Logo of pnasPNASInfo for AuthorsSubscriptionsAboutThis Article
Proc Natl Acad Sci U S A. 1981 Aug; 78(8): 4833–4837.
PMCID: PMC320266

DNA flexibility studied by covalent closure of short fragments into circles.


The ring closure probability, or j factor, has been measured for DNA restriction fragments of defined sequence bearing EcoRI cohesive ends and ranging in size from 126 to 4361 base pairs (bp). The j factor is defined as the ratio of the equilibrium constants for cyclization and for bimolecular association via the cohesive ends. The end-joining reactions are fast compared to covalent closure of the cohesive ends by T4 DNA ligase. The rate of ligase closure is shown to be proportional to the equilibrium fraction of DNA molecules with joined cohesive ends, both in cyclization and in bimolecular association reactions. The j factor changes by less than 10-fold between 242 and 4361 bp, whereas it decreases by more than 100-fold between 242 and 126 bp as the DNA reaches the size range of the persistence length (150 bp). As regards ring closure, short DNA fragments are surprisingly flexible. These data are in good agreement with predictions by others for the ring closure probability of a wormlike chain.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (950K), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Klug A, Rhodes D, Smith J, Finch JT, Thomas JO. A low resolution structure for the histone core of the nucleosome. Nature. 1980 Oct 9;287(5782):509–516. [PubMed]
  • Earnshaw WC, Harrison SC. DNA arrangement in isometric phage heads. Nature. 1977 Aug 18;268(5621):598–602. [PubMed]
  • Schellman JA. Flexibility of DNA. Biopolymers. 1974 Jan;13(1):217–226. [PubMed]
  • Wang JC, Davidson N. On the probability of ring closure of lambda DNA. J Mol Biol. 1966 Aug;19(2):469–482. [PubMed]
  • Wang JC, Davidson N. Thermodynamic and kinetic studies on the interconversion between the linear and circular forms of phage lambda DNA. J Mol Biol. 1966 Jan;15(1):111–123. [PubMed]
  • Pörschke D, Eigen M. Co-operative non-enzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic--oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH. J Mol Biol. 1971 Dec 14;62(2):361–381. [PubMed]
  • Bolivar F. Construction and characterization of new cloning vehicles. III. Derivatives of plasmid pBR322 carrying unique Eco RI sites for selection of Eco RI generated recombinant DNA molecules. Gene. 1978 Oct;4(2):121–136. [PubMed]
  • Kroeker WD, Kowalski D, Laskowski M., Sr Mung bean nuclease I. Terminally directed hydrolysis of native DNA. Biochemistry. 1976 Oct 5;15(20):4463–4467. [PubMed]
  • Mertz JE, Davis RW. Cleavage of DNA by R 1 restriction endonuclease generates cohesive ends. Proc Natl Acad Sci U S A. 1972 Nov;69(11):3370–3374. [PMC free article] [PubMed]
  • Olson WK. The flexible DNA double helix. I. Average dimensions and distribution functions. Biopolymers. 1979 May;18(5):1213–1233. [PubMed]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • PubMed
    PubMed citations for these articles
  • Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...