The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA.

Ho, P Shing

doi:10.1073/pnas.91.20.9549

Cited by 67 publications

(59 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This is ∼1.5 kcal/mol per dinucleotide, which is consistent with experimental data that give 0.66 kcal/mol per CG repeat (17), and in general, <2 kcal/mol per dinucleotide repeat (60). Lee et al (25) obtained 0.93 kcal/mol per dinucleotide with the base extrusion zipper mechanism at 0.1 M salt concentration in explicit water.…”

Section: Discussionsupporting

confidence: 90%

Reaction path ensemble of the B–Z-DNA transition: a comprehensive atomistic study

Moradi

Babin

Roland

et al. 2012

Nucleic Acids Research

View full text Add to dashboard Cite

Since its discovery in 1979, left-handed Z-DNA has evolved from an in vitro curiosity to a challenging DNA structure with crucial roles in gene expression, regulation and recombination. A fundamental question that has puzzled researchers for decades is how the transition from B-DNA, the prevalent right-handed form of DNA, to Z-DNA is accomplished. Due to the complexity of the B–Z-DNA transition, experimental and computational studies have resulted in several different, apparently contradictory models. Here, we use molecular dynamics simulations coupled with state-of-the-art enhanced sampling techniques operating through non-conventional reaction coordinates, to investigate the B–Z-DNA transition at the atomic level. Our results show a complex free energy landscape, where several phenomena such as over-stretching, unpeeling, base pair extrusion and base pair flipping are observed resulting in interconversions between different DNA conformations such as B-DNA, Z-DNA and S-DNA. In particular, different minimum free energy paths allow for the coexistence of different mechanisms (such as zipper and stretch–collapse mechanisms) that previously had been proposed as independent, disconnected models. We find that the B–Z-DNA transition—in absence of other molecular partners—can encompass more than one mechanism of comparable free energy, and is therefore better described in terms of a reaction path ensemble.

show abstract

Section: Discussionsupporting

confidence: 90%

Reaction path ensemble of the B–Z-DNA transition: a comprehensive atomistic study

Moradi

Babin

Roland

et al. 2012

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Although d(GT) n tracts possess a distinctly lower Z-DNA-forming potential than d(CG) n tracts (Ho et al, 1986), the filament proteins produced, related to the parental vector, a substantially stronger band-shift with plasmid pVimE23 containing a d(GT) 17 microsatellite repeat than with plasmid pCG17 harboring a perfect d(CG) 17 dinucleotide repeat or related plasmids carrying interrupted d(CG) 17 repeats. This discrepancy could at least partially be resolved by 2D-agarose gel electrophoresis of the protein-free plasmids, which showed that, in agreement with previous reports (Ho, 1994), the B-Z transition in pVimE23 DNA requires a higher negative superhelical density and is compensated for by relaxation of a lower number of superhelical turns than in pCG17 DNA. On the basis of these results, it seemed that, due to the strong affinity of cIF proteins for the helix-helix juxtapositions of supercoiled plasmids (Li et al, 2002a), their binding to pVimE23 DNA is favored just because of the higher number of DNA crossovers in the plasmid.…”

Section: Interaction Of Cif Proteins With Supercoiled Plasmids Contaisupporting

confidence: 86%

“…Moreover, in plasmid pVim23, the structural transition was observed at 2DLk 5 14, in comparison with 2DLk 5 9 in plasmid pCG17. This is in good correspondence with published data, which showed that the B-Z transition in d(GT) n sequences occurs at a higher superhelical density than required for d(CG) n sequences (Ho, 1994). The plasmids pBluescript II SK (1), pVimE23 and pCG17 were further analyzed for their capacities to associate with cIF proteins at physiological ionic strength.…”

Section: Binding Of If Proteins To Z-dna 145supporting

confidence: 53%

InteractionIn Vitroof Type III Intermediate Filament Proteins with Z-DNA and B-Z-DNA Junctions

Tolstonog

Traub

2003

DNA and Cell Biology

View full text Add to dashboard Cite

The selection of DNA fragments containing simple d(GT)(n) and composite d(GT)(m). d(GA)(n) microsatellites during affinity binding of mouse genomic DNA to type III cytoplasmic intermediate filaments (cIFs) in vitro, and the detection of such repeats, often as parts of nuclear matrix attachment region (MAR)-like DNA, in SDS-stable DNA-vimentin crosslinkage products isolated from intact fibroblasts, prompted a detailed study of the interaction of type III cIF proteins with left-handed Z-DNA formed from d(GT)(17) and d(CG)(17) repeats under the topological tension of negatively supercoiled plasmids. Although d(GT)(n) tracts possess a distinctly lower Z-DNA-forming potential than d(CG)(n) tracts, the filament proteins produced a stronger electrophoretic mobility shift with a plasmid carrying a d(GT)(17) insert than with plasmids containing different d(CG)(n) inserts, consistent with the facts that the B-Z transition of d(GT)(n) repeats requires a higher negative superhelical density than that of d(CG)(n) repeats and the affinity of cIF proteins for plasmid DNA increases with its superhelical tension. That both types of dinucleotide repeat had indeed undergone B-Z transition was confirmed by S1 nuclease and chemical footprinting analysis of the plasmids, which also demonstrated efficient protection by cIF proteins from nucleolytic and chemical attack of the Z-DNA helices as such, as well as of the flanking B-Z junctions. The analysis also revealed sensibilization of nucleotides in the center of one of the two strands of a perfect d(CG)(17) insert toward S1 nuclease, indicating cIF protein-induced bending of the repeat. In all these assays, vimentin and glial fibrillary acidic protein (GFAP) showed comparable activities, versus desmin, which was almost inactive. In addition, vimentin and GFAP exhibited much higher affinities for the Z-DNA conformation of brominated, linear d(CG)(25) repeats than for the B-DNA configuration of the unmodified oligonucleotides. While double-stranded DNA was incapable of chasing the Z-DNA from its protein complexes, and Holliday junction and single-stranded (ss)DNA were distinguished by reasonable competitiveness, phosphatidylinositol (PI) and, particularly, phosphatidylinositol 4,5-diphosphate (PIP(2)) turned out to be extremely potent competitors. Because PIP(2) is an important member of the nuclear PI signal transduction cascade, it might exert a regulatory influence on the binding of cIF proteins to Z- and other DNA conformations. From this interaction of cIF proteins with Z- and bent DNA and their previously detected affinities for MAR-like, ss, triple helical, and four-way junction DNA, it may be concluded that the filament proteins play a general role in such nuclear matrix-associated processes as DNA replication, recombination, repair, and transcription.

show abstract

“…This alternating purine-pyrimidine sequence is capable of forming Z DNA, a left-handed helix, whereas B DNA is a right-handed helix (Nordheim and Rich, 1983). As the CA repeat forms unstable Z DNA, it transitions between Z and B DNA, forming ss DNA during the transition (Ho, 1994), possibly explaining the ability of AID to attack these regions. Also, two extruded bases are present at the junction between Z and B DNA (Ha et al, 2005).…”

Section: Resultsmentioning

confidence: 99%

Activation-Induced Cytidine Deaminase Induces Reproducible DNA Breaks at Many Non-Ig Loci in Activated B Cells

et al. 2011

View full text Add to dashboard Cite

After immunization or infection, activation-induced cytidine deaminase (AID) initiates diversification of immunoglobulin (Ig) genes in B cells, introducing mutations within the antigen binding V regions (somatic hypermutation, SHM) and double-strand DNA breaks (DSBs) into switch (S) regions, leading to antibody class switch recombination (CSR). We asked if during B cell activation, AID also induces DNA breaks at genes other than IgH genes. Using a non-biased genome-wide approach, we have identified hundreds of reproducible AID-dependent DSBs in mouse splenic B cells shortly after induction of CSR in culture. Most interestingly, AID induces DSBs at sites syntenic with sites of translocations, deletions, and amplifications found in human B cell lymphomas, including within the oncogene B cell lymphoma11a (bcl11a)/evi9. Unlike AID-induced DSBs in Ig genes, genome-wide AID-dependent DSBs are not restricted to transcribed regions, and frequently occur within repeated sequence elements, including CA-repeats and non-CA tandem repeats, and SINEs.

show abstract

The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA.

Cited by 67 publications

References 34 publications

Reaction path ensemble of the B–Z-DNA transition: a comprehensive atomistic study

Reaction path ensemble of the B–Z-DNA transition: a comprehensive atomistic study

InteractionIn Vitroof Type III Intermediate Filament Proteins with Z-DNA and B-Z-DNA Junctions

Activation-Induced Cytidine Deaminase Induces Reproducible DNA Breaks at Many Non-Ig Loci in Activated B Cells

Contact Info

Product

Resources

About