Sequence‐Dependent Fluorescence of DNA‐Hosted Silver Nanoclusters

Artificial structures built from synthetic DNA are emerging as platforms for device science that offer greatly enhanced resolution and simplicity of fabrication compared to traditional solid-state structures. These advantages arise from the nanometer-scale control over geometry provided by aqueous self-assembly of designed DNA sequences, which yields robust “scaffolds” in a palette of nanometer-scale geometries ranging from octahedra to two-dimensional lattices of all types. [1–10] Future applications that arise from such DNA scaffolds may include nanometer-scale optics, nanometer-scale electronics, and single-molecule detection proteomics. Realizing the promise that DNA-based materials hold for nanometer-scale device science will require the development of functional nanoelements for patterning of DNA scaffolds. In analogy to the layout of logic and memory elements on a semiconductor chip, nanoelements with properties that can be varied in a controlled manner across the underlying scaffold are needed. Such nanoelements should have lateral dimensions no larger than a few nanometers, in order to take advantage of the ultrafine, 6 nm resolution currently available in DNA scaffolds. Nanoelements should be hosted within DNA strands that can integrate into the scaffold structure, to enable precise positioning. Finally, nanoelement properties should depend on the base sequence of their host DNA strand, to provide site-specific behavior. Such a combination of properties would increase flexibility and function in comparison to current approaches for patterning DNA scaffolds with attachments, such as Au nanoparticles and proteins, which are relatively bulky and lack sensitivity to the sequence of nearby DNA bases. Here we show that silver nanoclusters bound to short, synthetic DNA strands provide optically functional nanoelements with the desired small size, sequence sensitivity, and suitability for integration into DNA scaffolds. Our work builds on the initial discovery of fluorescence from few-atom silver clusters attached to a 12-base, single-stranded DNA sequence. We use six 19-base DNA oligomers to show that visibly fluorescent silver clusters form only in single-stranded regions of the DNA hosts. This selectivity opens the possibility of precise positioning of optical nanoelements on DNA scaffolds through use of DNA “hairpin” sequences, which have already been used to create patterns of high complexity, with resolution below 10 nm, upon double-stranded DNA scaffolds. We find that the spectral characteristics of these silver-DNA nanoelements can be controlled by the base sequence and secondary structure of the DNA strands that host the silver atoms, a result that may ultimately contribute to achieving sequence-programmed optical addressing with nanometer-scale resolution. Scheme 1 represents the oligomers studied here. Colored circles indicate the bases: blue = cytosine (C), green = thymine (T), red = guanine (G), and yellow = adenine (A). C-Strand and G-Strand are complementary sequences that, alone in solution, are each predominantly single-stranded (ss), but form a purely double-stranded (ds) “Duplex” when thermally annealed together under our solution conditions. The hairpin oligomers C-loop, G-loop, A-loop and T-loop are partially self-complementary sequences with a common, 7-base C O M M U N IC A IO N