LEADER 03992nam 22006015 450 001 9910155326503321 005 20200702123627.0 010 $a9783319451299 024 7 $a10.1007/978-3-319-45129-9 035 $a(CKB)3710000000964788 035 $a(DE-He213)978-3-319-45129-9 035 $a(MiAaPQ)EBC4751449 035 $a(PPN)197138543 035 $a(EXLCZ)993710000000964788 100 $a20161130d2017 u| 0 101 0 $aeng 135 $aurnn|008mamaa 181 $ctxt$2rdacontent 182 $cc$2rdamedia 183 $acr$2rdacarrier 200 10$aDynamics and Mechanism of DNA-Bending Proteins in Binding Site Recognition /$fby Yogambigai Velmurugu 205 $a1st ed. 2017. 210 1$aCham :$cSpringer International Publishing :$cImprint: Springer,$d2017. 215 $a1 online resource (XXI, 199 p. 112 illus., 105 illus. in color.) 225 1 $aSpringer Theses, Recognizing Outstanding Ph.D. Research,$x2190-5053 311 $a3-319-45128-6 311 $a3-319-45129-4 320 $aIncludes bibliographical references. 327 $aIntroduction -- Methods -- Integration Host Factor (IHF)-DNA interaction -- Lesion Recognition by Xeroderma Pigmentosum C (XPC) Protein -- DNA Mismatch Repair. 330 $aUsing a novel approach that combines high temporal resolution of the laser T-jump technique with unique sets of fluorescent probes, this study unveils previously unresolved DNA dynamics during search and recognition by an architectural DNA bending protein and two DNA damage recognition proteins. Many cellular processes involve special proteins that bind to specific DNA sites with high affinity. How these proteins recognize their sites while rapidly searching amidst ~3 billion nonspecific sites in genomic DNA remains an outstanding puzzle. Structural studies show that proteins severely deform DNA at specific sites and indicate that DNA deformability is a key factor in site-specific recognition. However, the dynamics of DNA deformations have been difficult to capture, thus obscuring our understanding of recognition mechanisms. The experiments presented in this thesis uncover, for the first time, rapid (~100-500 microseconds) DNA unwinding/bending attributed to nonspecific interrogation, prior to slower (~5-50 milliseconds) DNA kinking/bending/nucleotide-flipping during recognition. These results help illuminate how a searching protein interrogates DNA deformability and eventually ?stumbles? upon its target site. Submillisecond interrogation may promote preferential stalling of the rapidly scanning protein at cognate sites, thus enabling site-recognition. Such multi-step search-interrogation-recognition processes through dynamic conformational changes may well be common to the recognition mechanisms for diverse DNA-binding proteins. . 410 0$aSpringer Theses, Recognizing Outstanding Ph.D. Research,$x2190-5053 606 $aBiophysics 606 $aBiophysics 606 $aSpectrum analysis 606 $aMicroscopy 606 $aProteins 606 $aBiological and Medical Physics, Biophysics$3https://scigraph.springernature.com/ontologies/product-market-codes/P27008 606 $aSpectroscopy and Microscopy$3https://scigraph.springernature.com/ontologies/product-market-codes/P31090 606 $aProtein-Ligand Interactions$3https://scigraph.springernature.com/ontologies/product-market-codes/L14060 615 0$aBiophysics. 615 0$aBiophysics. 615 0$aSpectrum analysis. 615 0$aMicroscopy. 615 0$aProteins. 615 14$aBiological and Medical Physics, Biophysics. 615 24$aSpectroscopy and Microscopy. 615 24$aProtein-Ligand Interactions. 676 $a571.4 700 $aVelmurugu$b Yogambigai$4aut$4http://id.loc.gov/vocabulary/relators/aut$0819544 906 $aBOOK 912 $a9910155326503321 996 $aDynamics and Mechanism of DNA-Bending Proteins in Binding Site Recognition$91826398 997 $aUNINA