Many of the mutagenic or lethal effects of ionization radiation can be attributed to damage caused to the DNA by low-energy electrons. To gain insight on the parameters affecting this process, we measured the low-energy electron (<2 eV) transmission yield through self-assembled monolayers of short DNA oligomers. The electrons that are not transmitted are captured by the layer. Hence, the transmission reflects the capturing efficiency of the electrons by the layer. The dependence of the capturing probability on the base sequence was studied, as was the state of the captured electrons. It is found that the capturing probability scales with the number of G bases in the single-stranded oligomers and depends on their clustering level. Using two-photon photoelectron spectroscopy, we find that, once captured, the electrons do not reside on the bases. Rather, the state of the captured electrons is insensitive to the sequence of the oligomer. Double-stranded DNA does not capture electrons as efficiently as single-stranded oligomers; however, once captured, the electrons are bound more strongly than to the single strands.monolayer ͉ radiation damage ͉ guanine ͉ photoemission M any of the mutagenic or lethal effects of ionization radiation can be attributed to secondary electrons that are created within 10 Ϫ15 sec along radiation tracks and spurs and have kinetic energies Ͻ20 eV (1, 2). Experimental (3) and theoretical (4-6) studies indicate that electrons with subionization energies play an important role in inducing damage in DNA (7). Our goal in the present work is to determine the structural and chemical elements in the DNA that are governing the electron-capturing process by studying electron transmission through organized adsorbed layers of DNA.The detailed mechanism for electron-DNA interaction is difficult to address experimentally in vivo, where many parameters affect the electron-DNA interaction and the electron energy is not well defined. Therefore, we investigated the interaction of electrons possessing well defined energy, with monolayers of single-stranded (ss) and double-stranded (ds) DNA oligomers adsorbed on a gold surface. By methodically varying the bases in the oligomers, the effect of each base on the interaction with electrons could be determined, as could the difference between single and double strands. Furthermore, the binding energy of the captured electrons could be determined.Past findings hint that G bases act as ''DNA protectors.'' For example, G-rich telomeres found at the ends of chromosomes (8) were shown recently to increase the resistance of DNA to ionizing radiation (9). It is also well accepted that G is the most easily oxidized nucleotide (10,11). It has been demonstrated also that positive charges can transport over long distances in DNA through multistep hopping between G bases (12, 13). The putative role of G bases as protectors of the genome from electrons with kinetic energies greater than the ionization energy of the bases seems to result from their ability to easily form cations...

Here we show that self-assembled monolayers on gold of double-stranded DNA oligomers interact with polarized electrons similarly to a strong and oriented magnetic field. The direction of the field for right-handed DNA is away from the substrate. Moreover, the layer shows very high paramagnetic susceptibility. Interestingly, thiolated single-stranded DNA oligomers on gold do not show this effect. The new findings are rationalized based on recent results in which high paramagnetism was measured for diamagnetic films adsorbed on diamagnetic substrates.

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We present the assembly of gene brushes by means of a photolithographic approach that allows us to control the density of end-immobilized linear double-stranded DNA polymers coding for entire genes. For 2 kbp DNAs, the mean distance varies from 300 nm, where DNAs are dilute and assume relaxed conformations, down to 30 nm, where steric repulsion at dense packing forces stretching out. We investigated the gene-to-protein relationship of firefly luciferase under the T7/E.Coli-extract expression system, as well as transcription-only reactions with T7 RNA polymerase, and found both systems to be highly sensitive to brush density, conformation, and orientation. A 'structure-function' picture emerges in which extension of genes induced by moderate packing exposes coding sequences and improves their interaction with the transcription/translation machinery. However, tighter packing impairs the penetration of the machinery into the brush. The response of expression to two-dimensional gene crowding at the nanoscale identifies gene brushes as basic controllable units en route to multicomponent synthetic systems. In turn, these brushes could deepen our understanding of biochemical reactions taking place under confinement and molecular crowding in living cells.

We recently reported electrical transport measurements through double-stranded (ds)DNA molecules that are embedded in a self-assembled monolayer of single-stranded (ss)DNA and attached to a metal substrate and to a gold nanoparticle (GNP) on opposite ends. The measured current flowing through the dsDNA amounts to 220 nA at 2 V. In the present report we compare electrical transport through an ssDNA monolayer and dsDNA monolayers with and without upper thiol end-groups. The measurements are done with a conductive atomic force microscope (AFM) using various techniques. We find that the ssDNA monolayer is unable to transport current. The dsDNA monolayer without thiols in the upper end can transport low current on rare occasions and the dsDNA monolayer with thiols on both ends can transport significant current but with a much lower reliability and reproducibility than the GNP-connected dsDNA. These results reconfirm the ability of dsDNA to transport electrical current under the appropriate conditions, demonstrate the efficiency of an ssDNA monolayer as an insulating layer, and emphasize the crucial role of an efficient charge injection through covalent bonding for electrical transport in single dsDNA molecules.

Due to its coding nature, the many chemical and enzymatic manipulations that it can undergo, and its relative stability, DNA is being used as a scaffold and a building block outside the cellular context. The mode by which the DNA is connected to a solid surface is in the heart of technological advancements, such as DNA chips and biosensors. The desire is to connect the DNA to a given surface in a predesigned manner, tailored to any device specifications. In this work, DNA molecules were adsorbed specifically on gold surfaces. The specificity of the adsorption was controlled by a novel approach, in which the gold surface was first blocked with a hydrophobic layer (C18−SH) to various extents, followed by the adsorption of thiolated DNA. The technique was applied both for short and for long strands of DNA. We show that the reactivity of the thiolated short DNA in a ligation reaction is enhanced by more than an order of magnitude by the presence of the alkylthiol layer. Due to the hydrophobic and insulating nature of the C18−SH layer, this blocking method is advantageous for electronic measurements.

The electrical conduction through three short oligomers (26 base pairs, 8 nm long) with differing numbers of GC base pairs was measured. One strand is poly(A)-poly(T), which is entirely devoid of GC base pairs. Of the two additional strands, one contains 8 and the other 14 GC base pairs. The oligomers were adsorbed on a gold substrate on one side and to a gold nanoparticle on the other side. Conducting atomic force microscope was used for obtaining the current versus voltage curves. We found that in all cases the DNA behaves as a wide band-gap semiconductor, with width depending on the number of GC base pairs. As this number increases, the band-gap narrows. For applied voltages exceeding the band-gap, the current density rises dramatically. The rise becomes sharper with increasing number of GC base pairs, reaching more than 1 nA/nm2 for the oligomer containing 14 GC pairs.

Previously [Daube, S.S., & von Hippel, P.H. (1992) Science 258, 1320] we have shown that functional transcription elongation complexes can be formed by adding ribonucleotide triphosphates, Mg2+, and either Escherichia coli or T7 RNA polymerase to synthetic RNA-DNA bubble-duplex constructs. Here these observations are extended to show that the RNA transcripts synthesized from these bubble-duplex constructs are properly displaced from the DNA template during transcription. Some details of the displacement process differ between the polymerases tested. Thus the transcript is fully and processively displaced in the course of T7 polymerase-catalyzed synthesis from the bubble-duplex constructs, while the presence of a large excess of an RNA (or DNA) oligomer complementary to the DNA template sequence within the "permanent" DNA bubble is required to attain complete displacement of the nascent RNA from the construct during synthesis with the core E. coli enzyme. In addition, a correlation is shown between proper RNA displacement and the achievement of full-length transcript synthesis. We conclude that both the T7 polymerase and the E. coli core enzyme actively displace the nascent transcript during elongation and that the requirement for an RNA trap with the E. coli enzyme reflects its slower rate of synthesis. This suggests that these experiments may provide insight into the relative rates of transcript elongation and secondary structure formation within the nascent RNA in elongation and termination. By use of the RNA oligomer trap methodology, multiple rounds of transcript synthesis should be achievable on these bubble-duplex constructs with any polymerase.