Dynamics of DNA conformations and DNA-protein interaction

R. Metzler, T. Ambjörnsson, Michael Andersen Lomholt, O. Krichevsky

Publikation: Bidrag til tidsskriftKonferenceartikelForskning

Resumé

Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA denaturation (bubble breathing), deriving its dynamic response to external physical parameters and the DNA sequence in terms of the bubble relaxation time spectrum and the autocorrelation function of bubble breathing. The interaction with binding proteins that selectively bind to the DNA single strand exposed in a denaturation bubble are shown to involve an interesting competition of time scales, varying between kinetic blocking of protein binding up to full binding protein-induced denaturation of the DNA. We will also address the potential to use DNA physics for the design of nanosensors. Finally, we report recent findings on the search process of proteins for a specific target on the DNA.
OriginalsprogEngelsk
TidsskriftMaterials Research Society Symposium Proceedings
Vol/bind899
Sider (fra-til)7-18
Antal sider12
ISSN0272-9172
StatusUdgivet - 2005

Fingeraftryk

Conformations
DNA
deoxyribonucleic acid
proteins
Proteins
Denaturation
biopolymer denaturation
bubbles
Carrier Proteins
interactions
breathing
Nanosensors
Optical tweezers
DNA sequences
Autocorrelation
Relaxation time
Dynamic response
dynamic response
strands
Microscopes

Citer dette

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Dynamics of DNA conformations and DNA-protein interaction. / Metzler, R.; Ambjörnsson, T.; Lomholt, Michael Andersen; Krichevsky, O.

I: Materials Research Society Symposium Proceedings, Bind 899, 2005, s. 7-18.

Publikation: Bidrag til tidsskriftKonferenceartikelForskning

TY - GEN

T1 - Dynamics of DNA conformations and DNA-protein interaction

AU - Metzler, R.

AU - Ambjörnsson, T.

AU - Lomholt, Michael Andersen

AU - Krichevsky, O.

PY - 2005

Y1 - 2005

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AB - Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA denaturation (bubble breathing), deriving its dynamic response to external physical parameters and the DNA sequence in terms of the bubble relaxation time spectrum and the autocorrelation function of bubble breathing. The interaction with binding proteins that selectively bind to the DNA single strand exposed in a denaturation bubble are shown to involve an interesting competition of time scales, varying between kinetic blocking of protein binding up to full binding protein-induced denaturation of the DNA. We will also address the potential to use DNA physics for the design of nanosensors. Finally, we report recent findings on the search process of proteins for a specific target on the DNA.

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M3 - Conference article

VL - 899

SP - 7

EP - 18

JO - Materials Research Society Symposium Proceedings

JF - Materials Research Society Symposium Proceedings

SN - 0272-9172

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