1C1512 Site-specific integration of retrovirus onto palindromic sequence : Analysis of integration selectivity in relation to DNA local structure(Nucleic acid,The 49th Annual Meeting of the Biophysical Society of Japan)
1C1512 DNA回文配列に対するレトロウイルスの特異的挿入 : 反応特異性とDNA局部構造変化の定量的考察(核酸,第49回日本生物物理学会年会)

Weizhi Liu, Kenichi Yoshikawa, Tatsuaki Tsuruyama
2011 Seibutsu Butsuri  
TheBiophysicalSociety of Japan General IncorporatedAssociation nucleosome in mtro fonn thc so called 30nm hbei which ig gtabi]ized by 1inkLr histoneproteins Hl dnd H5 FIuctuations ofnucleosomc system are impertant for gene express]on dnd regulation For mono nucTcesotnc dynamics seLeral ]ntercstmg expeiiments are performed but for niulti nuclcosomc case the structure of30nm fibLr is highly Lontaoversial Recently -e combined a coaTsL grained (CG) protein mode] and a DNA model in which the protein
more » ... inodet can simulate foldmg pTecesses and largc confoimdtional changes and the DNA modLl rLpioduLes meLhdiniL pioperties ofDh"A duplLx and mLlung behavior In this study, wc simulaLe multi nuLleosome gystems that inctude 2 te 20 nucleosomes "ith and without 1inkcr histonL protems as d fiist step to addrenys the struLture and dynamics of higher leveJ nucleosomc structures via moleLuldr simulations IC1448 Atsush] YoshmoL Biotechnoiogr, Umverstty of fbk}o 5chool ofAgn"tttutat and Life S"enees B to Z DNA transition biomacromoleeules because it However the atomstic detai]s of the mechanism x ray Lrystal bindmg piotems featuteg of the pair at the B doublchdixstructurL part of B DNA To investigate moleculardynamics DNA]unctlon without the Z DNA bmding protetns tn explicit sokent We used the pannbscO force field parameter tor DNA We dindlyzed fluctuations of DNA and proteins and interactions bet"ccn prolem and DNA At present d transmon model termed stretched intermediate model has becn proposed This moder has been supported by seieral computationa] gnidies We wi11 discuss the validity ot tlns medel based on our simulation results While the paHt computationaT regearches did not consider the cffbct erthc protcms en thc lransition we -ill disLuss their roleg by companng the trveetones obtained from the simula"ons with and without the protems B-Z DNA Yv ;10Y i ;1utvaco"Ialh\Y:-= V-:l i ;, Molecular dlr namics simulahons ef B Z DNA Junttioll struLture TohTu TeTadia? KLntaro Shimizui' (i Dcparimeitt of Giaduate SLhool (V AgnLblititrai and Iife Saences TVic ?Agncuiturai BioiiijormartLs Retearch Unit Gradttate fhe Ln-ei stty of 7bkLo) is oiie ot the most Lomplex conformationat changes in [t is important to clarify the meLhdmsm of the transitson is invotued in genc transcnption and some kmds of diseases iemaincdunclLai tn2005 dn structure of the B Z DNAJunLtion in comp]ex wth four 7 DNA was detcirrimLd This ievealed the fo11owmg characteristic B L DNA Junction structurL (]) HydrogLn bonds ol ene bdise Z boundary were broken and the bases v"ere extrudLd from the (2) Neivertheless base stackmg was conunuous from the to the pait ol Z DNA the atomisuc mcchamsrn ot thL transitien we peiformed sirnu]ations for the BZ structurc with and IC1524 IlltmaraophiraweosopemtszaOM7f;,+itva Hmcan we know the chromatm emironment m Ii}ing LellsO gtriicturaL analysis of m]tot]c chromosomes m h}ing cells Saera Hiharaii Chang PaLki Kazun'ui Kdizu4 Yasushi Sako' Masataka KirljoS Koichi Takahashi4 Kazuhllo Mdeshimai 2 dynamic to ensure accessibility foi the di ffusing piotLins IC1536 Fluorescence microseope study of DNA motLoll near s]hcon based nano scale pere Cenki Andoi Kenta Tsukahlla' Yuk] MoTtya3 ToshiyLiki Vitsui4 (HGntd ldat Sci Aoutma thnv 2C,'ndergrad Phly 14itth Aoiama LimL iL)idetgtad Phys WLith A(oama Uhn 4Assoc PJof WatSa AQJama bn-) Siticon baged solid state nanomctcT sLale pore LallLd nanopore is one of powertul tools foi rapid gmg!e DNA molecute detection Thc translocatlon thrcadmg DNA through nanopore eleLtrephoietiLally produceny ionic current LhdngLs and proNides the mformation ofDNA ie length One ofissues m this dctcction mLthod is clogging DNA molecules mto nanopore OnLe DNA rnolecu]eg are clogged the me]ecuTes aTe not able to be removed byJust i arying the apphed bias ioltages acroHs ndnopore We have been studying how a DNA molccule move trap and translocate or Llog mto ndnopore by directly obgerving the DNA using a nuorcsecncL microscopL By analy-ng the DNA motion the current induced electric field around nanopore was estimated ]ntercstmgly the field ls not sphenLal aroulld nallopore and the tield strength reduces regions less than 2 Lun awa} from the nanepore guriace FurthcnnorL clcctncallv modit]ed nallepore surtace vL as prepared by coatmg Au and the profiTe ofthe etectnc field areund nanoporc -as cstimatLd In this presentation we -ill disLuss the infiuence of gurface conductivities applied ioTtages and iomc cencentrations en the eleLtrit field profiles around nanopore dind the probabiTity of the cloggmg DNA undeT thLnye fietd profiZeg IC1512 "eizhi Liui iC;oto bniv lntegration many physiological oncogenes cxpTcsglon been debated retrovirus (N{LV) oLLurs seleLtwely on certam base wL have shown gpectfied sequenee N ta the experimentg both on leveIs ot who]e antmal and ot in vrtro model system i e large enhdnLement of the integration tor d palmdromic sequLncc (T Tsuruyama, ct al PLeS ONF 5 11 (2010)) It ig known that palmdromic sequences in a double stmng DNA can form specific secondary struLtuie Ldlled as Lruuform under Lertam condition m m -tro sysLcm In the presenLpapcr we have pLrtormed the quantitauLe analysis on the experimenta] data giNen by Dr Tguru>ama concernmg the base gpecificity on the mtegration reaLtion dround the pal]ndromie region It will be argucd that thc intLgiation sLlecuvity is attributable to the occurrence of crueiform structure on the pahndromic sequence geneiated m hving cdls This study is LxpLctLd to piovide a lle-msight on the mechanism how mfec"on of retrovirus is caused in 1iving cells depending on the specific DNA structure induced by the em ironmenta] change DNAu"dieijlll[stv6vFavtrJvxoptssctsfix mmsnscma eDNAmEtsmEgttcoremeqgpt Site specific integratson of retrovirus onte palindrom]c sequence Anal}sis ofJntegration se]ettiv]ts ]n relat]on to DNA loca] structure KLmchi Yoshika-ai Tatsuaki Tsuruyama2 (ierad Sch Sct ?Dept Dmgnobtic Pathologr KJoto Omv) tnto the host cell genome by retro-iug p]a}s the ciiticaholes in and pathological processes EspLcially the in ± lucnLL to is one of the most talked about topies no-adavs lt has long time that whether the integtation of muiine Teukern]a sequenee or not ReLently that MLV has the potentiat to selectiLeTy mtegrate into aICt548 Direct obsenation of Pl pLasm]d movement on an opticaL mlLrosLope (iiCeArs 1{)]vto Omiersin iAtzODK ww US4 iDcpaFtment of ldbiecular Genetics Onivefsit) of fotfmto Canada) The segregation ot genome DNA is LrmLal proLess for hvmg organisms In erder to mamtam laithful iiiheritance of genetic informauon the replicated genome DNAg should be paititToned to the ddughter Lells pioperly before Lell division The samc]b truc foi le" Lopy numberplasmid Plasmids arc uscful ior inLesttgaling these proceKseny Pl pTasmid ts a Tocopy ptasrnid in Eschenchia coh dnd the plasmid segregation system is simple Only t-o Pl plasmid encodcd protems ParA and ParB and a cis actmg ccntremciL 1ikc DNA pat5 are required for the Pl plastnid segregation ParA is a Walker type ATPase interdLts with DNA non speLifiLdlly Jn vMo and LoloLalize with the bactertal nuLleoid Jn vivo ParB is parS speLific DNA bmdmg protein and PaiBparg -S35 -NII-Electronic
doi:10.2142/biophys.51.s35_2 fatcat:vgv5u4g7mvhp3hrp55jhjiwizy