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Panyutin IG, Hsieh P: The kinetics of spontaneous branch migration. Proc Natl Acad Sci USA 1994, 91:2021-2025. An improved assay was developed to determine the kinetics parameters of spontaneous branch migration as a function of temperature and ionic conditions. It appears that the structure of the branch point plays a key role in determining the rate of spontaneous branch migration.
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Proc Natl Acad Sci USA
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Panyutin, I.G.1
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A pivotal role for the structure of the Holliday junction in DNA branch migration
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Panyutin IG, Biswas I, Hsieh P: A pivotal role for the structure of the Holliday junction in DNA branch migration. EMBO J 1995, 14:1819-1826. The rate of spontaneous branch migration in mobile 4H junctions was measured as a function of magnesium ion concentration. The rate increases dramatically at ionic concentrations below 0.5 mM with the steepest acceleration occurring between 0.3 and 0.1 mM. It is concluded that coaxial base stacking constitutes a kinetic barrier to branch migration.
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EMBO J
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Panyutin, I.G.1
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Formation of a single base mismatch impedes spontaneous DNA branch migration
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Panyutin IG, Hsieh P: Formation of a single base mismatch impedes spontaneous DNA branch migration. J Mol Biol 1993, 230:413-424.
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J Mol Biol
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NMR studies of complex DNA structures: The Holliday intermediate in genetic recombination
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Carlström G, Chen S-m, Miick S, Chazin WJ: NMR studies of complex DNA structures: the Holliday intermediate in genetic recombination. Methods Enzymol 1995, 261:163-182. The authors present a full account of the experimental NMR techniques and resonance assignment strategies which were employed in the analysis of the conformational problems of 4H junction J2P1.
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Methods Enzymol
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Carlström, G.1
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Helical stacking in DNA three-way junctions containing two unpaired pyrimidines: Proton NMR studies
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2 junctions having either unpaired TT or TC on one strand reveal a coaxial stacking preference that differs from the one found in [36] and in [35••]; thus far, this remains the only example of an A/C stacking arrangement (in the present nomenclature) studied by NMR.
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Biophys J
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Leontis, N.B.1
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Refinement of the solution structure of a branched DNA three-way junction
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Ouporov IV, Leontis NB: Refinement of the solution structure of a branched DNA three-way junction. Biophys J 1995, 68:266-274.
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Rosen MA, Patel DJ: Structural features of a three-stranded DNA junction containing a C-C functional bulge. Biochemistry 1993, 32:6576-6587.
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Construction of a DNA four-way junction: Design and NMR spectroscopy
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Edited by Pullman B, Jortner J. Dordrecht: Kluwer Academic Publishers
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Altona C, Pikkemaat JA: Construction of a DNA four-way junction: design and NMR spectroscopy. In Modelling of Biomolecular Structures and Mechanisms. Edited by Pullman B, Jortner J. Dordrecht: Kluwer Academic Publishers; 1995:289-304. The authors supply the first description of a small 4H model junction that consists of a self-folding linear 46-mer DNA strand.
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1H NMR studies of immobile Holliday junctions: Nonlabile proton assignments and identification of cross-over isomers
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1H NMR studies of immobile Holliday junctions: nonlabile proton assignments and identification of cross-over isomers. Biochemistry 1994, 33:11453-11459. This is the final report on NMR studies of two 32-base-pair models of the Holliday junction, J1 and J2. The overlap of resonances in proton NOESY spectra necessitated the use of a multipathway strategy for obtaining sequence-specific assignments, wherein all possible NOE connectivities are analyzed in parallel. Several unambiguous cross-arm NOE connectivities were identified, directly establishing the stacking arrangement of each contiguous (two-arm) helical domain. J2 differs from J1 by the exchange of two base pairs in neighbouring arms and this exchange results in a different conformer selection.
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(1994)
Biochemistry
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Chen, S.-M.1
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1H NMR studies of 32-base-pair synthetic immobile Holliday junctions: Complete assignment of the labile protons and identification of the base-pairing scheme
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1H NMR studies of 32-base-pair synthetic immobile Holliday junctions: complete assignment of the labile protons and identification of the base-pairing scheme. Biochemistry 1993, 32:319-326.
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Biochemistry
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Chen, S.-M.1
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NMR studies and conformational analysis of a DNA four-way junction formed in a linear synthetic oligonucleotide
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Pikkemaat JA, Van den Elst H, Van Boom JH, Altona C: NMR studies and conformational analysis of a DNA four-way junction formed in a linear synthetic oligonucleotide. Biochemistry 1994, 33:14896-14907. The design of a 46-mer model Holliday junction, described in [56•], was studied by means of proton NMR. The data confirm the expected existence of minihairpin loop structures at the three 5′-CTTG-3′ motifs in the sequence. Watson-Crick type base pairing is preserved for all residues in the stem domain, including the residues at the centre of the junction. The relatively large number of identified NOE contacts at the branch point indicates that quasi-continuous stacking occurs at the interface between arms A and D and at the interface between arms B and C (A/D stack).
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Biochemistry
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Sequence dependence and direct measurement of crossover isomer distribution in model Holliday junctions using NMR spectroscopy
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1H-detected experiments point to the coexistence of a minor amount of the second conformer in equilibrium with the major form and provide a direct measure of the equilibrium distribution.
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Wemmer DE, Wand AJ, Seeman NC, Kallenbach NR: NMR analysis of DNA junctions. Biochemistry 1985, 24:5745-5749.
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Macke T, Chen S-M, Chazin WJ: Analysis of the structure and dynamics of synthetic 32 base-pair models of the Holliday junction intermediate in genetic recombination. In Structure and Function Volume 1: Nucleic Acids. Edited by Sarma RH, Sarma MH. Schenectady: Adenine Press; 1992:213-227.
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The global folding of four-way junctions in RNA, including that in U1 snRNA
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2+ (between the same arms as in their DNA analogues). However, the two continuous helical axes are approximately at right angles to each other. The RNA junctions exhibit significant sequence-dependent differences in their structures as a function of ionic conditions.
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Cell
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Symmetric Holliday junction crossover isomers
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-1) at 4°C. It is concluded that large cross-over preferences are not characteristic of junctions with extensive symmetry, and are thus unlikely to have important consequences for genetic recombination.
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Pieters JML, Mans RMW, Van den Elst H, Van der Marel GA, Van Boom JH, Altona C: Conformation and thermodynamic consequences of the introduction of a nick in duplexed DNA fragments: an NMR study augmented by biochemical experiments. Nucleic Acids Res 1989, 17:4551-4565.
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Conformation and thermodynamics of DNA necks. Models for three-arm branch formation in a duplex
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Zhong M, Kallenbach NR: Conformation and thermodynamics of DNA necks. Models for three-arm branch formation in a duplex. J Mol Biol 1993, 230:766-778.
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Zhong, M.1
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