Magnetic control over the fundamental structure of atomic wires.

When reducing the size of materials towards the nanoscale, magnetic properties can emerge due to structural variations. Here, we show the reverse effect, where the structure of nanomaterials is controlled by magnetic manipulations. Using the break-junction technique, we find that the interatomic distance in platinum atomic wires is shorter or longer by up to ∼20%, when a magnetic field is applied parallel or perpendicular to the wires during their formation, respectively. The magnetic field direction also affects the wire length, where longer (shorter) wires are formed under a parallel (perpendicular) field. Our experimental analysis, supported by calculations, indicates that the direction of the applied magnetic field promotes the formation of suspended atomic wires with a specific magnetization orientation associated with typical orbital characteristics, interatomic distance, and stability. A similar effect is found for various metal and metal-oxide atomic wires, demonstrating that magnetic fields can control the atomistic structure of different nanomaterials when applied during their formation stage.

Transcription Factor Binding in Embryonic Stem Cells Is Constrained by DNA Sequence Repeat Symmetry.

Transcription factor (TF) recognition is dictated by the underlying DNA motif sequence specific for each TF. Here, we reveal that DNA sequence repeat symmetry plays a central role in defining TF-DNA-binding preferences. In particular, we find that different TFs bind similar symmetry patterns in the context of different developmental layers. Most TFs possess dominant preferences for similar DNA repeat symmetry types. However, in some cases, preferences of specific TFs are changed during differentiation, suggesting the importance of information encoded outside of known motif regions. Histone modifications also exhibit strong preferences for similar DNA repeat symmetry patterns unique to each type of modification. Next, using an in vivo reporter assay, we show that gene expression in embryonic stem cells can be positively modulated by the presence of genomic and computationally designed DNA oligonucleotides containing identified nonconsensus-repetitive sequence elements. This supports the hypothesis that certain nonconsensus-repetitive patterns possess a functional ability to regulate gene expression. We also performed a solution NMR experiment to probe the stability of double-stranded DNA via imino proton resonances for several double-stranded DNA sequences characterized by different repetitive patterns. We suggest that such local stability might play a key role in determining TF-DNA binding preferences. Overall, our findings show that despite the enormous sequence complexity of the TF-DNA binding landscape in differentiating embryonic stem cells, this landscape can be quantitatively characterized in simple terms using the notion of DNA sequence repeat symmetry.