Research projects

Biomolecular systems; DNA


   The structure of DNA, with its wire-like double helix, and pi-electron-rich stacked base pairs, has led to considerable interest in the molecule’s electronic properties for decades. The interest in charge transport through DNA is driven both by biological considerations, involving radiation damage and repair, as well as by the molecule’s potential use as molecular wire in nanoelectronics.
   The focus of our DNA research is on the experimental charge transport measurements through DNA molecules and assemblies. Literature reports on charge transport through DNA portray a range of conductivity values. But, the experiments are typically performed under a variety of conditions where important factors, including the surface of the substrate, contacts to the electrodes, DNA sequence, counterions, and DNA secondary structure (bends, nicks, stacking distance between base pairs, width of the DNA molecule), are not kept constant. To establish the relationship of DNA structure to its charge transport properties, we perform comparative measurements on lambda DNA assemblies. To ensure repeatable attachment of DNA molecules to electrodes, with utilize thiol or disulfide affinity to gold. In the case lambda DNA (16 micron long, ~48,000 bp), we employ the two overhanging ends on the molecules to attach disulfide labeled complementary oligonucleotides to lambda. The disulfide labeled DNA molecules are aligned between 2 gold electrodes under the application of an ac electric field. A schematic picture is on the left below, whereas an AFM picture (18 x 18 micron, height variation, 54 nm) of aligned bundles, between gold electrodes on mica, is found on the right below.


   To probe the relationship of structure to DNA electrical properties, we have investigated linear lambda DNA molecules functionalized with disulfide groups at both ends. The procedure of attaching disulfide end groups to lambda DNA molecules generates two gaps or nicks in the phosphate backbone, between the DNA and the short oligonucleotide segment (indicated on the left above). These nicks can be repaired by the addition of a ligation enzyme, and the I-V characteristics shown on the left reveal a change in curve shapes as a function of structure. The repaired DNA double helices show a close-to-linear I-V characteristic, with a DC conductivity estimated at ~ 1x10-3 S cm-1. In contrast, the nicked lambda DNA shows pronouncedly non-linear and rectifying behavior, with a conductivity gap of ~ 3 eV. The low-field conductivity of the nicked lambda DNA is approximately a factor 10 lower than the repaired lambda DNA’s conductivity. [B. Hartzell et al. “Comparative current-voltage characteristics of nicked and repaired lambda-DNA”, Applied Physics Letters 82, 4800 (2003)].


   We have further investigated the effect of nicks in the lambda backbone on charge transport. Nineteen nicks were introduced using the artificial endonuclease, N.Bpu101, which recognizes a double stranded DNA sequence but instead of cutting both strands it nicks the phosphate backbone of only one of the strands at the nineteen recognition sites present in lambda DNA. Comparative I-V measurements of lambda DNA versus lambda DNA with 19 nicks is shown in the figure on the left. The introduction of 19 nicks reduces the magnitude of the measured current to that of the airgap, again indicating to the interplay between structure and electronic properties of DNA.


   To assess the influence of disulfide termination on charge transport, we have synthesized lambda DNA molecules labeled with disulfide end groups in two configurations: at the 3’ ends of opposing strands, or on the 3’ and 5’ ends of the same strand. In the latter configuration, only one strand is attached and contacted to the two Au electrodes utilized in the measurement. I-V measurements of these two types of lambda DNA show no appreciable differences in curve shapes, indicating that the position of the disulfide is less important than the fidelity of the double helical structure. [B. Hartzell et al. “Current-voltage characteristics of diversely disulfide terminated labmda-DNA” Journal of Applied Physics 95, 2764 (2003)].


   To further evaluate the influence of the double helical structure, we measure the I-V characteristics of double stranded (dsDNA) versus single-stranded (ssDNA) molecules. For these measurements, we utilize lambda DNA molecules that possess disulfide linkers on the 3’ and 5’ ends of the same strand. This allows us to first measure lambda in the double stranded form, and then single strand the molecules on the device itself and compare the results. The ssDNA was formed from the dsDNA using two different methods: a thermal/chemical denaturation and enzymatic digestion utilizing lambda exonuclease. Resulting I-V characteristics for both the double stranded and single stranded samples are close-to-linear when measured at room temperature. However, the ssDNA samples consistently give conductivity values about a factor 50 smaller in amplitude, as seen in the figure on the left. These observations reinforce the importance of the double helical structure in DNA charge transport. Support from NSF NIRT grant 0103034.