TY - JOUR
T1 - Effects of localized bending on DNA supercoiling
AU - Yang, Yang
AU - Westcott, Timothy P.
AU - Pedersen, Scott C.
AU - Tobias, Irwin
AU - Olson, Wilma K.
N1 - Funding Information:
contactS. uchc hangesin, turn,s uggest here.T herei s also a suggestiofnr om curveds egmentasn dl endss upportto structuraml echanismws herebys pe-the existingru leso f DNA bendingt hat the idea2" ~t hat curvedd ouble-helicalc ific base-pairs equencecsa n regulate thel dnetoplasfrta gmentasr es uperheli-fragmentsc an uniquely orient the intramoleculianrt eractionasn drelated cal rathetrh anp lanacr urve1s4 ,xsw, hich topology of supercoUedD NA. The biochemicaplr ocesses. would furthera ltert he globalf olding. correspondencbee tweent he current Rnally,t he allowed( 4.5°/bp)t wisting modela nde xperimenist thus qualita-Acknowledgements fluctuationins them odeal res omewhatt iver athetrh anq uantitativTeh. ati s, the Wet hankL . Couchman/ohre ri nvalu-lowert hant hosef oundi n recents ur-theoreticaml odelp redictst hat three ables upportA, . Gorin for his insights veyso f DNA crystals (~5,5°/bp~) 2,s ug- curveds egmentasr er equiredto fix the into DNA bendinga ndt wistinga t the gesting that the twisting energy has shape of a DNA supercoilu niquely, atomicl evel,a ndA. Olson and A. De been overestimatedh ere, Larger twist- whereasth e experimentaolb servationF alco for their generoush elp in the ing contributions (ATu)=3.9 in the is thatt wos egmenatsr en eeded. preparationo f color pictures.T his three.armedc onfigurationin Fig. 5b and The curved inserts divide the research was supported by the US 2.2 in the bent linear structurei n Fig. straightD NA into regionso f uniform, Public Health Service (grant GM34809) 5c), includingp ronouncecdh angesin althougdhi fferentlo, calt wist.T hesub-and the US Naval Research Laboratory twistw ithint hec urveds egmentsg,i ve tle distinctionsin twisting in the (contract N00014-92-C-2094)C. ompu- rise to the substantiallhyi gheren-straightli nkersm akeo ne part of the tations were carried out at the Rutgers ergieso f the branchedc,o mparewd lth chain potentiallmy ores usceptiblteo University Center for Computational thel inears, upercolls. meltinga ndm ayp referentialldye stabi-Chemistry and the Physical Acoustics It takest hreec urvedfr agmenttso flx lizet hec losec ontactosf doubleh elices Branch of the US Naval Research thec urrenDt NA modeiln toa branched in one of the interwounda rmsof a LaboratoryW, ashingtonD C, USA. form at naturalle vels of superhellcal branchesdt ructureF.u rthermoruep, on densityi n the current model. The supercollingt,h etwo insertsa re often insertsi n Fig. 5(I are equallys paced positionedd ifferentlyw ith respectt o alongt heD NA contouar nda ssumetdo the abuttinlgin kerD NA (e.g.t heasym-be co-planarin the 'open'r eference metricaol rientationosf curvedin serts stateA. s witho therY -shapedco nfigura-in thet woh airpinl oopsi n Fig.5 b) and, tions,t het wistingc ontributioins large as a result,s howc ompleteldyi fferent in this structure( ATw=4.5)S. ignifi-changesin local twisting.S ince the cantlyn, o linearlyin terwuunadr range-changein twist at the base-pailre vel mentas ref oundf ort hisD NA sequence. can substantialalyff ectt he bindingo f The superhellcafol ldingo f thec haini s proteintso DNA,t hea ffinityo f a protein uniquelyd eterminedb y the three for a naturallyc urveds egmenct an 1 TrifonovE, . N. andS ussmanJ., L. (1980P) roc. Natl Acad. ScL USA 77,3 816-3820 2 SussmanJ,. L. andT rifonovE, . N. (1978P) roc. Natt Acad. Sci. USA 75, 103-107 3 LevittM, . (1978P) roc. Natl Acad. '3eL USA 75, 640-644 40lson,W . K. (1979B) iopolymers1 8, 1235-1260 5 Zi=uddVn,. B., LysovY, . P. annI vanovV, . (1979) Nudelc Acids Res. 6, 1081-1096 6 SelsingE, ., Wells,R . D.,A ldenC, . J. and AmottS, . (1979J) . BioL Chem2. 54, 5417-5422
Funding Information:
If. Ifang is at SFA, Inc., 1401 McCormick Drive, Landover,M D 20785, USA, under contract to the US Naval Research Laboratory, Washington,D C 20375-5000, USA; and 1". P. Weft©eft, S. C. Pede~en, I. Teblas and W. K. Olsen are at the Department of Chemistry,R utgers,t he State Universityo f New Jersey, New Brunswick, NJ 08903, USA.
PY - 1995/8
Y1 - 1995/8
N2 - The DNA double helix is straight only in the idealized case. In reality, it bends, twists and stretches in response to local base sequence and to specific interactions with proteins and other bound ligands. Naturally occurring bends appear to promote the assembly of nucleosomes, and in some cases can effectively replace regulatory DNA-binding proteins in vivo. Recently, a computational method known as 'finite element analysis', which is used routinely by engineers to analyse the stability of buildings and bridges, has been applied to the quantitative assessment of natural curvature in supercoiled DNA structures, providing new insight into the relationship between local, sequence-dependent features and the overall topology of these chains.
AB - The DNA double helix is straight only in the idealized case. In reality, it bends, twists and stretches in response to local base sequence and to specific interactions with proteins and other bound ligands. Naturally occurring bends appear to promote the assembly of nucleosomes, and in some cases can effectively replace regulatory DNA-binding proteins in vivo. Recently, a computational method known as 'finite element analysis', which is used routinely by engineers to analyse the stability of buildings and bridges, has been applied to the quantitative assessment of natural curvature in supercoiled DNA structures, providing new insight into the relationship between local, sequence-dependent features and the overall topology of these chains.
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U2 - 10.1016/S0968-0004(00)89058-1
DO - 10.1016/S0968-0004(00)89058-1
M3 - Review article
C2 - 7667890
AN - SCOPUS:0029087424
SN - 0968-0004
VL - 20
SP - 313
EP - 319
JO - Trends in Biochemical Sciences
JF - Trends in Biochemical Sciences
IS - 8
ER -