A convenient method of aligning large DNA molecules on bare mica surfaces for atomic force microscopy

Nanotemplate-directed DNA segmental thermal motion

Nanotemplate directed DNA segmental thermal motion on molecular nanotemplates on graphite was directly observed and characterized using AFM in a liquid.

Microfluidic transfer of liquid interface for parallel stretching and stamping of terminal-unmodified single DNA molecules in zigzag-shaped microgrooves

The molecular stretching of DNA is an indispensable tool for the optical exploration of base sequences and epigenomic changes of DNA at a single molecule level. In stretching terminal-unmodified DNA molecules parallel to each other on solid substrate, the receding meniscus assembly and capillary force through the dewetting process are quite useful. These can be achieved by pulling the substrate out of the DNA solution or sliding a droplet of DNA solution between a pair of substrates. However, currently used methods do not allow control over liquid interface motion and single-molecule DNA positioning. Here, we show a microfluidic device for stretching DNA molecules by syringing through microgrooves. The device can trap single DNA molecules at vertices of the microgrooves, which were designed as parallel zigzag lines. Different zigzag pattern depths, sizes, and shapes were studied to evaluate the adsorption possibility of DNA on the surface. The microfluidic transfer of the liquid interface stretched over 1500 DNA molecules simultaneously. The stretched DNA molecules could be stamped to a silanized surface. The device will therefore serve as a template preparation for high-resolution DNA imaging studies.

Statistical analysis of molecular nanotemplate driven DNA adsorption on graphite

In this work, we have studied the conformation of DNA molecules aligned on the nanotemplates of octadecylamine, stearyl alcohol, and stearic acid on highly oriented pyrolytic graphite (HOPG). For this purpose, fluctuations of contours of adsorbed biopolymers obtained from atomic force microscopy (AFM) images were analyzed using the wormlike chain model. Moreover, the conformations of adsorbed biopolymer molecules were characterized by the analysis of the scaling exponent ν, which relates the mean squared end-to-end distance and contour length of the polymer. During adsorption on octadecylamine and stearyl alcohol nanotemplates, DNA forms straight segments, which order along crystallographic axes of graphite. In this case, the conformation of DNA molecules can be described using two different length scales. On a large length scale (at contour lengths l > 200-400 nm), aligned DNA molecules have either 2D compact globule or partially relaxed 2D conformation, whereas on a short length scale (at l ≤ 200-400 nm) their conformation is close to that of rigid rods. The latter type of conformation can be also assigned to DNA adsorbed on a stearic acid nanotemplate. The different conformation of DNA molecules observed on the studied monolayers is connected with the different DNA-nanotemplate interactions associated with the nature of the functional group of the alkane derivative in the nanotemplate (amine, alcohol, or acid). The persistence length of λ-DNA adsorbed on octadecylamine nanotemplates is 31 ± 2 nm indicating the loss of DNA rigidity in comparison with its native state. Similar values of the persistence length (34 ± 2 nm) obtained for 24-times shorter DNA molecules adsorbed on an octadecylamine nanotemplate demonstrate that this rigidity change does not depend on biopolymer length. Possible reasons for the reduction of DNA persistence length are discussed in view of the internal DNA structure and DNA-surface interaction.

Robust deposition of lambda DNA on mica for imaging by AFM in air

Long DNA molecules remain difficult to image by atomic force microscopy (AFM) because of their tendency to entanglement and spontaneous formation of networks. We present a comparison of two different DNA deposition methods operating at room temperature and humidity conditions, aimed at reproducible imaging of isolated and relaxed λ DNA conformations by AFM in air. We first demonstrate that a standard deposition procedure, consisting in adsorption of DNA in the presence of divalent cations followed by washing and air-drying steps, yields a coexistence of different types of λ DNA networks with a only a few isolated DNA chains. In contrast, deposition using a spin-coating-based technique results in reproducible coverage of a significant fraction of the substrate area by isolated and relaxed λ DNA molecules, with the added benefit of a reduction in the effect of a residual layer that normally embeds DNA strands and leads to an apparent DNA height closer to the expected value. Furthermore, we show that deposition by spin-coating is also well-suited to visualize DNA-protein complexes. These results indicate that spin-coating is a simple, powerful alternative for reproducible sample preparation for AFM imaging.

Simple method of DNA stretching on glass substrate for fluorescence imaging and spectroscopy

We demonstrate a simple method of stretching DNA to its full length, suitable for optical imaging and atomic force microscopy (AFM). Two competing forces on the DNA molecules, which are the electrostatic attraction between positively charged dye molecules (YOYO-1) intercalated into DNA and the negatively charged surface of glass substrate, and the centrifugal force of the rotating substrate, are mainly responsible for the effective stretching and the dispersion of single strands of DNA. The density of stretched DNA molecules could be controlled by the concentration of the dye-stained DNA solution. Stretching of single DNA molecules was confirmed by AFM imaging and the photoluminescence spectra of single DNA molecule stained with YOYO-1 were obtained, suggesting that our method is useful for spectroscopic analysis of DNA at the single molecule level.

Nanostructure-induced DNA condensation

The control of the DNA condensation process is essential for compaction of DNA in chromatin, as well as for biological applications such as nonviral gene therapy. This review endeavours to reflect the progress of investigations on DNA condensation effects of nanostructure-based condensing agents (such as nanoparticles, nanotubes, cationic polymer and peptide agents) observed by using atomic force microscopy (AFM) and other techniques. The environmental effects on structural characteristics of nanostructure-induced DNA condensates are also discussed.

Electrically conductive magnetic nanowires using an electrochemical DNA-templating route

The fabrication of electrically conducting magnetic nanowires has been achieved using electrochemical DNA-templating of iron. In this approach, binding of the Fe(2+) cations to the DNA "template" molecules has been utilised to promote growth along the molecular axis. Formation of Fe within the product material was verified by XRD and XPS studies, which confirmed an iron/oxide "core-shell" structure. The effectiveness of the DNA duplex to direct the metal growth in one dimension was highlighted by AFM which reveals the product material to comprise high aspect ratio nanostructured architectures. These "nanowires" were observed to have morphologies consisting of densely packed linear arrangements of metal particles along the template, with wire diameters up to 26 nm. The structures were confirmed to be electrically conductive, as expected for such Fe-based materials, and to display superparamagnetic behaviour, consistent with the small size and particulate nature of the nanowires.

Transplatin enhances effect of cisplatin on both single DNA molecules and live tumor cells

Cisplatin is the main platinum antitumor drug applied in clinical settings. However, its trans isomer, transplatin, is known to have an ineffective antitumor activity. Despite intensive studies in this field, the structural and biophysical properties of DNA molecules reacting with these two platinum complexes have not been fully elucidated. In the present study, we observed that transplatin made efficient cross-linking of DNA in the vicinity of cisplatin adducts. High-resolution atomic force microscopy studies revealed that the transplatin-induced cross-linkings of nucleotides flanking cisplatin adducts were characterized by kinked-loop structures with rod-like shapes of nanometer scales (∼10-60nm). The results were further confirmed by denaturing gel electrophoresis and single-molecule experiment using magnetic tweezers. In vivo studies revealed that transplatin and cisplatin co-treatment could induce a considerable amount of kinked loops with smaller sizes (∼15nm) in cellular DNA. Furthermore, compared with cisplatin treatment alone, the co-treatment resulted in enhanced cytotoxicity, increased amount of interstrand cross-links, and cell lesions more reluctant to cellular repair system. The results of the present study provide a new clue for understanding the stepwise reactions of DNA with platinum drugs and might serve as a basis for the development of a new antitumor strategy.

Magnetic and conductive magnetite nanowires by DNA-templating

The synthesis of nanowires made of magnetite (Fe(3)O(4)) phase iron oxide was achieved using DNA as a template to direct formation of the metal oxide and confine its growth in two dimensions. This simple solution-based approach involves initial association of Fe(2+) and Fe(3+) to the DNA "template" molecules, and subsequent co-precipitation of the Fe(3)O(4) material, upon increasing the solution pH, to give the final metal oxide nanowires. Analysis of the DNA-templated material, using a combination of FTIR, XRD, XPS, and Raman spectroscopy, confirmed the iron oxide formed to be the Fe(3)O(4) crystal phase. Investigation of the structural character of the nanowires, carried out by AFM, revealed the metal oxide to form regular coatings of nanometre-scale thickness around the DNA templates. Statistical analysis showed the size distribution of the nanowires to follow a trimodal model, with the modal diameter values identified as 5-6 nm, 14-15 nm, and 23-24 nm. Additional scanning probe microscopy techniques (SCM, MFM) were also used to verify that the nanowire structures are electrically conducting and exhibit magnetic behaviour. Such properties, coupled with the small dimensions of these materials, make them potentially good candidates for application in a host of future nanoscale device technologies.

Assembly of single-stranded DNA onto HOPG surface at different temperature: atomic force microscopy study

Assembly of long single-stranded DNA (ssDNA) and short oligodeoxynucleotides onto bare highly oriented pyrolytic graphite (HOPG) at different temperature has been studied. It was indicated that both long ssDNA and oligodeoxynucleotides can sequentially form network, straight chains, and layer structures when the adsorption temperature was changed from room temperature, 37-55°C. High-resolution atomic force microscopy (AFM) imaging of the layer structures revealed that they are composed of parallel ssDNA chains with relatively higher height and tend to form patterns with three-fold symmetry. These new findings are significantly important for understanding assembly characterization of ssDNA. In addition, this assembly method for ssDNA is expected to be used for preparation of DNA structures in biosensing and DNA-based nanodevices.

Single-molecule studies of DNA transcription using atomic force microscopy

Atomic force microscopy (AFM) can detect single biomacromolecules with a high signal-to-noise ratio on atomically flat biocompatible support surfaces, such as mica. Contrast arises from the innate forces and therefore AFM does not require imaging contrast agents, leading to sample preparation that is relatively straightforward. The ability of AFM to operate in hydrated environments, including humid air and aqueous buffers, allows structure and function of biological and biomolecular systems to be retained. These traits of the AFM are ensuring that it is being increasingly used to study deoxyribonucleic acid (DNA) structure and DNA-protein interactions down to the secondary structure level. This report focuses in particular on reviewing the applications of AFM to the study of DNA transcription in reductionist single-molecule bottom-up approaches. The technique has allowed new insights into the interactions between ribonucleic acid (RNA) polymerase to be gained and enabled quantification of some aspects of the transcription process, such as promoter location, DNA wrapping and elongation. More recently, the trend is towards studying the interactions of more than one enzyme operating on a single DNA template. These methods begin to reveal the mechanics of gene expression at the single-molecule level and will enable us to gain greater understanding of how the genome is transcribed and translated into the proteome.

A silanized mica substrate suitable for high-resolution fiber FISH analysis by scanning near-field optical/atomic force microscopy

We applied a novel silanized mica substrate with an extremely flat surface constructed according to Sasou et al. (Langmuir 19, 9845-9849 (2003)) to high-resolution detection of a specific gene on a DNA fiber by scanning near-field optical/atomic force microscopy (SNOM/AFM). The interaction between the substrate and fluorescence-dye conjugated peptide nucleic acid (PNA) probes, which causes fluorescence noise signal, was minimal. By using the substrate, we successfully obtained a fluorescence in situ hybridization signal from the ea47 gene on a λphage DNA labeled with an Alexa 532-conjugated 15-base PNA probe. As the results, no fluorescence noises were observed, indicating that the surface adsorbed almost none of the PNA probe. The combination of the substrate and SNOM/AFM is an effective tool for visualizing DNA sequences at nanometer-scale resolution.

Evaluation of the radial deformability of poly(dG)-poly(dC) DNA and G4-DNA using vibrating scanning polarization force microscopy

Poly(dG)-poly(dC) DNA and G4-DNA are two types of synthetic molecules that are regarded as promising candidates for molecular nanodevices. In this work, vibrating scanning polarization force microscopy (VSPFM) was employed to study the radial deformability of these two molecules coadsorbed on a Ni(2+)-modified mica surface. The values of the radial compressive elastic modulus of these two types of molecules were found to be similar (approximately 5-10 MPa) when the external loading force was between approximately 0.04 and approximately 0.12 nN. However, G4-DNA molecules possessed higher stiffness than poly(dG)-poly(dC) DNA (approximately 20-40 vs approximately 10-20 MPa) when the loading force was larger than approximately 0.12 nN. The results will aid us in understanding these molecule's mechanical performances.

Micrometer-sized DNA-single-fluorophore-DNA supramolecule: synthesis and single-molecule characterization

The synthesis of single-fluorophore-bis(micrometer-sized DNA) triblock supramolecules and the optical and structural characterization of the construct at the single-molecule level is reported. A fluorophore-bis(oligodeoxynucleotide) triblock is synthesized via the amide-coupling reaction. Subsequent protocols of DNA hybridization/ligation are developed to form the supramolecular triblock structure with lambda-DNA fragments on the micrometer length scale. The successful synthesis of the micrometer-sized DNA-single-fluorophore-DNA supramolecule is confirmed by agarose gel electrophoresis with fluorescence imaging under UV excitation. Single triblock structures are directly imaged by combined scanning force microscopy and single-molecule fluorescence microscopy, and provide unambiguous confirmation of the existence of the single fluorophore inserted in the middle of the long DNA. This type of triblock structure is a step closer to providing a scaffold for single-molecule electronic devices after metallization of the DNAs.

DNA-templated synthesis of ZnO thin layers and nanowires

In this paper, we report a novel synthetic approach towards electrically conductive ZnO nanowires close to ambient conditions using lambda-DNA as a template. Initially, the suitability of DNA to assemble ZnO nanocrystals into thin coatings was investigated. The ZnO nanowires formed on stretched and aligned lambda-DNA molecules were prepared via chemical bath deposition (CBD) of zinc acetate in methanol solution in the presence of polyvinylpyrrolidone (PVP). After 10 deposition cycles, the nanowires exceed 10 microm in length and the height can be varied from 12 to around 40 nm. The nanocrystalline structure of the ZnO wires was confirmed by high-resolution transmission electron microscopy (HRTEM). The electrical conductivity was found to be of the order of several Omega cm at room temperature in two terminal measurements.

A comparative analysis of Dmc1 and Rad51 nucleoprotein filaments

The eukaryotic RecA homologs Rad51 and Dmc1 are essential for strand exchange between homologous chromosomes during meiosis. All members of the RecA family of recombinases polymerize on DNA to form helical nucleoprotein filaments, which is the active form of the protein. Here we compare the filament structures of the Rad51 and Dmc1 proteins from both human and budding yeast. Previous studies of Dmc1 filaments suggested that they might be structurally distinct from filaments of other members of the RecA family, including Rad51. The data presented here indicate that Rad51 and Dmc1 filaments are essentially identical with respect to several structural parameters, including persistence length, helical pitch, filament diameter, DNA base pairs per helical turn and helical handedness. These data, together with previous studies demonstrating similar in vitro recombinase activity for Dmc1 and Rad51, support the view that differences in the meiotic function of Rad51 and Dmc1 are more likely to result from the influence of distinct sets of accessory proteins than from intrinsic differences in filament structure.

Synthesis, Manipulation and Conductivity of Supramolecular Polymer Nanowires

The synthesis of supramolecular conducting nanowires can be achieved by using DNA and pyrrole. Oxidation of pyrrole in DNA-containing solutions yields a material that contains both the cationic polypyrrole (PPy) and the anionic DNA polymers. Intimate interaction of the two polymer chains in the self-assembled nanowires is indicated by FTIR spectroscopy. AFM imaging shows individual nanowires to be continuous, approximately 5 nm high and conformationally flexible. This feature allows them to be aligned by molecular combing in a similar manner to bare DNA and provides a convenient method for fabricating a simple electrical device by stretching DNA/PPy strands across an electrode gap. Current-voltage measurements confirm that the nanowires are conducting, with values typical for a polypyrrole-based material. In contrast to polymerisation of pyrrole on a DNA template in bulk solution, attempts to form similar wires by polymerisation at surface-immobilised DNA do not give a continuous coverage; instead, a beads-on-a-string appearance is observed suggesting that immobilisation inhibits the assembly process.

Ionic effect on combing of single DNA molecules and observation of their force-induced melting by fluorescence microscopy

Molecular combing is a powerful and simple method for aligning DNA molecules onto a surface. Using this technique combined with fluorescence microscopy, we observed that the length of lambda-DNA molecules was extended to about 1.6 times their contour length (unextended length, 16.2 microm) by the combing method on hydrophobic polymethylmetacrylate coated surfaces. The effects of sodium and magnesium ions and pH of the DNA solution were investigated. Interestingly, we observed force-induced melting of single DNA molecules.

A simple DNA stretching method for fluorescence imaging of single DNA molecules

Stretching or aligning DNA molecules onto a surface by means of molecular combing techniques is one of the critical steps in single DNA molecule analysis. However, many of the current studies have focused on λ-DNA, or other large DNA molecules. There are very few studies on stretching methodologies for DNA molecules generated via PCR (typically smaller than 20 kb). Here we describe a simple method of stretching DNA molecules up to 18 kb in size on a modified glass surface. The very low background fluorescence allows efficient detection of single fluorescent dye labels incorporated into the stretched DNA molecules.

Imaging DNA molecules on mica surface by atomic force microscopy in air and in liquid

DNA molecules immobilized on mica surface by various methods have been observed by atomic force microscopy both in air and in liquid. Divalent cations and 3-aminopropyltriethoxysilane (APTES) modified mica surface have been used to immobilize the DNA molecules. Optimal DNA and divalent cations concentration for AFM imaging are presented. Among the different methods of modifying mica surface with APTES, the water solution modifying method appears to get the best results. When using high DNA concentration for AFM imaging, DNA networks can be formed. A simple method to extend long DNA molecules is demonstrated. The optimal imaging conditions and AFM operating techniques are discussed. Different DNA immobilizing methods have been compared and evaluated.

Construction and deconstruction of PLL/DNA multilayered films for DNA delivery: Effect of ionic strength

Through the layer-by-layer (LbL) self-assembly technique, DNA was incorporated into the multilayered films with poly-l-lysine (PLL). The effect of ionic strength on the construction and deconstruction of the PLL/DNA films was investigated. It was found that the salt concentration of the deposition solution had a significant effect on the construction of the films, which might attribute to the effect of salt ions on the conformation of polyelectrolytes and interaction between PLL and DNA molecules. A salt-induced deconstruction of the PLL/DNA films was observed. The extent of the deconstruction increased with the salt concentration in the incubation solution. The mechanism of the deconstruction was discussed. Taking the advantages of the LbL technique, the erasable PLL/DNA films could deposit onto a variety of surfaces, such as vascular stent, intervention catheter and tissue engineering scaffold, to serve as a novel DNA delivery system.

Single molecular imaging and spectroscopy of conjugated polyelectrolytes decorated on stretched aligned DNA

DNA is the prototype template for building nanoelectronic devices by self-assembly. The electronic functions are made possible by coordinating electronic polymer chains to DNA. This paper demonstrates two methods for fabrication of aligned and ordered DNA nanowires complexed with conjugated polyelectrolytes (CPEs). The complex can be formed either in solution prior to stretching or after stretching of the bare DNA on a surface. Molecular combing was used to stretch the complexes on surface energy patterned surfaces, and PMMA for the bare DNA. Single molecular spectroscopy, in fluorescence, and microscopy, in atomic force microscopy, give evidence for coordination of the short CPE chains to the aligned DNA.

Combing DNA on CTAB-coated surfaces

A fluorescence microscope (FM) coupled with an intensified charge-coupled device (ICCD) camera was used to investigate the combing of DNA on cetyltrimethyl ammonium bromide (CTAB)-coated glass surfaces. DNA molecules can be combed uniform and straight on CTAB-coated surfaces. Different combing characteristics at different pH values were found. At lower pH (ca. 5.5), DNA molecules were stretched 30% longer than the unextended and DNA extremities bound with CTAB-coated surfaces via hydrophobic interaction. At high pH values (e.g., 6.4 and 6.5), DNA molecules were extended about 10% longer and DNA extremities bound with CTAB-coated surfaces via electrostatic attraction. At pH 6.0, DNA molecules could be extended 30% longer on 0.2-mM CTAB-coated surfaces. CTAB cationic surfactant has both a hydrophobic motif and a positively charged group. So, CTAB-coated surfaces can bind DNA extremities via hydrophobic effect or electrostatic attraction at different pH values. It was also found that combing of DNA on CTAB-coated surfaces is reversible. The number of DNA base pairs binding to CTAB-coated surfaces was calculated.

Extended, relaxed, and condensed conformations of hyaluronan observed by atomic force microscopy

The conformation of the polysaccharide hyaluronan (HA) has been investigated by tapping mode atomic force microscopy in air. HA deposited on a prehydrated mica surface favored an extended conformation, attributed to molecular combing and inhibition of subsequent chain recoil by adhesion to the structured water layer covering the surface. HA deposited on freshly cleaved mica served as a defect in a partially structured water layer, and favored relaxed, weakly helical, coiled conformations. Intramolecularly condensed forms of HA were also observed, ranging from pearl necklace forms to thick rods. The condensation is attributed to weak adhesion to the mica surface, counterion-mediated attractive electrostatic interactions between polyelectrolytes, and hydration effects. Intermolecular association of both extended and condensed forms of HA was observed to result in the formation of networks and twisted fibers, in which the chain direction is not necessarily parallel to the fiber direction. Whereas the relaxed coil and partially condensed conformations of HA are relevant to the native structure of liquid connective tissues, fully condensed rods may be more relevant for HA tethered to a cell surface or intracellular HA, and fibrous forms may be relevant for HA subjected to shear flow in tight intercellular spaces or in protein-HA complexes.

Aminoglycoside antibiotics aggregate to form starch-like fibers on negatively charged surfaces and on phage lambda-DNA

The water-soluble (> 200 mg/mL) antibiotics tobramycin, kanamycin, and neomycin spontaneously produce rigid fibers on negatively charged surfaces (mica, graphite, DNA). Atomic force microscopy showed single strands of tobramycin on mica at pH 7 with a length of several hundred nanometers and a diameter of 0.5 nm and double helices with a diameter of 1.0 nm and a helical pitch of 7 nm. At pH 13 (NaOH) up to 15 microm long, rigid fibers with a uniform height of 2.4 nm and an apparent helical pitch of 30 nm were formed along the sodium silicate channels on the surface of mica. Kanamycin and neomycin behaved similarly. Fibers of similar length and width, but without secondary structure, were obtained from aqueous solutions at pH 7 on amorphous, hydrophilized carbon and characterized by transmission electron microscopy. Overstretched phage lambda-DNA strands with a height of 1.0 nm on mica did not interact with tobramycin coils at pH 7. After treatment with EDTA, however, the height of the magnesium-free lambda-DNA strands grew from 1.0 to 3.8 nm after treatment with tobramycin, which suggests a wrapping by the supramolecular fibers. Such fibers may interact with F-actin fibers in biological cells, which would explain the known aggressiveness of aminoglycosides toward bacterial cell membranes and their ototoxicity.

Method for patterning stretched DNA molecules on mica surfaces by soft lithography

Lambda DNA was stretched and patterned on mica surface using soft lithography. A highly diluted solution of amino propyl trimethoxy silane in hexane was deposited on a line patterned polydimethylsiloxane (PDMS) stamp. The functionalized stamp was then used to pick up DNA by molecular combing while the line patterns are parallel to the liquid surface. The stamp was then microcontact printed on freshly cleaved mica. We successfully obtained stretched DNA pattern on mica surface. DNA was found to be stretched in patterns perpendicular to those carved on the stamp. The stretched DNA population was large enough to be used for molecular biology mapping studies. Furthermore, the possibility of locating stretched DNA molecules in the desired position by stamping makes this method a good candidate for assembling non-semiconductor molecular devices.

Atomic force microscope investigation of large-circle DNA molecules

A circular bacterial artificial chromosome of 148.9kbp on human chromosome 3 has been extended and fixed on bare mica substrates using a developed fluid capillary flow method in evaporating liquid drops. Extended circular DNA molecules were imaged with an atomic force microscope (AFM) under ambient conditions. The measured total lengths of the whole DNA molecules were in agreement with sequencing analysis data with an error range of +/-3.6%. This work is important groundwork for probing single nucleotide polymorphisms in the human genome, mapping genomic DNA, manipulating biomolecular nanotechnology, and studying the interaction of DNA-protein complexes investigated by AFM.

Accuracy of AFM measurements of the contour length of DNA fragments adsorbed on mica in air and in aqueous buffer

The measurement by atomic force microscope of the contour length of DNA fragments adsorbed on mica has been made as accurate as possible by revisiting the different steps of image acquisition and processing. In air, the DNA helical rise was estimated at 2.97 +/- 0.15 A per base pair (bp) (mean +/- standard deviation) by imaging a 648-bp DNA fragment and 2.95 +/- 0.14 A per bp for a 115-bp fragment. This confirms earlier observations suggesting that drying DNA fragments on mica in the presence of nickel induces limited conformational changes. At this point the exact nature of these conformational changes remains unknown. Simple hypotheses are the transconformation of stretches of the DNA molecules to the A-form of the double helix or alteration of the helix structure at the points of contact between DNA and mica. By contrast, in aqueous buffer, the measured helical rise was 3.14 +/- 0.15 A per bp for the 648-bp fragment and 3.17 +/- 0.13 A per bp for the 1115-bp fragment. Thus, measured helical rises do not depend on the fragment length and are significantly shorter than the 3.38 A per bp measured by crystallography, but close to the 3.18 A per bp found in NMR studies. These findings are discussed with respect to discrepancies in earlier results published in the literature.

Method for orienting DNA molecules on mica surfaces in one direction for atomic force microscopy imaging

An efficient method was developed to stretch DNA molecules on an atomically flat surface for AFM imaging. This method involves anchoring DNA molecules from their 5' ends to amino silanized mica surfaces. N-Succinimidyl6-[3'-(2-pyridyldithio) propionamido]hexanoate (LC-SPDP), a heterobifunctional cross-linker with a flexible spacer arm was used for this purpose. Immobilization was carried out by introducing a thiol group to the 5' end of DNA by PCR. Thiolated molecules were then reacted with the cross linker to conjugate with its 2-pyridyl disulphide group via sulfhydryl exchange. The resulting complex was deposited on amino silanized mica where NHS-ester moiety of the cross linker reacted with the primary amino group on the surface. Samples were washed by a current of water and dried by an air jet in one direction parallel to the surface. DNA molecules were fully stretched in one direction on imaging them by AFM.

Behavior of DNA fibers stretched by precise meniscus motion control

A modified DNA combing method, which can precisely locate straightened DNA fibers on a substrate, has been developed. Precise motion control of a DNA solution droplet on hydrophobic surfaces has allowed detailed analyses of DNA straightening behavior. Our method provides a technique for consistently straightening lambda phage DNA on a trace of droplet motion, though the straightened DNAs had several variations in their alignments. The dependence of the straightened DNA frequency upon motion rate, fluidity in the droplet and environmental humidity was investigated. Visualization of the solution flow in the moving droplet indicated that flows circulating parallel to the contour of the droplet markedly bias the direction of straightening in relation to the site in the droplet. As a result, the alignment variations caused by the site specificity of the bias direction revealed that environmental humidity significantly alters the straightening behavior.