DNA bending induced by Cro protein binding as demonstrated by gel electrophoresis.

Lyubchenko, Yuri L.; Shlyakhtenko, Luda S.; Chernov, B. K.; Harrington, R. M.

doi:10.1073/pnas.88.12.5331

Cited by 58 publications

(58 citation statements)

References 27 publications

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“…Much less effort has been made towards unraveling the global structure of three-way junctions with no irregularities at the junction. An oligonucleotide ligation-cyclization analysis approach (22,23) was consistent with the junction adopting a pyramidal geometry with an angle of 60-90°between the arms (24). This conclusion was also supported by FRET data (15).…”

Section: Introductionmentioning

confidence: 77%

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Structure and dynamics of three-way DNA junctions: atomic force microscopy studies

Shlyakhtenko¹

2000

Nucleic Acids Research

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We have used atomic force microscopy (AFM) to study the conformation of three-way DNA junctions, intermediates of DNA replication and recombination. Immobile three-way junctions with one hairpin arm (50, 27, 18 and 7 bp long) and two relatively long linear arms were obtained by annealing two partially homologous restriction fragments. Fragments containing inverted repeats of specific length formed hairpins after denaturation. Three-way junctions were obtained by annealing one strand of a fragment from a parental plasmid with one strand of an inverted repeat-containing fragment, purified from gels, and examined by AFM. The molecules are clearly seen as three-armed molecules with one short arm and two flexible long arms. The AFM analysis revealed two important features of three-way DNA junctions. First, three-way junctions are very dynamic structures. This conclusion is supported by a high variability of the inter-arm angle detected on dried samples. The mobility of the junctions was observed directly by imaging the samples in liquid (AFM in situ). Second, measurements of the angle between the arms led to the conclusion that threeway junctions are not flat, but rather pyramid-like. Non-flatness of the junction should be taken into account in analysis of the AFM data.

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Section: Introductionmentioning

confidence: 77%

“…Earlier we used an oligonucleotide ligation-cyclization technique (22) to estimate a mean angle between the arms of a three-way junction of 60-90° (16,24). This suggests that a three-way junction should be a trigonal pyramid in structure (16,24).…”

Section: Discussionmentioning

confidence: 99%

Structure and dynamics of three-way DNA junctions: atomic force microscopy studies

Shlyakhtenko¹

2000

Nucleic Acids Research

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“…The assay was performed essentially as described (27)(28)(29)(30)(31)(32)(33)(34). Reaction mixtures (10 l) contained 20 mM HEPES (pH 7.5), 1 mM DTT, 100 g/ml bovine serum albumin, 0.5-1 nM 189-bp fragment, and protein as indicated.…”

Section: Cloning Overexpression and Purification Of Bsmc1 And Bsmc3mentioning

confidence: 99%

“…For investigating DNA bending by proteins, including those that do not bind a specific DNA sequence, the ring closure or circularization assay has been widely used (27)(28)(29)(30)(31)(32)(33)(34). This assay, whose theoretical foundation was worked out in 1981 (27), generally uses an end-labeled, linear DNA substrate of a length between 70 and 200 bp with cohesive ends.…”

Section: Mammalian Smc C-terminal Domainsmentioning

confidence: 99%

Mammalian SMC3 C-terminal and Coiled-coil Protein Domains Specifically Bind Palindromic DNA, Do Not Block DNA Ends, and Prevent DNA Bending

Akhmedov¹,

Gross²,

Jessberger³

1999

Journal of Biological Chemistry

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The C-terminal domains of yeast structural maintenance of chromosomes (SMC) proteins were previously shown to bind double-stranded DNA, which generated the idea of the antiparallel SMC heterodimer, such as the SMC1/3 dimer, bridging two DNA molecules. Analysis of bovine SMC1 and SMC3 protein domains now reveals that not only the C-terminal domains, but also the coiled-coil region, binds DNA, while the N terminus is inactive. Duplex DNA and DNA molecules with secondary structures are highly preferred substrates for both the C-terminal and coiled-coil domains. Contrasting other cruciform DNA-binding proteins like HMG1, the SMC3 C-terminal and coiled-coil domains do not bend DNA, but rather prevent bending in ring closure assays. Phosphatase, exonuclease, and ligase assays showed that neither domain renders DNA ends inaccessible for other enzymes. These observations allow modifications of models for SMC-DNA interactions.

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“…B: A curved sequence motif (A)CTCTAAAAAT(A) designed by Ulanovsky et al [6]. C: A straight sequence from the lambda phage OR3 operator region [8,36]. (C)ACCCA;AAGGG(A).…”

Section: A Vector Representation Of Dna Bendabilitymentioning

confidence: 99%

Distribution of bending propensity in DNA sequences

Gabrielian¹,

Simoncsits²,

Pongor³

1996

FEBS Letters

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Local bending propensity and curvature of DNA can he characterized using a vector description of DNA bendability, based on a set of parameters derived from deoxyribonuclease I (DNase I) cleavage experiments. Two characteristics -arithmetic and vector averages of bendability -were successfully used to predict experimentally known bendable, rigid and curved segments in DNA. A characteristic distribution of bendability is conserved in evolutionarily related kinetoplast sequences. An analysis of the M. genitalium and H. influenzae genomes as well as fragments of human and yeast genomes shows, on the other hand, that highly curved segments -similar to artificially designed curved oligonucleotides -are extremely rare in natural DNA.bendable segments [2]. Bendability plots were drawn by first dividing a DNA sequence into overlapping trinucleotides, then assigning a bendability value given in Table 1 to the center of each trinucleotide. (In this way the first and last nucleotides will have no values so a sequence of 32 residues will have 30 values.) Average bendability and helical asymmetry (see below at Eq. 1) were calculated for segments of 32 bp, i.e. approximately three helical turns. The calculated profiles do not significantly depend on this window length. Random sequences were generated by random shuffling the sequence of entire genomes. The shuffled sequences were then divided into overlapping segments of 32 residues for the calculation of the values given in Table 1 which are averages and standard deviations calculated from 10 runs of randomization. Results and discussion

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DNA bending induced by Cro protein binding as demonstrated by gel electrophoresis.

Cited by 58 publications

References 27 publications

Structure and dynamics of three-way DNA junctions: atomic force microscopy studies

Structure and dynamics of three-way DNA junctions: atomic force microscopy studies

Mammalian SMC3 C-terminal and Coiled-coil Protein Domains Specifically Bind Palindromic DNA, Do Not Block DNA Ends, and Prevent DNA Bending

Distribution of bending propensity in DNA sequences

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