Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Proofreading01:31

Proofreading

6.3K
Synthesis of new DNA molecules is carried out by the enzyme DNA polymerase, which adds nucleotides on the daughter strand complementary to the template DNA strand. DNA polymerase has a higher affinity to add the correct base and ensures fidelity during DNA replication. Furthermore,  it exhibits proofreading activity during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.
Errors During Replication are Corrected by the DNA Polymerase...
6.3K
Nucleic Acid Structure01:25

Nucleic Acid Structure

6.1K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
6.1K
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

9.2K
Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
9.2K
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

14.1K
For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
14.1K
The Replisome03:01

The Replisome

33.5K
DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with...
33.5K
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

29.5K
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
29.5K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

SATB2 dysregulation generates a novel circular RNA and drives KRAS-like transcriptional reprogramming and transformation-associated phenotypes.

Cell communication and signaling : CCS·2026
Same author

DNA methylation, nucleic acid structure, and rett mutations tune MeCP2 binding affinity and cooperativity.

The Journal of biological chemistry·2026
Same author

Single amino-acid differences define H2B variants and modify chromatin accessibility to induce EMT in breast cancer.

Oncogene·2026
Same author

SELEX identifies high-affinity RNA targets for chromatin-binding proteins PARP1 and MeCP2.

iScience·2025
Same author

Histone variants: The bricks that fit differently.

The Journal of biological chemistry·2024
Same author

Beyond the Usual Suspects: Examining the Role of Understudied Histone Variants in Breast Cancer.

International journal of molecular sciences·2024

Related Experiment Video

Updated: Jun 29, 2025

Analyzing DNA-Protein Interactions with Streptavidin-Based Biolayer Interferometry
08:07

Analyzing DNA-Protein Interactions with Streptavidin-Based Biolayer Interferometry

Published on: January 17, 2025

1.3K

Cooperative nucleic acid binding by Poly ADP-ribose polymerase 1.

Manana Melikishvili1, Michael G Fried2, Yvonne N Fondufe-Mittendorf3

  • 1Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA.

Scientific Reports
|March 30, 2024
PubMed
Summary

Poly (ADP)-ribose polymerase 1 (PARP1) binds single-stranded DNA and RNA with positive cooperativity, a function independent of its catalytic domain. Nucleic acid secondary structure influences PARP1 binding stoichiometry, revealing its versatile ligand recognition.

More Related Videos

Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events
10:59

Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events

Published on: May 13, 2019

9.7K
An Assay for Quantifying Protein-RNA Binding in Bacteria
07:02

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

6.6K

Related Experiment Videos

Last Updated: Jun 29, 2025

Analyzing DNA-Protein Interactions with Streptavidin-Based Biolayer Interferometry
08:07

Analyzing DNA-Protein Interactions with Streptavidin-Based Biolayer Interferometry

Published on: January 17, 2025

1.3K
Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events
10:59

Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events

Published on: May 13, 2019

9.7K
An Assay for Quantifying Protein-RNA Binding in Bacteria
07:02

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

6.6K

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • Poly (ADP)-ribose polymerase 1 (PARP1) is a nuclear protein involved in DNA repair, replication, transcription, and splicing.
  • PARP1's interaction with undamaged DNA and RNA is crucial for its diverse cellular functions.
  • Understanding PARP1's nucleic acid binding mechanisms is key to elucidating its roles in chromatin and RNA biology.

Purpose of the Study:

  • To investigate the binding characteristics of wild-type (WT) PARP1 and its mutants to various nucleic acid structures.
  • To determine the role of PARP1's catalytic domain and zinc fingers in nucleic acid binding and cooperativity.
  • To explore how nucleic acid secondary structure influences PARP1 binding stoichiometry and mechanism.

Main Methods:

  • Analysis of PARP1 binding to single-stranded DNA (T20), single-stranded RNA (U20), and double-stranded DNA (19mer).
  • Comparison of full-length WT PARP1 with mutants lacking the catalytic domain (ΔCAT) or zinc fingers 1 and 2 (ΔZn1ΔZn2).
  • Characterization of protein-nucleic acid complex stoichiometry and binding patterns.

Main Results:

  • WT PARP1, ΔCAT, and ΔZn1ΔZn2 PARP1 formed saturated 2:1 complexes with single-stranded oligonucleotides (T20, U20) with positive binding cooperativity.
  • Neither the catalytic domain nor zinc fingers 1 and 2 are essential for cooperative binding to single-stranded nucleic acids.
  • WT PARP1 formed a 4:1 complex with double-stranded DNA, while the ΔZn1Zn2 mutant showed 1:1 stoichiometry, indicating structure-dependent binding.

Conclusions:

  • PARP1 exhibits structure-dependent binding mechanisms influenced by nucleic acid secondary structure.
  • PARP1's interactions with diverse oligonucleotides are critical for its functional versatility in chromatin and RNA biology.
  • These findings provide a foundation for understanding how PARP1 recognizes different nucleic acid ligands in cellular contexts.