Single Strand DNA Molecules

Single Strand DNA MoleculesNC-AFM Imaging of Bio-molecular SamplesPark Systems Inc 0 2010 Sample：G4 DNA Image Conditions： NC-AFM Scan size (1um)Scan rate (0.5Hz) Z servo gain (3.0) Pixel (256 x256) System Requirement： XE-100 SLD Head (Optional： Liquid probehand， Liquid Cell) The Benefits： The true non-contactimaging mode of XE-AFM series insuresminimal disruption ofsensitive biologicalsamples such as DNAmolecules. Thenegligibleinteractionforce between tip andsample allows accurateheight measurements ofsmall bio-molecularsamples. Deoxyribonucleic Acid (DNA) is a polymer chain that stores hereditary information of species. It ismade from repeating units called nucleotides. In its natural state， the chain is 22 to 26 A ngstroms wide(2.2 to 2.6 nanometres)， and one nucleotide unit is 3.3 A (0.33 nm) long. Although each individualrepeating unit is very small， DNA polymers can be very large molecules containing millions ofnucleotides. While X-ray crystallography and electron microscopy are the main tools used to resolve thestructure of DNA in 3-dimensions， scanning probe techniques have gradually gained importance in thefield of high resolution DNA imaging due to their ease of sample preparation (in-necessity to crystallizethe DNA prior to imaging) as well as the possibility of functional studies (e.g.， study of protein-DNAinteraction processes) under physiological conditions. In preparation for AFM imaging， DNA samplesare usually immobilized onto a stiff， flat substrate surface. The negatively charged backbone of the DNAcan be utilized for immobilization onto charged substrates such as freshly cleaved mica via electrostaticinteractions. After the DNA molecules are adsorbed onto the substrate， the surface can be washed， air-dried， and promptly imaged. Alternatively， the imaging process can be carried out in physiologicalsolutions. Publications Using the XE-AFM on DNA Molecules Journal： Nucleic Acids Research. 33(20) November 2005. 6515. Title： Synthesis of novel poly(dG)-poly(dG)-poly(dC) triplex structure by Klenow exo- fragment of DNA polymerase I Authors： A. Kotlyar， N. Borovok1， T. Molotsky1， D.Klinov， B. Dwir and E. Kapon； System： Park Systems XE-100 Park Systems Inc3040 Olcott StSanta Clara， CA 95054Tel： 408.986.1110Fax： 408.986.1199www.parkAFM.cominfo@parkAFM.com Abstract： The extension of the G-strand of long (700 bp)poly(dG)-poly(dC) by the Klenow exo-fragment of DNApolymerase I yields a complete triplex structure of the H-DNA type. Atomic force microscopy morphology imagingshows that the synthesized structures lack single-strandedfragments and have approximately the same length as theparent 700 bp poly(dG)-poly(dC). CD spectrum of thepolymer has a large negative peak at 278 nm， which ischaracteristic of the poly(dG)-poly(dG)-poly(dC) triplex.The polymer is resistant to DNase and interacts much moreweakly with ethidium bromide as compared with thedouble-stranded DNA. Fig. 2. AFM images of (A) synthesized poly(dG-dG)-poly(dC) molecules ， (B) ~700 bp parentpoly(dG)-poly(dC) and (C) poly(dG-dG)-poly(dC)molecules co-deposited with a linear plasmid pSK+DNA on mica. Statistical length analyses of single，well-separated molecules from several images atseveral areas are shown in the inserts to (A) and(B).