DNA-Based Scaffolds for Sensing Applications

DNA nanotechnology employs synthetic nucleic acid strands to design and engineer nanoscale structural and functional systems of increasing complexity that may find applications in sensing,1-7 computing,8-10 molecular transport,11-13 information processing14 and catalysis.15,16 Several features make synthetic DNA a particularly appealing and advantageous biomaterial for all the above applications but more specifically for sensing. First, synthetic DNA sequences, especially if of limited length (<100 nucleotides), have highly predictable interactions and thermodynamics. This allows to develop spatio-temporally controlled nanostructures with quasi-Amstrong precision and to engineer supramolecular devices with well controlled secondary structures.17-22 DNA is also quite easy and inexpensive to synthetize: currently the cost of 150 µg of an unmodified single stranded DNA strand of 20 nucleotides is about 8 euros if purchased from one of the many commercial vendors available in the market. Finally, DNA is relatively stable if compared to other biomolecules like enzymes or antibodies. The other important feature of synthetic DNA is the wide range of possibilities that it offers for sensing applications if used as recognition element. Of course the most obvious use of a single stranded synthetic DNA sequence as recognition element is for the detection of a specific target complementary sequence. Countless applications of such use, especially if coupled with PCR, have been reported to date which resulted in many commercially available sensing devices.23,24 Synthetic DNA can also be used as recognition element for targets other than DNA. This is the case, for example, of DNA aptamers, a class of high-affinity nucleic acid ligands, which are selected through alternate cycles in vitro to bind a specific target molecule.25-29 To date, thousands of DNA and RNA aptamers have been selected which bind to specific targets including small molecules, proteins, peptides, bacteria, virus, and live cells.30-32 Other aptamers can bind to surface molecules and membrane proteins of live cells.33-35 A DNA aptamer is usually a short DNA sequence (<100 nucleotides) that can bind with high affinity (nM-µM) and high specificity its specific target. While the affinity of the aptamers is usually not as high as that of other biomolecular recognition elements (i.e. antibodies) there are some advantages connected with their use including the lower cost and the higher stability. Synthetic DNA can also be used as recognition element to detect metal ions through the use of thymine-thymine (T-T) and cytosine-cytosine (C-C) mismatches, which specifically bind mercury(II)36-38 and silver(I)39,40 ions respectively or through the use of copper-dependent DNAzymes.41 Similarly, the use of non-conventional DNA interactions can be used to rationally design pH-sensitive DNA switches that can be used as nanometer scale pH meters.42-44 Such probes typically exploit DNA secondary structures that display pH dependence due to the presence of specific protonation sites. These structures include I-motif,45-50 inter and intra molecular triplex DNA,51-55 DNA tweezers56 and catenanes.57 Recently, we have also reported on the rational design of programmable DNA-based nanoswitches whose closing/opening can be triggered over specific different pH windows by simply changing the relative content of TAT/CGC triplets in the switches.58 Finally, DNA can be employed as convenient recognition element for the detection of transcription factors, proteins that control the transcription of genetic information and that specifically recognize double-stranded or single-stranded DNA and RNA sequences.59-63.