Immobilization of DNA for scanning probe microscopy

Electronic Level Structure of Novel Guanine Octuplex DNA Single Molecules

Throughout the past few decades, guanine quadruplex DNA structures have attracted much interest both from a fundamental material science perspective and from a technologically oriented perspective. Novel guanine octuplex DNA, formed from coiled quadruplex DNA, was recently discovered as a stable and rigid DNA-based nanostructure. A detailed electronic structure study of this new nanomaterial, performed by scanning tunneling spectroscopy on a subsingle-molecule level at cryogenic temperature, is presented herein. The electronic levels and lower energy gap of guanine octuplex DNA compared to quadruplex DNA dictate higher transverse conductivity through guanine octads than through guanine tetrads.

Formation of Novel Octuplex DNA Molecules from Guanine Quadruplexes

Guanine quadruplex (G4)-DNA structures have sparked the interest of many scientists due to their important biological roles and their potential use in molecular nanoelectronics and nanotechnology. The high guanine content in G4-DNA endows it with mechanical stability, robustness, and improved charge transport properties-attractive attributes for a molecular nanowire. The self-driven formation of a novel G4-DNA-based nanostructure, coined guanine octuplex (G8)-DNA, is reported herein. Atomic force microscopy and scanning tunneling microscopy characterization of this molecule reveal its organized coiled-coil structure, which is found to be stable under different temperatures and surrounding conditions. G8-DNA exhibits enhanced stiffness, mechanical and thermodynamic stability when compared to its parent G4-DNA. These, along with its high guanine content, make G8-DNA a compelling new molecule, and a highly prospective candidate for molecular nanoelectronics.

Electronic Level Structure of Silver-Intercalated Cytosine Nanowires

Metal-mediated base-paired DNA has long been investigated for basic scientific pursuit and for nanoelectronics purposes. Particularly attractive in these domains is the Ag⁺-intercalated polycytosine DNA duplex. Extensive studies of this molecule have led to our current understanding of its self-assembly properties, high thermodynamic and structural stability, and high longitudinal conductivity. However, a high-resolution morphological characterization of long Ag⁺-intercalated polycytosine DNA has hitherto not been carried out. Furthermore, the electronic level structure of this molecule has not been studied before. Here we present a scanning tunneling microscopy and spectroscopy study of this intriguing nanowire. Its temperature-independent morphological and electronic properties suggest substantial stability, while its emergent electronic levels and energy gap provide the basis for its high conductivity.

Temperature Dependence of the STM Morphology and Electronic Level Structure of Silver-Containing DNA

Understanding the effect of external conditions, temperature in particular, on novel nanomaterials is of great significance. The powerful ability of scanning tunneling microscopy (STM) to characterize topography and electronic levels on a single molecule scale is utilized herein to characterize individual silver-containing poly(dG)-poly(dC) DNA molecules, at different temperatures. These measurements indicate that the molecule is a truly hybrid metal-organic nanomaterial with electronic states originating from both the DNA and the embedded silver. The temperature dependence of this density of states (DOS) leads to the temperature dependent STM apparent height of the molecule-a phenomenon that has not been observed before for other complex nanostructures.

Scanning Tunneling Microscopy and Spectroscopy of Novel Silver-Containing DNA Molecules

The quest for a suitable molecule to pave the way to molecular nanoelectronics has been met with obstacles for over a decade. Candidate molecules such as carbon nanotubes lack the appealing trait of self-assembly, while DNA seems to lack the desirable feature of conductivity. Silver-containing poly(dG)-poly(dC) DNA (E-DNA) molecules have recently been reported as promising candidates for molecular electronics, owing to the selectivity of their metallization, their thin and uniform structure, their resistance to deformation, and their maximum possible high conductivity. Ultrahigh vacuum (UHV) scanning tunneling microscopy (STM) of E-DNA presents an elaborate high-resolution morphology characterization of these unique molecules, along with a detailed depiction of their electronic level structure. The energy levels found for E-DNA indicate a novel truly hybrid metal-molecule structure, potentially more conductive than other DNA-based alternatives.

A Review on Surface Stress-Based Miniaturized Piezoresistive SU-8 Polymeric Cantilever Sensors

In the last decade, microelectromechanical systems (MEMS) SU-8 polymeric cantilevers with piezoresistive readout combined with the advances in molecular recognition techniques have found versatile applications, especially in the field of chemical and biological sensing. Compared to conventional solid-state semiconductor-based piezoresistive cantilever sensors, SU-8 polymeric cantilevers have advantages in terms of better sensitivity along with reduced material and fabrication cost. In recent times, numerous researchers have investigated their potential as a sensing platform due to high performance-to-cost ratio of SU-8 polymer-based cantilever sensors. In this article, we critically review the design, fabrication, and performance aspects of surface stress-based piezoresistive SU-8 polymeric cantilever sensors. The evolution of surface stress-based piezoresistive cantilever sensors from solid-state semiconductor materials to polymers, especially SU-8 polymer, is discussed in detail. Theoretical principles of surface stress generation and their application in cantilever sensing technology are also devised. Variants of SU-8 polymeric cantilevers with different composition of materials in cantilever stacks are explained. Furthermore, the interdependence of the material selection, geometrical design parameters, and fabrication process of piezoresistive SU-8 polymeric cantilever sensors and their cumulative impact on the sensor response are also explained in detail. In addition to the design-, fabrication-, and performance-related factors, this article also describes various challenges in engineering SU-8 polymeric cantilevers as a universal sensing platform such as temperature and moisture vulnerability. This review article would serve as a guideline for researchers to understand specifics and functionality of surface stress-based piezoresistive SU-8 cantilever sensors.

Potential role of atomic force microscopy in systems biology

Systems biology is a quantitative approach for understanding a biological system at its global level through systematic perturbation and integrated analysis of all its components. Simultaneous acquisition of information data sets pertaining to the system components (e.g., genome, proteome) is essential to implement this approach. There are limitations to such an approach in measuring gene expression levels and accounting for all proteins in the system. The success of genomic studies is critically dependent on polymerase chain reaction (PCR) for its amplification, but PCR is very uneven in amplifying the samples, ineffective in scarce samples and unreliable in low copy number transcripts. On the other hand, lack of amplifying techniques for proteins critically limits their identification to only a small fraction of high concentration proteins. Atomic force microscopy (AFM), AFM cantilever sensors, and AFM force spectroscopy in particular, could address these issues directly. In this article, we reviewed and assessed their potential role in systems biology.

Unraveling DNA dynamics using atomic force microscopy

The elucidation of structure-function relationships of biological samples has become important issue in post-genomic researches. In order to unveil the molecular mechanisms controlling gene regulations, it is essential to understand the interplay between fundamental DNA properties and the dynamics of the entire molecule. The wide range of applicability of atomic force microscopy (AFM) has allowed us to extract physicochemical properties of DNA and DNA-protein complexes, as well as to determine their topographical information. Here, we review how AFM techniques have been utilized to study DNA and DNA-protein complexes and what types of analyses have accelerated the understanding of the DNA dynamics. We begin by illustrating the application of AFM to investigate the fundamental feature of DNA molecules; topological transition of DNA, length dependent properties of DNA molecules, flexibility of double-stranded DNA, and capability of the formation of non-Watson-Crick base pairing. These properties of DNA are critical for the DNA folding and enzymatic reactions. The technical advancement in the time-resolution of AFM and sample preparation methods enabled visual analysis of DNA-protein interactions at sub-second time region. DNA tension-dependent enzymatic reaction and DNA looping dynamics by restriction enzymes were examined at a nanoscale in physiological environments. Contribution of physical properties of DNA to dynamics of nucleosomes and transition of the higher-order structure of reconstituted chromatin are also reviewed.

Nanoengineering with DNA

DNA is a tractable medium for controlling the structure of matter on the nanometer scale. We have explored ligating together stable branched DNA molecules to form geometrical objects. By this means, we have assembled a 3-connected molecule whose helix axes have the connectivity of a cube. The construct is a hexacatenane, each of whose cyclic strands corresponds to a face of the object. Each of its twelve edges contains a unique recognition site for cleavage by a restriction enzyme; these sites are used to demonstrate the assembly of the object. The plectonemic structure of DNA also permits the directed synthesis of molecular knots. Recently, we have constructed trefoil knots from B-DNA and an amphichiral figure-8 knot whose helical domains contain both B-DNA and Z-DNA.

We have developed a solid-support methodology for the synthesis of geometrical objects. This approach provides greater control over products and topological purity, and lends itself better to automation. Branched molecules containing 3–6 double helical arms can be formed from equimolar mixtures of their component strands, thereby enabling the construction of 3–6 connected networks. The goals of this work include the construction of periodic multiply-connected networks of DNA. The aims of these DNA constructions include using them as scaffolding to build periodic macromolecular arrays for diffraction purposes, as well as directing the assembly of molecular electronic devices. There are wellcharacterized molecular transformations of DNA that make nano-scale machines feasible to build in this molecular context. These materials are likely to be useful for understanding crystallization processes and structure-function relationships.

Atomic force microscopy of biological samples

The ability to evaluate structural-functional relationships in real time has allowed scanning probe microscopy (SPM) to assume a prominent role in post genomic biological research. In this mini-review, we highlight the development of imaging and ancillary techniques that have allowed SPM to permeate many key areas of contemporary research. We begin by examining the invention of the scanning tunneling microscope (STM) by Binnig and Rohrer in 1982 and discuss how it served to team biologists with physicists to integrate high-resolution microscopy into biological science. We point to the problems of imaging nonconductive biological samples with the STM and relate how this led to the evolution of the atomic force microscope (AFM) developed by Binnig, Quate, and Gerber, in 1986. Commercialization in the late 1980s established SPM as a powerful research tool in the biological research community. Contact mode AFM imaging was soon complemented by the development of non-contact imaging modes. These non-contact modes eventually became the primary focus for further new applications including the development of fast scanning methods. The extreme sensitivity of the AFM cantilever was recognized and has been developed into applications for measuring forces required for indenting biological surfaces and breaking bonds between biomolecules. Further functional augmentation to the cantilever tip allowed development of new and emerging techniques including scanning ion-conductance microscopy (SICM), scanning electrochemical microscope (SECM), Kelvin force microscopy (KFM) and scanning near field ultrasonic holography (SNFUH).

Electron transfer of plurimodified DNA SAMs

An STM-based current-voltage (I/V) investigation of deoxyribonucleic acid (DNA) 18 base pair (bp) oligonucleotide monolayers on gold is presented. Three bases of each of the immobilized and complementary strands were modified with either iodine or phenylethylene moieties. The oligonucleotides were immobilized on template stripped gold (tsg) surfaces and characterized by atomic force microscopy (AFM) and scanning tunneling microscopy (STM). AFM imaging showed that monolayers of the expected height were formed. A comparative study of normal, halogenated, and phenyl-modified DNA was made with the STM in tunneling spectroscopy (TS) mode. I/V spectroscopic measurements in the range +/-250 mV on both single- and double-stranded (ds) DNA monolayers (modified and unmodified) showed that for negative substrate bias (U(sub)) electron transfer is more efficient through a phenyl-modified monolayer than through normal or halogenated DNA. This effect was particularly clear below a threshold bias of -100 mV. For positive U(sub), unmodified ds DNA was found to conduct slightly better than the modified strands. This is presumably caused by greater order in the unmodified versus modified DNA monolayers. Modifications on the immobilized (thiolated) strand seem to improve electron transport through the DNA monolayer more than modifications on the complementary (not surface-bound) strand.

The Puzzle of Contrast Inversion in DNA STM Imaging

DNA has been at the center of an imaging effort since the invention of the scanning tunneling microscope (STM). In some of the STM imaging reports the molecules appeared with negative contrast, i.e., "submerged" under the metal background and darker. We demonstrate the phenomenon of contrast inversion in DNA STM imaging by controlled and spontaneous contrast inversions and by the dependence of the DNA apparent height with respect to the surface on the imaging bias voltage. Using these characterizations, we formulate a model explaining the above phenomenon by resonant tunneling through virtual states in the vacuum between the STM tip and the DNA molecule.

Immobilization of DNA on 11-mercaptoundecanoic acid-modified gold (111) surface for atomic force microscopy imaging

Immobilized DNA on preformed 11-mercaptoundecanoic acids (MUDA) self-assembled monolayers (SAMs) on a gold (111) surface was bound by a divalent cation bridges was imaged by atomic force microscopy (AFM). The DNA immobilization was attributed to the formation of ionic bridges between the carboxylate groups of MUDA and the phosphate groups of DNA. AFM images revealed that DNA molecules could be immobilized strongly enough to permit stable and reproducible imaging. The effect of different bridge cations, such as Mg(2+), Zn(2+) and Cu(2+), and the pH of DNA assembled solution on immobilization and conformation of DNA was studied. Plasmid DNA pBR 322/Pst I molecules were straightened by using a molecular combing technique on the MUDA surface.

Mapping individual cosmid DNAs by direct AFM imaging

Individual cosmid clones have been restriction mapped by directly imaging, with the atomic force microscope (AFM), a mutant EcoRI endonuclease site-specifically bound to DNA. Images and data are presented that locate six restriction sites, predicted from gel electrophoresis, on a 35-kb cosmid isolated from mouse chromosome 7. Measured distances between endonuclease molecules bound to lambda DNA, when compared to known values, demonstrate the accuracy of AFM mapping to better than 1%. These results may be extended to identify other important site-specific protein-DNA interactions, such as transcription factor and mismatch repair enzyme binding, difficult to resolve by current techniques.

Scanning tunneling microscopy of mercapto-hexyl-oligonucleotides attached to gold

6-mercapto hexyl-oligonucleotides bind to a gold surface strongly enough to permit imaging by a scanning tunneling microscope (STM). STM images showed worm-like chains that were approximately 12-(A-wide for single-stranded DNA and 20-(A-wide for double-stranded DNA. The chain lengths corresponded to 3.4 +/- 0.4 A per basepair for double-stranded DNA and 2.2 +/- 0.4 A per base for single-stranded DNA. This unexpectedly short length for single-stranded DNA was confirmed using oligomers with both single- and double-stranded regions. When the attachment of the samples was weakened (by imaging in water or scraping with the STM tip) the images changed to pairs of "blobs," apparently reflecting the attachment points of the molecules to the gold surface. Given this interpretation, images of DNA containing a five-base bulge imply that the bulge bends the oligomer by 90 degrees +/- 20 degrees.

Method for immobilizing microbial cells on gel surface for dynamic AFM studies

The processes of cell growth and budding of the yeast cells Saccharomyces cerevisiae, which were gently immobilized on 3% agar and submerged in culture medium, were successfully imaged with an atomic force microscope for 6-7 h. Similar experiments on chemically fixed cells did not detect any appreciable change in their appearance except in a few scannings at the very beginning, indicating that the dissolution of agar and/or scraping of its surface by the scanning tip, if any, did not significantly interfere with the images taken thereafter. The increment in the height of many of the untreated cells, accompanied by their lateral enlargement, was taken as an indication of successful imaging of the growth process of yeast cells, together with an image of a growing daughter cell attached to its mother cell.

DNA loops induced by cooperative binding of transcriptional activator proteins and preinitiation complexes

DNA conformational changes are essential for the assembly of multiprotein complexes that contact several DNA sequence elements. An approach based on atomic force microscopy was chosen to visualize specific protein-DNA interactions occurring on eukaryotic class II nuclear gene promoters. Here we report that binding of the transcription regulatory protein Jun to linearized plasmid DNA containing the consensus AP-1 binding site upstream of a class II gene promoter leads to bending of the DNA template. This binding of Jun was found to be essential for the formation of preinitiation complexes (PICs). The cooperative binding of Jun and PIC led to looping of DNA at the protein binding sites. These loops were not seen in the absence of either PICs, Jun, or the AP-1 binding site, suggesting a direct interaction between DNA-bound Jun homodimers and proteins bound to the core promoter. This direct visualization of functional transcriptional complexes confirms the theoretical predictions for the mode of gene regulation by trans-activating proteins.

Molecular electronics of a single photosystem I reaction center: studies with scanning tunneling microscopy and spectroscopy

Thylakoids and photosystem I (PSI) reaction centers were imaged by scanning tunneling microscopy. The thylakoids were isolated from spinach chloroplasts, and PSI reaction centers were extracted from thylakoid membranes. Because thylakoids are relatively thick nonconductors, they were sputter-coated with Pd/Au before imaging. PSI photosynthetic centers and chemically platinized PSI were investigated without sputter-coating. They were mounted on flat gold substrates that had been treated with mercaptoacetic acid to help bind the proteins. With tunneling spectroscopy, the PSI centers displayed a semiconductor-like response with a band gap of 1.8 eV. Lightly platinized (platinized for 1 hr) centers displayed diode-like conduction that resulted in dramatic contrast changes between images taken with opposite bias voltages. The electronic properties of this system were stable under long-term storage.

Structure of hydrated oligonucleotides studied by in situ scanning tunneling microscopy

We have used the scanning tunneling microscope (STM) to image several synthetic oligonucleotides adsorbed onto a positively charged Au(111) electrode. The molecules were deposited and imaged in aqueous electrolyte under potential control, a procedure that eliminated the problem of the substrate artifacts that had limited some previous STM studies. Experiments were carried out with two types of single-stranded molecules (11 and 20 bases long) and three types of double-stranded molecules (20 and 61 base pairs and 31 bases with 25 bases paired and 6-base "sticky" ends). The molecules lie along symmetry directions on the reconstructed (23 x square root of 3) gold surface, and length measurements indicate that they adopt simple base-stacked structures. The base stacking distances are, within experimental uncertainty, equal to the 0.33 nm measured for polymeric aggregates of stacked purines by direct imaging in identical conditions. The images show features consistent with helical structures. Double helices have a major-groove periodicity that is consistent with a 36 degrees twist. The single helices appear to be more tightly twisted. A simple tunneling model of STM contrast generates good agreement between measured and calculated images.

Masking generates contiguous segments of metal-coated and bare DNA for scanning tunneling microscope imaging

To date, no microscopic methods are available to confirm scanning tunneling microscope (STM) images of DNA. The difficulties encountered in repeating these images may be attributed to inadequate distribution of molecules on the substrate, poor adhesion to the substrate, or the low conductivity of the molecules. However, these factors are difficult to assess in an STM experiment where they may act simultaneously. A method to isolate these factors involves partly masking the deposited molecules before coating them with a conductive film to produce adjacent segments of coated and bare DNA after the mask is removed. The coated DNA segments are conductive and mechanically stable to allow easy identification of DNA by the STM. Furthermore, the path of a molecule can be traced from a coated to an uncoated region to test STM imaging of bare DNA. Masked preparations of DNA deposited on platinum/carbon-coated mica and highly oriented pyrolytic graphite were examined with a tunneling current 1000 times lower than the usual nanoamps. The tip apparently displaces molecules adsorbed to graphite to preclude imaging whereas more stably bound DNA on platinum/carbon-coated mica appears in reversed contrast.