(Q71187124)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:8679953%20AND%20SRC:MED&resulttype=core&format=json

16 October 2019

title

Molecular dynamics simulations of small DNA plasmids: effects of sequence and supercoiling on intramolecular motions (English)

1 reference

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16 October 2019

author name string

R K Tan

series ordinal

1

1 reference

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16 October 2019

D Sprous

series ordinal

2

1 reference

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16 October 2019

S C Harvey

series ordinal

3

1 reference

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16 October 2019

publication date

1 August 1996

1 reference

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16 October 2019

1 reference

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16 October 2019

volume

39

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:8679953%20AND%20SRC:MED&resulttype=core&format=json

16 October 2019

issue

2

1 reference

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16 October 2019

page(s)

259-278

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:8679953%20AND%20SRC:MED&resulttype=core&format=json

Enhancer-origin interaction in plasmid R6K involves a DNA loop mediated by initiator protein

16 October 2019

cites work

1 reference

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Hin-mediated site-specific recombination requires two 26 bp recombination sites and a 60 bp recombinational enhancer.

21 January 2018

1 reference

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Functional replacement of a protein-induced bend in a DNA recombination site

21 January 2018

1 reference

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Alternative DNA loops regulate the arabinose operon in Escherichia coli

21 January 2018

1 reference

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DNA looping and unlooping by AraC protein

21 January 2018

1 reference

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In vivo sequence requirements of the SV40 early promoter region

21 January 2018

1 reference

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An operator at -280 base pairs that is required for repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repression

21 January 2018

1 reference

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Upstream repression and CRP stimulation of the Escherichia coli L-arabinose operon

21 January 2018

1 reference

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AraC-DNA looping: Orientation and distance-dependent loop breaking by the cyclic AMP receptor protein

21 January 2018

1 reference

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Transcription activation at a distance by phage phi 29 protein p4. Effect of bent and non-bent intervening DNA sequences

21 January 2018

1 reference

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DNA looping generated by DNA bending protein IHF and the two domains of lambda integrase

21 January 2018

1 reference

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Positive and negative effects of DNA bending on activation of transcription from a distant site

21 January 2018

1 reference

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Site-specific relaxation and recombination by the Tn3 resolvase: recognition of the DNA path between oriented res sites

21 January 2018

1 reference

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Computer simulation of DNA supercoiling

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0282%28199608%2939%3A2%3C259%3A%3AAID-BIP12%3E3.0.CO%3B2-9

Conformational and thermodynamic properties of supercoiled DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0282%28199608%2939%3A2%3C259%3A%3AAID-BIP12%3E3.0.CO%3B2-9

Monte Carlo analysis of the conformation of DNA catenanes.

21 January 2018

1 reference

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The effect of intrinsic curvature on supercoiling: predictions of elasticity theory.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0282%28199608%2939%3A2%3C259%3A%3AAID-BIP12%3E3.0.CO%3B2-9

Molecular modeling and energy refinement of supercoiled DNA.

21 January 2018

1 reference

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Supercoiled DNA energetics and dynamics by computer simulation

21 January 2018

1 reference

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Twist and writhe of a DNA loop containing intrinsic bends

21 January 2018

1 reference

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Molecular mechanics model of supercoiled DNA.

21 January 2018

1 reference

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Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA.

21 January 2018

1 reference

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Optimization by Simulated Annealing

21 January 2018

1 reference

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Definitions and nomenclature of nucleic acid structure parameters.

21 January 2018

1 reference

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Base sequence and helix structure variation in B and A DNA

21 January 2018

1 reference

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The locus of sequence-directed and protein-induced DNA bending

21 January 2018

1 reference

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Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles

21 January 2018

1 reference

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The ten helical twist angles of B-DNA.

21 January 2018

1 reference

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A comparison of six DNA bending models

21 January 2018

1 reference

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Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G

21 January 2018

1 reference

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Analysis of local helix geometry in three B-DNA decamers and eight dodecamers

21 January 2018

1 reference

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Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G

21 January 2018

1 reference

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Calculated compression, bending, shearing, torsion, and base-tilting force constants of B- and A-form poly(dG).poly(dC)

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0282%28199608%2939%3A2%3C259%3A%3AAID-BIP12%3E3.0.CO%3B2-9

Dependence of DNA helix flexibility on base composition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0282%28199608%2939%3A2%3C259%3A%3AAID-BIP12%3E3.0.CO%3B2-9

Sedimentation of homogeneous double-strand DNA molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0282%28199608%2939%3A2%3C259%3A%3AAID-BIP12%3E3.0.CO%3B2-9

Dependence of laser light scattering of DNA on NaCl concentration

21 January 2018

1 reference

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Investigation of the flexibility of DNA using transient electric birefringence

21 January 2018

1 reference

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Flow dichroism of T7 DNA as a function of salt concentration

21 January 2018

1 reference

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Chain flexibility and hydrodynamics of the B and Z forms of poly(dG-dC).poly(dG-dC).

21 January 2018

1 reference

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Theory of twisting and bending of chain macromolecules; analysis of the fluorescence depolarization of DNA

21 January 2018

1 reference

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Energetics of DNA twisting. I. Relation between twist and cyclization probability.

21 January 2018

1 reference

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Interactions of highly charged colloidal cylinders with applications to double-stranded

21 January 2018

1 reference

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Osmotic pressure of DNA solutions and effective diameter of the double helix

21 January 2018

1 reference

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Self-Linking and the Gauss Integral in Higher Dimensions

21 January 2018

1 reference

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Crystallographic R factor refinement by molecular dynamics

21 January 2018

1 reference

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Crystallographic refinement by simulated annealing. Application to a 2.8 A resolution structure of aspartate aminotransferase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0282%28199608%2939%3A2%3C259%3A%3AAID-BIP12%3E3.0.CO%3B2-9

Curved helix segments can uniquely orient the topology of supertwisted DNA.

21 January 2018

1 reference

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Structure of plectonemically supercoiled DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0282%28199608%2939%3A2%3C259%3A%3AAID-BIP12%3E3.0.CO%3B2-9

Catastrophic variation of twist and writhing of circular DNAs with constraint?

21 January 2018

1 reference

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Elastic model of highly supercoiled DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0282%28199608%2939%3A2%3C259%3A%3AAID-BIP12%3E3.0.CO%3B2-9

On higher buckling transitions in supercoiled DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0282%28199608%2939%3A2%3C259%3A%3AAID-BIP12%3E3.0.CO%3B2-9

Base sequence effects in double helical DNA. I. Potential energy estimates of local base morphology

21 January 2018

1 reference

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Base sequence effects in double-helical DNA. II. Configurational statistics of rodlike chains

21 January 2018

1 reference

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Static and statistical bending of DNA evaluated by Monte Carlo simulations

21 January 2018

1 reference

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The sampling properties of some distance geometry algorithms applied to unconstrained polypeptide chains: a study of 1830 independently computed conformations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0282%28199608%2939%3A2%3C259%3A%3AAID-BIP12%3E3.0.CO%3B2-9

10.1002/(SICI)1097-0282(199608)39:2<259::AID-BIP12>3.0.CO;2-9

21 January 2018

Identifiers

DOI

0 references

1 reference