ArticleNucleic acids research2004
The stability of Seeman JX DNA topoisomers of paranemic crossover (PX) molecules as a function of crossover number.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed, 85 citations in OpenAlex.
- Paranemic Cohesion of DNA under Isothermal Conditions.JACS Au · 2026Article
- Repurposing of drug molecules from FDA database against Hepatitis C virus E2 protein using ensemble docking approach.Molecular diversity · 2024Article
- Mechanism of DNA origami folding elucidated by mesoscopic simulations.Nature communications · 2024Article
- Diameter Dependent Melting and Softening of dsDNA Under Cylindrical Confinement.Frontiers in chemistry · 2022Article
- Exceptional Nuclease Resistance of Paranemic Crossover (PX) DNA and Crossover-Dependent Biostability of DNA Motifs.Journal of the American Chemical Society · 2020Article
- DNA Translocation through Hybrid Bilayer Nanopores.The journal of physical chemistry. C, Nanomaterials and interfaces · 2019Article
- Structure and electrical properties of DNA nanotubes embedded in lipid bilayer membranes.Nucleic acids research · 2018Article
- Terahertz Frequency Spectroscopy to Determine Cold Shock Protein Stability upon Solvation and Evaporation - A Molecular Dynamics Study.IEEE transactions on terahertz science and technology · 2017Article
- The unusual and dynamic character of PX-DNA.Nucleic acids research · 2015Article
- Computational Docking Study of p7 Ion Channel from HCV Genotype 3 and Genotype 4 and Its Interaction with Natural Compounds.PloS one · 2015Article
- Complex reconfiguration of DNA nanostructures.Angewandte Chemie (International ed. in English) · 2014Article
- Elasticity of DNA and the effect of dendrimer binding.The European physical journal. E, Soft matter · 2013Article
- Structural rigidity of paranemic crossover and juxtapose DNA nanostructures.Biophysical journal · 2011Article
- Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin.Journal of molecular modeling · 2009Article
- Thermodynamics of forming a parallel DNA crossover.Biophysical journal · 2009Article
- The poly dA helix: a new structural motif for high performance DNA-based molecular switches.Nucleic acids research · 2009Article
- Molecular-dynamics simulations of insertion of chemically modified DNA nanostructures into a water-chloroform interface.Biophysical journal · 2008Article
- Architecture with GIDEON, a program for design in structural DNA nanotechnology.Journal of molecular graphics & modelling · 2006Article
- Atomic-level simulations of seeman DNA nanostructures: the paranemic crossover in salt solution.Biophysical journal · 2006Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We use molecular dynamics simulations in explicit water and salt (Na+) to determine the effect of varying the number of crossover points on the structure and stability of the PX65 paranemic crossover DNA molecule and its JXM topoisomers (M denotes the number of missing crossover points), recently synthesized by the Seeman group at New York University. We find that PX65, with six crossover points, is the most stable, and that the stability decreases monotonically with the number of crossover points PX65 > JX1 > JX2 > JX3 > JX4, with 6, 5, 4, 3 and 2 crossover points, respectively. Thus, for PX65/JX1, the strain energy is approximately 3 kcal/mol/bp, while it is approximately 13 kcal/mol/bp for JX2, JX3 and JX4. Another measure of the stability is the change in the structure from the minimum energy structure to the equilibrium structure at 300 K, denoted as root-mean-square deviation in coordinates (CRMSD). We find that CRMSD is approximately 3.5 A for PX65, increases to 6 A for JX1 and increases to 10 A for JX2/JX3/JX4. As the number of crossover points decreases, the distance between the two double helical domains of the PX/JX molecules increases from approximately 20 A for PX65 to 23 A for JX4. This indicates that JX2, JX3 and JX4 are less likely to form, at least in with Na+. However, in all the cases, the two double helical domains have average helicoidal parameters similar to a typical B-DNA of similar length and base sequence.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.