficulty of adequately sampling its heterogeneous conformational space within accessible timescales (D’Annessa et al., 2014; Wang et al., 2024). Coarse-grained (CG) simulations offer a way to overcome these limitations by reducing the number of degrees of freedom and smoothing the ruggedness of the free-energy landscape. Recently, a five-bead CG model of PAR has been developed to investigate its structure, providing a promising tool for studying the conformational properties of PAR and contrasting its behaviors with RNA (Baidya et al., 2026; Nguyen et al., 2019). Similar efforts have also been pursued by other groups (Liu et al., 2025a; Yang et al., 2026).

Structural features

PAR structure is strongly governed by chain length, branching architecture, and ionic environment. Recent advances in experimental techniques (Badiee et al., 2023; Wang et al., 2024) and simulations (Wang et al., 2024; Baidya et al., 2026; D’Annessa et al., 2014) have begun to elucidate PAR structure, revealing that it differs markedly from nucleic acids. Circular dichroism spectroscopy indicated that PAR lacks well-defined secondary structure and instead adopts an extended, disordered random-coil-like conformation (Minaga and Kun, 1983). NMR studies further showed that adenine bases in PAR predominantly adopt the anti conformation, a topology that disfavors the base stacking and hydrogen-bonding interactions commonly observed in nucleic acids (Schultheisz et al., 2009). Consistent with this observation, SAXS-based modeling and computer simulations suggested that base stacking in PAR is either absent or occurs with very low probability (Wang et al., 2024; Baidya et al., 2026) (Figure 2B). Consequently, although it contains adenine bases capable of forming stacking interaction, PAR does not adopt the stacked or weakly helical structures characteristic of poly-adenylic acid (poly(rA)) or poly-deoxyadenylic acid (poly(dA)) (Plumridge et al., 2020; Zhang et al., 2026; Mondal et al., 2024).

Physiochemical factors that influence PAR structure

Polymer length

In most biological polymers, greater sequence complexity often leads to greater structural diversity. However, PAR is a homopolymer and therefore lacks the former. Notably, alternative analogs such as GDP-ribose, CDP-ribose, or UDP-ribose are not found in cells. This raises an important question: if PAR lacks sequence variation, how does it tune its structure to perform diverse biological functions?

In cells, the length of PAR can vary widely, typically ranging from 2 to about 200 ADP-ribose units (Reber and Mangerich, 2021). SAXS experiments and CG simulations revealed that PAR length plays a central role in dictating its structure (Wang et al., 2024; Baidya et al., 2026). In particular, PAR undergoes a length-dependent coil-to-globule transition, a behavior that is not observed in disordered RNAs such as poly(rA) or poly(rU) (Plumridge et al., 2020; Zhang et al., 2026) (Figure 3b). Short PAR chains typically adopt extended conformations, intermediate-length chains behave as random coils, and longer chains form compact globular structures. Thus, even without sequence complexity, PAR can access a broad range of structures simply by varying its chain length (Wang et al., 2024; Baidya et al., 2026). This structural transition is driven by ion-mediated bridging, which promotes chain collapse (Figure 3c). The number of bridging ions increases with PAR length, further enhancing the emergence of length-dependent structural diversity (Figure 3d). See more discussions of ion-PAR interactions below.

Such differences at variable lengths may influence PAR function (Reber and Mangerich, 2021; Dasovich et al., 2021; Löffler et al., 2023; Liu et al., 2025b). For example, PAR recruits a wide range of proteins to initiate processes such as DNA repair and SG assembly. Several biochemical studies (Reber and Mangerich, 2021; Dasovich et al., 2021; Löffler et al., 2023) have shown that the interactions of many of these proteins with PAR depend strongly on its length. PAR-binding proteins contain specialized PAR reader modules, including PAR-binding motifs, zinc finger domains, macrodomains, WWE domains, RNA-binding motifs, SR/KR repeats, and RGG-rich disordered regions (Löffler et al., 2023; Krietsch et al., 2013; Leung, 2020). PAR reader modules are highly diverse in both length (20–150 residues) and structural properties, ranging from well-folded domains to IDRs. PAR structural variability may enable selective recognition by specific PAR reader modules and PAR-binding proteins. For example, DEK forms stable complexes with longer PAR chains (≥ 54 ADP-ribose units) but shows no interaction with shorter chains (≤ 18 units) (Fahrer et al., 2010). Similarly, p53 forms three distinct complexes with longer PAR chains at different PAR:protein ratios, whereas shorter chains form only a single complex (Fahrer et al., 2007). Comparable length-dependent interactions have also been reported for several DNA repair proteins, including XPA, NONO, polβ, APE1, and XRCC1 (Teloni and Altmeyer, 2016; Fahrer et al., 2007). In contrast, proteins such as H1, FUS, TAF15, and EWS can interact with both short and long PAR chains (Teloni and Altmeyer, 2016; Fahrer et al., 2007; Leung, 2014; Gagne et al., 2008; Sang et al., 2024).

This suggests that PAR of specific lengths can selectively recruit distinct sets of proteins. Such length dependence further implies that PARylation may regulate the sequential recruitment of proteins at DNA damage sites. Proteins capable of binding short PAR chains, such as FUS and EWS, may be recruited during the early stages of PARylation when PAR chains are relatively short. In contrast, proteins such as DEK, p53, and XPA preferentially associate with longer PAR chains and are therefore likely recruited at later stages as PAR polymers elongate. Thus, PAR length may contribute to the temporal and sequential recruitment of proteins to DNA repair foci, nucleoli, or SGs.

In addition to regulating protein recruitment, PAR length also influences condensate formation, as well as their dynamics and material properties. In vitro studies show that a minimum PAR length (≥ 5 ADP-ribose units) is required for condensate formation, and increasing PAR length enhances condensate assembly (Rhine et al., 2022). Condensates formed by medium-length PAR are typically dynamic and liquid-like, whereas longer PAR chains (≥ 32 units) tend to form more solid-like aggregates.

Branching pattern

In addition to linear chains, PAR can also exist as a branched polymer, which is typically synthesized by PARP1 and PARP2 (Juarez-Salinas et al., 1982; Alemasova and Lavrik, 2022b; Reber and Mangerich, 2021; Aberle et al., 2020). PAR branching occurs approximately every 20-50 ADP-ribose units (Alvarez-Gonzalez and Jacobson, 1987; Miwa et al., 1979), which gives rise to a unique star-like topology that alters the spatial distribution and accessibility of negative charges compared with linear PAR of similar size. As a result, branched PAR may act as a more effective scaffold, enabling the simultaneous recruitment of multiple proteins due to its increased multivalency compared to linear chains (Löffler et al., 2023; Reber and Mangerich, 2021; Aberle et al., 2020). Branch points within PAR could also serve as specific recognition motifs for proteins that preferentially bind branched PAR. For example, the histone chaperone APLF specifically recognizes and binds to PAR branching points, facilitating the removal of histone H3 from chromatin and thereby increasing the accessibility of damaged DNA for repair (Chen et al., 2018).

PAR branching might also influence the dynamics and material properties of condensates. In vitro studies showed that PAR maintains fluidity of ASK3 condensates (Watanabe et al., 2021) probably due to its flexible nature. Similarly, the structural features of branched PAR may affect condensate organization by creating internal voids that could enhance molecular mobility and promote more dynamic condensate states compared with those formed by linear PAR. Conversely, hyperbranched PAR is more effective in promoting protein phase separation, such as seen in FUS (Sukhanova et al., 2024b; Aberle et al., 2020), compared to linear chains and may lead to less dynamic, more solid-like condensates that might transition into pathological aggregates (Figure 1b, bottom). Furthermore, hyperbranched PAR is less efficiently degraded by the PARG enzyme, making it more stable than linear PAR and thereby contributing to the stabilization and persistence of PAR-mediated condensates (Aberle et al., 2020). However, the impact of PAR branching on condensate formation, dynamics, and function in cellular contexts remains poorly understood, with limited direct evidence currently available. Therefore, elucidating how PAR branching modulates the structural, biophysical, and functional properties of condensates represents an important direction for future investigation.

Multivalent ions

PAR is a highly charged polyelectrolyte whose physicochemical behavior is strongly governed by its interaction with surrounding ions. Single-molecule FRET experiments reveal that under monovalent salt conditions, PAR is significantly stiffer and less flexible than RNA or DNA, presumbaly due to its higher charge content compared to nucleic acids of the same length (approximately twice that of single-stranded RNA or DNA) (Badiee et al., 2023; Baidya et al., 2026; Baidya et al., 2025a). Both experimental and computational studies have observed that ions regulate PAR conformations through a combination of electrostatic screening and specific ion-phosphate interactions (Badiee et al., 2023; Wang et al., 2024; Baidya et al., 2026). In particular, multivalent cations such as Mg 2 +, Ca 2 +, and polyamines induce highly cooperative transitions from extended to compact states at significantly lower concentrations than monovalent ions, highlighting the importance of ion valency (Figures 3a,b). This behavior contrasts with RNA, where structural transitions are often less cooperative in multivalent ions (Nguyen and Thirumalai, 2020; Zhang et al., 2026), suggesting distinct underlying mechanisms. Recent CG simulations with explicit ions demonstrated that PAR exhibits enhanced sensitivity to multivalent ions, with critical concentrations an order of magnitude lower than those required for RNA (Baidya et al., 2026) (Figure 2a). Such transitions occur mainly due to the higher ion binding and bridging in PAR than RNA (Figure 2c). Moreover, length-dependent structural changes in PAR are strongly coupled with enhanced ion-phosphate interactions (Figures 3c,d).

At the molecular level, the differences between PAR and RNA can be traced to their charge distributions and ion-binding modes (Figures 2d–f). Computational studies suggested that while RNA exhibits a relatively uniform charge distribution along its backbone and interacts with ions predominantly in a diffuse manner (Maity et al., 2025; Zhang et al., 2026), PAR contains clustered phosphate groups that promote localized, direct ion binding and facilitate long-range ion-mediated bridging interactions (Baidya et al., 2026). As a result, PAR forms a more compact ion atmosphere compared to the extended ion cloud surrounding RNA. This distinction may have important functional consequences: the diffuse ion environment of RNA can enable long-range electrostatic recruitment of protein partners, whereas the compact ion atmosphere of PAR potentially favors selective and spatially localized interactions, which are essential for cellular functions like DNA repair, SG assembly, etc. Ion identity further modulates these effects (Sukhanova et al., 2024a), with divalent ions such as Ca 2 + often promoting stronger condensation than Mg 2 + due to the differences in ion-binding modes similar to RNA (Baidya et al., 2026; Habibullah et al., 2024; Mondal et al., 2025; Onuchic et al., 2019). Consistent with this, the higher condensation propensity of Ca 2 + has been shown to drive the formation of dense Ca 2 +-PAR droplets in the extracellular matrix, which deposit on collagen surfaces and contribute to the initiation of bone mineralization (Zecca et al., 2025; Mueller et al., 2019).

These unique ion-responsive properties suggest that PAR may serve as an efficient scaffold for biomolecular condensate formation. Despite its lower cellular abundance relative to RNA, PAR can effectively compete for protein binding and contribute to phase separation under physiological conditions. Its ability to form compact, ion-mediated networks could facilitate selective recruitment of functionally relevant proteins while minimizing nonspecific interactions. Despite their chemical similarity, PAR and RNA exhibit fundamentally different ion-coupled behaviors arising from differences in charge distribution and ion association. This distinction likely underlies the preferential utilization of PAR in cellular processes requiring rapid, localized, and tightly regulated assembly of biomolecular condensates.

Temperature

Growing evidence (Wadsworth et al., 2023; Pullara et al., 2022; Wadsworth et al., 2025; Merindol et al., 2018) indicates that RNA and DNA can exhibit thermoresponsive phase behavior, where phase separation is enhanced with increasing temperature in the presence of multivalent ions such as Mg 2 +, Ca 2 +, spermine, spermidine, etc. This phenomenon, the so-called lower critical solution temperature (LCST), has been attributed to ion desolvation, in which water molecules are released from the ion solvation shells, enabling stronger ion–phosphate interactions that facilitate condensate formation (Ramachandran and Potoyan, 2025; Li and Chen, 2025). Given the chemical similarities between PAR and RNA, it is plausible that PAR may also exhibit LCST behavior. However, experimental studies directly examining the temperature dependence of PAR condensation are currently lacking, making this an important area for future investigation. Notably, this phenomenon can be modulated by ion concentration, ion identity, and sequence (Chen et al., 2026; Wadsworth et al., 2023; 2025). Therefore, systematic studies examining the effects of temperature coupled with ionic conditions, PAR chain length, and branching architecture will be necessary to establish a comprehensive understanding of the thermoresponsive behavior of PAR condensates.

Therapeutic potential

PAR plays a dual role in cellular physiology, functioning in both survival and death pathways. Under mild DNA damage, PAR contributes to DNA repair and cell protection (Figure 1b, top). However, severe damage induces excessive PAR synthesis, or hyperPARylation, which consumes large amounts of NAD + required for PAR production (Berger, 1985) (Figure 1b, bottom). NAD + depletion impairs ATP generation, causing an energy crisis that disrupts essential metabolic and repair processes, ultimately triggering a regulated cell death pathway known as parthanatos (David et al., 2009). Under normal conditions, PAR levels are tightly controlled by PAR-degrading enzymes such as PARG and ARH3. When hyperPARylation overwhelms these mechanisms, ATP depletion ensues, tipping the balance toward cell death. Thus, PAR functions as a molecular switch governing cell fate, and modulation of its levels has been explored as a therapeutic strategy to promote cell survival or induce cell death (Jeong and Kang, 2024; Bai, 2015).

Exploiting this principle, PARP inhibitors have emerged as targeted cancer therapeutics (Morales et al., 2014). PARP enzymes normally repair single-strand DNA breaks, but their inhibition leads to the accumulation of lesions that are converted into lethal double-strand breaks during replication. While healthy cells can repair such damage via homologous recombination, mediated by proteins like BRCA1 and BRCA2, many cancers carry mutations in these genes and are deficient in this pathway. In such contexts, PARP inhibition results in catastrophic DNA damage and selective tumor cell death, the so-called synthetic lethality (Petropoulos et al., 2024). This mechanism underlies the clinical efficacy of PARP inhibitors such as Olaparib, representing a precision approach in cancer therapy (Zhou et al., 2025).

Beyond cancer, aberrant PAR accumulation has been implicated in neurodegeneration (McGurk et al., 2018a; Lüscher et al., 2018; McGurk et al., 2018c; Park et al., 2020; Virag, 2005; Jeong and Kang, 2024; Zhu et al., 2021) (Figure 1b, bottom). Excessive PAR promotes aggregation of disease-associated proteins, including α-synuclein (Kam et al., 2018), TDP-43, FUS (Rhine et al., 2022), and hnRNPA1, forming pathological inclusions that contribute to disorders such as Parkinson’s disease, Alzheimer’s disease, Amyotrophic Lateral Sclerosis (ALS), and Frontotemporal Dementia (FTD). Emerging therapeutic strategies seek to combine PARP inhibitors with other agents that modulate the DNA damage response, tailored to disease stage and patient-specific factors, offering promising avenues for mitigating neurodegeneration (Kam et al., 2018; McGurk et al., 2018c).

Future directions

Studies on PAR have proposed its multifaceted role in regulating both cellular function and dysfunction, acting as a molecular scaffold, sieve, and switch. It could function as a scaffold to initiate phase separation, as a molecular sieve that selectively recruits proteins into condensates, and its cellular levels act as a switch governing cell survival and death. Consequently, PAR currently represents a critically important area of research. Despite extensive biochemical investigations, biophysical studies on PAR remain comparatively limited. This imbalance highlights a key opportunity for future studies to develop a quantitative, mechanistic understanding of PAR-driven condensates and their roles in cellular organization and stress response.

Many important questions remain unanswered, in part due to limitations in current experimental techniques and computational approaches: (1) how the branching architecture influences PAR structural organization and specificity toward particular binding proteins; (2) how sequence length and ion interactions collectively govern the emergent material properties of PAR condensates; (3) how cellular environmental factors such as temperature, pH, and macromolecular crowding modulate these properties and translate into functional outcomes; (4) how PAR-driven condensates differ from RNA condensates in terms of formation mechanisms, structure, dynamics, material properties, and the physicochemical nature of their microenvironments including ion composition, dielectric properties, hydration, and local pH; (5) whether PAR condensates with defined length and branching architectures can be rationally engineered to selectively recruit therapeutic molecules for applications in drug delivery and biomaterial design and (6) whether hybrid PAR-RNA condensates exhibit emergent properties that are not accessible to either component alone, and how such properties can be tuned for functional or synthetic applications. Answering these questions will be essential for establishing a predictive, mechanistic framework of PAR-driven phase behavior, enabling the rational design of therapeutics and the engineering of condensate based biomaterials with tunable structure, dynamics, and function.

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Footnotes

Edited by: Jianhan Chen, University of Massachusetts Amherst, United States

Reviewed by: Vysakh Ramachandran, Iowa State University, United States

Xinming Su, Hangzhou City University, China