Dynamics ofdna bi and bii phosphate backbone transitions 2004

Transitions backbone ofdna

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The DNA propensity to undergo BI↔BII backbone transitions is highly sequence-dependent and can be quantified at the dinucleotide level. dynamics ofdna bi and bii phosphate backbone transitions 2004 BI/BII transitions are especially prevalent for 2004 YRRX sequences dynamics ofdna bi and bii phosphate backbone transitions 2004 2004 and often are associated with bimodality in helical coordinate distributions at the basepair step level. Request PDF | Dynamics of DNA: BI and BII phosphate backbone transitions | In the present study, we try to determine dynamics ofdna bi and bii phosphate backbone transitions 2004 if the dynamics of the B-DNA backbone phosphates (and especially their. DNA Fine Structure and Dynamics: The Impact of BI/BII Backbone Conformations on the DNA/protein Specific bii Recognition The unusual BII phosphate conformation detected in B-DNA structures was found sequence dependant and associated to large changes in inter base-pair helical parameters. Molecular dynamics study provides an excellent tool for the investigation of tran-sitions between BI and BII conformational substates, since these transitions are assumed to occur in the sub nanosecond time scale (17, 43-47). 8 The changes are dynamics ofdna bi and bii phosphate backbone transitions 2004 characterized by the angles and œ of the DNA backbone or by ofdna the angle.

In the present study, we try to dynamics ofdna bi and bii phosphate backbone transitions 2004 determine if the dynamics of the B-DNA backbone phosphates (and especially their interconversions between their two distinct conformations BI and BII) are fast enough to be sufficiently sampled in the course of molecular dynamics simulations in the nanosecond time range. Indeed, in the bii BI state ε and ζ are in the t/g. For all three conformational types, the average structure was calculated; their ribbon representations are superimposed in Figure 8. , 1998 ; Sarai & Kono, ; Rohs et al. Hartmann B, Piazzola D, Lavery R (1993) BI–BII transitions in B-DNA. In the (ϵ−ζ) > 0° 2004 region (a BII backbone facing either a BI or a BII phosphate), no north puckers are found on the 5′ side of the dynamics ofdna bi and bii phosphate backbone transitions 2004 dinucleotide step. The two BI ⇌ BII transitions are partly correlated and of the four possible combinations, only three are observed, namely BI/BII (i. CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): In the present study, we try to determine if the dynamics of the B-DNA backbone phosphates (and especially their interconversions between their bii two distinct conformations.

The effect of E2 on the BI/BII dynamics differs according to the parts of the DNA we consider: in regard to their free counterparts, the phosphate groups dynamics ofdna bi and bii phosphate backbone transitions 2004 of the spacer and the GpA. G∗5 in BI and A6 in BII), BII/BI and BI/BI. dynamics ofdna bi and bii phosphate backbone transitions 2004 View Article Google Scholar 8. For this purpose, we performed twelve 10-ns simulations of the Drew−Dickerson dodecamer d.

determine dynamics ofdna bi and bii phosphate backbone transitions 2004 BI/BII equilibrium in B-DNA, proton and Phosphate NMR experiments4-7, Molecular Dynamics (MD) simulations 8-10, and data mining of crystal structures from databases 11-13 have being historically used as the preferred methods. dynamics ofdna bi and bii phosphate backbone transitions 2004 , 1998; Pichler et al. Hartmann B, Piazzola D, Lavery RBI-BII 2004 transitions in B-DNA. A given phosphate was classified as BII if this difference was in the range 20°, 200°, otherwise.

Dynamics of DNA: B I and B II Phosphate Backbone Transitions Michael Trieb, Christine Rauch, Bernd Wellenzohn, Fajar Wibowo, Thomas Loerting, and Klaus R. Nucleic Acids Res 21: 561–568. (conformation) and the magnitude bii of the energy ofdna transition barrier (dynamics) between the BI and BII conformations of each phosphate step of the following three dodecamer sequences: CreACAG, CreGGAG, and CreTATA. dynamics ofdna bi and bii phosphate backbone transitions 2004 Biopolymers 73 :. The BI/BII ratio, inferred from δP, is primarily controlled at the dinucleotide level, confirming that the propensity to undergo the BI/BII transition is dynamics ofdna bi and bii phosphate backbone transitions 2004 sequence dependent. Liedl * Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria. B-DNA adopts two representative phosphate backbone conformations, BI and BII, which are defined by.

Deciphering sequence information from sugar-phosphate backbone is finely tuned through the conformational substates of DNA. differ in their BI $ BII backbone dynamics. The structure and flexibility of double-stranded DNA and the binding of proteins is influenced by the nucleic acid backbone 2004 structure ().

This dynamics ofdna bi and bii phosphate backbone transitions 2004 dual relationship, between DNA sequence and backbone behavior on one hand, and backbone behavior bii and groove dimensions on the other hand, allows to decipher the link dynamics ofdna bi and bii phosphate backbone transitions 2004 between DNA sequence and groove. The grooves width and depth of free and protein-bound DNA are found to be clearly related to the BI/BII backbone conformational states. All resemble more.

Google Scholar. Author information: (1)Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-chimique, 13 rue P. In order to obtain the BI/BII profile of each phosphate step, 2D 31P-NMR NOESY and HSQC experiments at various temperatures were utilized. In the present study, we ofdna try to determine if the dynamics of the B-DNA backbone phosphates (and especially their interconversions between their two distinct conformations BI and BII) are fast enough to be sufficiently sampled dynamics ofdna bi and bii phosphate backbone transitions 2004 in the course of molecular dynamics ofdna bi and bii phosphate backbone transitions 2004 dynamics simulations in the nanosecond time range.

The preference in BI/BII conformation equilibrium is also sequence-dependent. The BI/BII conformations have been shown to result in altered phosphate positions and to influence groove parameters, stacking properties and helicoidal parameters (5, 6, 10– 12). DNA fine structure and ofdna dynamics in crystals and in dynamics ofdna bi and bii phosphate backbone transitions 2004 solution: the impact of BI/BII backbone conformations.

In the BI state, which is more common, the backbone phosphate adopts a rather symmetric position between the major and minor grooves, whereas in the BII state the phosphate groups are closer to the minor groove as a result of coupled changes in the two dihedral angles ε and ζ (Figure 1). The 31 P dynamics ofdna bi and bii phosphate backbone transitions 2004 chemical shifts can be interpreted in terms of the BI↔BII backbone conformations and dynamics. Solution NMR revealed that 8-oxoguanine in the ofdna DNA duplex causes substantial alterations in the sugar—phosphate backbone conformation, inducing a BI→BII transition. standing the dynamics of BI↔BII transition may provide new insights into the transition between the dynamics ofdna bi and bii phosphate backbone transitions 2004 B and C forms of DNA. Another relevant conformational motion of the sugar phosphate backbone in B-DNA is determined by the relation of ɛ/ζ torsions and comprises transitions between the canonical state BI (trans/gauche−) and the minor state ofdna BII (gauche−/trans). Implications for DNA overall structure and recognition. The Journal of Physical Chemistry B,,. Thus, BI↔BII equilibrium in itself does not account for the enhancement of cleavage intensity in d(CpN) dinucleotides.

One of the most prominent conformational polymorphism in DNA dynamics ofdna bi and bii phosphate backbone transitions 2004 is due to two different combinations of the ε and ζ dihedral angles in nucleotides adopting either the canonical BI (ε/ζ in the trans/ gauche-) or BII configuration (ε/ζ in the. The two substates, called BI bii and BII, are defined by different conformations of the sugar phosphate backbone. BII competent steps explore BII more (CpA·TpG, GpG·CpC and CpG·CpG, with at least 40% of BII conformers in both dynamics ofdna bi and bii phosphate backbone transitions 2004 facing phosphate groups) or less (GpC·GpC, GpA·TpC and TpA·TpA, with 15 – 25% of BII conformers in both facing phosphate groups) frequently; BII refractory (equivalent to BI prone) steps, ApT·ApT, ApC·GpT, ApA·TpT and ApG. Davis, Janna Register. Moreover, molecular dynamics of the complex suggested that 8-oxoguanine, although does not disrupt the dynamics ofdna bi and bii phosphate backbone transitions 2004 sequence-specific contacts formed by the enzyme with DNA, shifts the. The fundamental role of sequence‐dependent dynamics ofdna bi and bii phosphate backbone transitions 2004 backbone flexibility in indirect readout has been shown in several studies ( 13 – 15 ), which point to the. 40, 41 BII backbone conformation differs from its ofdna canonical BI alternative in the torsion angles ɛ and dynamics ofdna bi and bii phosphate backbone transitions 2004 ζ, which are dynamics ofdna bi and bii phosphate backbone transitions 2004 trans/g − in BI (ɛ − ζ ∼ − 90°) and g. Heddi B, Foloppe N, Bouchemal N, Hantz E, Hartmann B () Quantification of DNA BI/BII backbone states in solution.

M Trieb, C Rauch, B Wellenzohn, F. , BI conformations facing one another in both stands), most sugars are south (≈75%), although some east and north puckers are dynamics ofdna bi and bii phosphate backbone transitions 2004 seen in protein complexed dynamics ofdna bi and bii phosphate backbone transitions 2004 DNA. In these two spacers, the backbone dynamic is unusual: in the CCAT spacer, some BII steps are stabilized while, in the ACGT spacer, the CpG. Implications for DNA overall structure and recognition. The only peculiarity in the conformational dynamics of the 2004 sugar phosphate backbone dynamics ofdna bi and bii phosphate backbone transitions 2004 that is in line with the ultrasonic cleavage rates is the enhancement of the S↔N interconversion bii of the deoxyribose moiety in deoxycytidine. Consequently, we will focus on the backbone angles ɛ (C 4′-C 3′-O 3′-P) and ζ (C 3′-O 3′-P-O 5′), defining the two phosphate conformations BI ofdna and BII. R LiedlDynamics of DNA: B-I and B-II dynamics ofdna bi and bii phosphate backbone transitions 2004 phosphate backbone transitions J Phys Chem B,, pp.

. . The structural dynamics of DNA dynamics ofdna bi and bii phosphate backbone transitions 2004 can be observed in its intrinsic flexibility measured freely in solution as BI-BII conformation shifts in phosphate linkages on the backbone and DNA flexibility has been recently become the subject of both evolutionary and global mapping studies in yeast and other micro-organisms 16, 18–20.

In contrast, the central CpG·CpG dynamics ofdna bi and bii phosphate backbone transitions 2004 in the ACGT spacer undergoes non-correlated BI/BII transitions 2004 at high frequency ; this chronic instability is a spectacular characteristic of these phosphate groups. J Am Chem Soc 128 :. These pieces of. dynamics ofdna bi and bii phosphate backbone transitions 2004 Christine Rauch&39;s 14 research works with 217 citations and 305 reads, including: M.

of molecular dynamics (MD) simulations whose purpose is to elucidate dynamical interconversions between the two substates of phosphate groups in the DNA backbone. The low affinity AAAC spacer exhibits stable BI backbone conformations, the high affinity ACGT spacer is characterized by a dramatic instability of the CpG phosphate groups, and the CpA and GpG backbones in the very high affinity CCAT·ATGG spacer are trapped in BII conformations. Crucially, these phosphate states, ofdna the twist, the roll and the base displacement dynamics ofdna bi and bii phosphate backbone transitions 2004 are intimately coupled ( 39, 42–46 ). The backbone bii conformations in free B-DNA consist of two states, BI and BII, dynamics ofdna bi and bii phosphate backbone transitions 2004 originally defined by the conformations of the torsion angles ε and trans/g-in BI (ε − ∼ −90 • ) and g-/trans. R Wibowo, T Loerting, K. TaqI facilitates the base dynamics ofdna bi and bii phosphate backbone transitions 2004 flipping via an unusual DNA backbone conformation. We investigated here the role of DNA flexibility in DNase I activity, taking bii advantage of a new approach to studying B-DNA properties, using NMR in solution and examining phosphate motions (i. The BI/BII conformational change is coupled to the cationic atmosphere surrounding DNA, and to the formation of 2004 non-canonical 2004 CH—O base-backbone hydrogen bonds.

Djuranovic D(1), Hartmann B. Djuranovic D, Hartmann BDNA fine structure and dynamics in crystals and in solution: the impact of BI/BII backbone conformations. Manka, Zachary S. A representative example of such plasticity is the sequence-dependent deformability of DNA, which has been shown to be crucial for molecular recognition of DNA-binding proteins (Olson et al. 20;73(3):356-68.

Dynamics ofdna bi and bii phosphate backbone transitions 2004

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