Abstract
Poly (ADP)‑ribose polymerase 1 (PARP1) is an abundant nuclear protein well‑known for its role in DNA repair yet also participates in DNA replication, transcription, and co‑transcriptional splicing, where DNA is undamaged. Thus, binding to undamaged regions in DNA and RNA is likely a part of PARP1’s normal repertoire. Here we describe analyses of PARP1 binding to two short single‑stranded DNAs, a single‑stranded RNA, and a double stranded DNA. The investigations involved comparing the wild‑ type (WT) full‑length enzyme with mutants lacking the catalytic domain (∆CAT) or zinc fingers 1 and 2 (∆Zn1∆Zn2). All three protein types exhibited monomeric characteristics in solution and formed saturated 2:1 complexes with single‑stranded T 20 and U 20 oligonucleotides. These complexes formed without accumulation of 1:1 intermediates, a pattern suggestive of positive binding cooperativity. The retention of binding activities by ∆CAT and ∆Zn1∆Zn2 enzymes suggests that neither the catalytic domain nor zinc fingers 1 and 2 are indispensable for cooperative binding. In contrast, when a double stranded 19mer DNA was tested, WT PARP1 formed a 4:1 complex while the ∆Zn1Zn2 mutant binding saturated at 1:1 stoichiometry. These deviations from the 2:1 pattern observed with T 20 and U 20 oligonucleotides show that PARP’s binding mechanism can be influenced by the secondary structure of the nucleic acid. Our studies show that PARP1:nucleic acid interactions are strongly dependent on the nucleic acid type and properties, perhaps reflecting PARP1’s ability to respond differently to different nucleic acid ligands in cells. These findings lay a platform for understanding how the functionally versatile PARP1 recognizes diverse oligonucleotides within the realms of chromatin and RNA biology.
Document Type
Article
Publication Date
2024
Funding Information
Research reported in this publication was supported by the National Science Foundation grant, MCB 2016515 (Y.N.F.-M.) and the National Institutes of Environmental Health grants, R01 R01ES031846, R01ES034253 (Y.N.F.-M.).
Repository Citation
Melikishvili, Manana; Fried, Michael G.; and Fondufe‑Mittendorf, Yvonne N., "Cooperative nucleic acid binding by Poly ADP‑ribose polymerase 1" (2024). Markey Cancer Center Faculty Publications. 221.
https://uknowledge.uky.edu/markey_facpub/221
Notes/Citation Information
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