An explanation for rotor speed effects observed during sedimentation of large folded DNA molecules

Pettijohn, David E.; Hecht, Ralph M.; Stimpson, Don; Scoyk, Susan Van

doi:10.1016/0022-2836(78)90441-2

Cited by 12 publications

(3 citation statements)

References 14 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It is known experimentally that circular DNA exhibits a rotor speed dependence of the sedimentation constant similar to linear DNA with half the length . Circular chains are also relevant in the context of DNA supercoiling and bacterial nucleoids. , The series of conformations for circular N = 200 chains at different field strengths in Figure is similar to the series of linear N = 100 chains in Figure a. A direct comparison is made in Figure d at a driving force G̃ = 1: The circular chain with N = 200 forms a tadpole similar in size and shape to the linear N = 100 chain except that the tail is double-stranded.…”

Section: Circular Polymersmentioning

confidence: 82%

Anomalous Sedimentation of Self-Avoiding Flexible Polymers

Schlagberger

Netz

2008

Macromolecules

View full text Add to dashboard Cite

We investigate the conformational changes of a single self-avoiding flexible polymer in strong sedimentation fields using hydrodynamic simulations and scaling arguments. For small fields or short chains hydrodynamic recirculation leads to compaction. For elevated fields or long chains the hydrodynamic drag leads to stretching of the coil and a decrease of the sedimentation coefficient for both linear and circular DNA, in agreement with results in ultracentrifuge experiments. At very large fields a spontaneous symmetry breaking takes place, and the polymer adopts a conformation consisting of a compact head and a trailing straight tail.

show abstract

Section: Circular Polymersmentioning

confidence: 82%

Anomalous Sedimentation of Self-Avoiding Flexible Polymers

Schlagberger

Netz

2008

Macromolecules

View full text Add to dashboard Cite

show abstract

“…Modal mineralogy of feldspathic litharenite and litharenites of Kuldana Formation. Moreover, displaying the end factors of quartzose parts of the sandstone was reevaluated for the diamond diagram of Pettijohn, et al[48].…”

mentioning

confidence: 99%

Petrography and Provenance of the Sub-Himalayan Kuldana Formation: Implications for Tectonic Setting and Palaeoclimatic Conditions

et al. 2022

View full text Add to dashboard Cite

In this paper, the depositional environment, age, and tectonic context of the Sub-Himalayan Kuldana Formation are discussed in detail. To determine the Kuldana Formation’s depositional environment, age, and tectonic setting, sedimentological, palaeontological, and petrographic investigations have been conducted accordingly. The Kuldana Formation lithologically consists of both siliciclastic and carbonate rocks. Petrographically, the Kuldana Formation’s sandstone is divided into litharenite and feldspathic litharenite petrofacies. The sandstone plots on the QtFL and QmFLt suggest that the sandstone of the Kuldana Formation derived from a recycled orogen provenance field that developed during the collision of the Indian and Eurasian plates in the Lesser and Higher Himalayas. The plots in the diamond diagram further demonstrate that the detritus of the Kuldana Formation was derived from low and middle-to-upper rank metamorphic rocks of the Himalayas. Throughout the deposition of sandstone, paleo-climate conditions were semi-humid to semiarid. Dolostone and limestone are the two main types of carbonate rocks found in the Kuldana Formation. According to Dunham’s Classification, the Kuldana Formation limestone is classified as mudstone, wackstone, and packstone. These petrofacies suggest that the limestone was deposited in an inner-outer ramp setting. The bioclasts include bivalves, brachiopods, crinoid, gastropods, Globigerinoides spp, Lockhartia pustulosa, miliolids, Nummulites atacicus, Nummulites discorbina, Nummulites mamillatus, Nummulites djodjokartae, Nummulites vascus, and ostracods suggesting that the age of Kuldana Formation is Middle Eocene- early Oligocene. The Kuldana Formation was deposited during the initial stages of the Himalayan Orogeny as a result of the Ceno-Tethys Ocean’s regression and transgression, as revealed by a succession of siliciclastic and non-clastic rocks.

show abstract

“…Sometimes, before the gradients were centrifuged, 360 PELLON, ULMER, AND GOMEZ trifuge at 4°C. To minimize any rotor-speed effects (8,17), the rotor speed employed was usually 3,000 or A 4,000 rpm (except when the rotor speed effect itself 5 was being investigated). The final w2t was 6 x 109 rad2/ S.…”

mentioning

confidence: 99%

Heat damage to the chromosome of Escherichia coli K-12

Pellón¹,

Ulmer²,

Gómez³

1980

Appl Environ Microbiol

View full text Add to dashboard Cite

The folded chromosome or nucleoid of Escherichia coli was analyzed by lowspeed sedimentation in neutral sucrose gradients after-in vivo heat treatment. Heat treatment of cultures at 50°C for 15, 30, and 60 min resulted in in vivo association of the nucleoids with cellular protein. Structural changes, determined by the increase in speed dependence of the nucleoids from heated cells, also occurred. These changes were most likely due to the unfolding of the typical compact nucleoid structure. The nucleoids from heated cells also had notably higher sedimentation coefficients (3,000 to 4,500S) than nucleoids from control cells (1,800S). These nucleoids did not contain greater than normal amounts of membrane phospholipids or ribonucleic acid. We propose that the protein associated with the nucleoids from heated cells causes the observed sedimentation coefficient increases. MATERIALS AND METHODS Chemicals and enzymes. Sarkosyl NL-95 (sodium N-lauroylsarcosinate) was a gift of CIBA-GEIGY (Dyestuffs and Chemicals Division, Greensboro, N.C.). Fluorinert FC-48 was a gift of the 3M Co. (Commercial Chemicals Division, St. Paul, Minn.). Angio-CONRAY (sodium iothalamate) was purchased from Mallinckrodt, Inc. (Pharmaceutical Division, St. Louis, Mo.). Sucrose was density gradient grade (RNase free), obtained from Schwarz/Mann (Orangeburg, N.Y.). All other chemicals were purchased from Sigma Chemical Co. (St. Louis, Mo.). [Methyl-'H]thymidine (40 Ci/ mmol), [methyl-'4C]thymidine (47.5 mCi/mmol), L-[4,5-3H]leucine (60 Ci/mmol), [2-'H]glycerol (200 mCi/mol), [5-'H]uracil (30 Ci/mmol), Aquasol, and mini-vials were all purchased from New England Nuclear Corp. (Boston, Mass.). Egg-white lysozyme (EC 3.2.1.17; muramidase; grade I; 3x crystallized; 38,500 U/mg) was obtained from Sigma Chemical Co. Beef pancreas DNase I was obtained from Miles Laboratories (Elkhart, Ind.). Microorganism. The bacterial strain used in this study was a derivative of E. coli K-12 originating from the culture collection of Howard Flanders and desig-358

show abstract

An explanation for rotor speed effects observed during sedimentation of large folded DNA molecules

Cited by 12 publications

References 14 publications

Anomalous Sedimentation of Self-Avoiding Flexible Polymers

Anomalous Sedimentation of Self-Avoiding Flexible Polymers

Petrography and Provenance of the Sub-Himalayan Kuldana Formation: Implications for Tectonic Setting and Palaeoclimatic Conditions

Heat damage to the chromosome of Escherichia coli K-12

Contact Info

Product

Resources

About