Download PDF by Yogambigai Velmurugu: Dynamics and Mechanism of DNA-Bending Proteins in Binding

By Yogambigai Velmurugu

ISBN-10: 3319451286

ISBN-13: 9783319451282

ISBN-10: 3319451294

ISBN-13: 9783319451299

Using a unique process that mixes excessive temporal solution of the laser T-jump approach with designated units of fluorescent probes, this research unveils formerly unresolved DNA dynamics in the course of seek and popularity through an architectural DNA bending protein and DNA harm attractiveness proteins.

Many mobile methods contain detailed proteins that bind to precise DNA websites with excessive affinity. How those proteins realize their websites whereas speedily looking amidst ~3 billion nonspecific websites in genomic DNA is still a superb puzzle. Structural experiences convey that proteins critically deform DNA at particular websites and point out that DNA deformability is a key think about site-specific popularity. even if, the dynamics of DNA deformations were tough to seize, therefore obscuring our realizing of popularity mechanisms.

The experiments provided during this thesis discover, for the 1st time, swift (~100-500 microseconds) DNA unwinding/bending attributed to nonspecific interrogation, ahead of slower (~5-50 milliseconds) DNA kinking/bending/nucleotide-flipping in the course of popularity. those effects aid remove darkness from how a looking protein interrogates DNA deformability and finally “stumbles” upon its aim website. Submillisecond interrogation might advertise preferential stalling of the swiftly scanning protein at cognate websites, therefore permitting site-recognition. Such multi-step search-interrogation-recognition procedures via dynamic conformational adjustments might be universal to the popularity mechanisms for various DNA-binding proteins.

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Get Dynamics and Mechanism of DNA-Bending Proteins in Binding PDF

Utilizing a unique method that mixes excessive temporal answer of the laser T-jump method with distinctive units of fluorescent probes, this learn unveils formerly unresolved DNA dynamics in the course of seek and popularity through an architectural DNA bending protein and DNA harm popularity proteins. Many mobile approaches contain designated proteins that bind to precise DNA websites with excessive affinity.

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B) The same experiment as in (a) was repeated with a new IR laser, which shows very stable IR beam energy and hence reflects as a stable high temperature jump (measured with a free 2AP reference sample) and I ð0þ Þ, respectively, in the T-jump experiment. The relationship between the intensities from the equilibrium and T-jump measurements, given by: I f ðT f Þ I ð0þ Þ ¼ I i ðT i Þ I ð0À Þ ð2:6Þ is used to estimate the value of If(Tf) in terms of the experimentally measured Ii(Ti), I ð0À Þ, and I ð0þ Þ, and interpolated on the equilibrium fluorescence intensity versus temperature plot of Fig.

Wiggins, R. C. Nelson, Exact theory of kinkable elastic polymers. Phys. Rev. E 71(2 Pt 1), 021909 (2005) 23. A. , High flexibility of DNA on short length scales probed by atomic force microscopy. Nat. Nanotechnol. 1(2), 137–141 (2006) 24. A. Travers, DNA dynamics: bubble ‘n’ flip for DNA cyclisation? Curr. Biol. 15(10), R377– R379 (2005) 25. J. F. Marko, Localized single-stranded bubble mechanism for cyclization of short double helix DNA. Phys. Rev. Lett. 93(10), 108108 (2004) 26. B. J. Hagerman, Origin of the intrinsic rigidity of DNA.

A. C. Correll, Protein-Nucleic Acid Interactions. 2008, Cambridge [11] with permission by The Royal Society of Chemistry DNA such as shape and mechanical deformability/flexibility. Thus, many indirect readout proteins interrogate potential binding sites by inspecting the ease of bending, twisting, or deforming DNA sites in order to fit into the binding interface of the protein. 2 Induced-Fit Mechanism Structural and thermodynamics studies of several protein–DNA complexes show that the bound protein also undergoes conformational changes in order to facilitate favorable interactions with the deformed DNA structure and these interactions stabilize the complex (Fig.

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Dynamics and Mechanism of DNA-Bending Proteins in Binding Site Recognition by Yogambigai Velmurugu


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