DNA strands

Fig. XVin-3. AFM image of DNA strands on mica. Lower figure image obtained in the contact mode under water. The contrast shown covers height variations in the range of 0-2 nm. Upper figure observed profile along the line A-A of the lower figure. (From S. N. Magnov and M.-H. Whangbo, Surface Analysis with STM and AFM, VCH, New Yoric, 1996.)...

Calculate the magnification factor in Fig. XVIII-3. Assuming the scanning tip to be 2 A wide and the tip force to be 3 nN, calculate the pressure exerted on the DNA strand. 

An equally important challenge for nanocrystal assembly is the fonnation of specific nanocrystal arrangements in solution. By using complementary DNA strands as tethers, Mirkin et al [102, 103] fonned aggregates of gold nanocrystals with specific sizes Alivisatos et al also used DNA to stmcture semiconductor nanocrystal molecules, though in this case the molecules contained only a few nanocrystals placed controlled distances from each other [104, 105 and 106]. The potential applications of biomolecular teclmiques to this area of nanoscience are immense, and the opportunities have been reviewed in several recent publications [107, 108, 109 and 110]. 

A helical structure for DNA strands had been suggested in 1949 by Sven Furberg in his Ph D dissertation at the University of London... 

Each pair contains one purine and one pyrimidine base This makes the A T and G C pairs approximately the same size and ensures a consistent distance between the two DNA strands... 

Figure 28 4 supplements Figure 28 3 by showing portions of two DNA strands arranged side by side with the base pairs m the middle... 

The viruses responsible for AIDS are human immunodeficiency virus 1 and 2 (HIV 1 and HIV 2) Both are retroviruses, meaning that their genetic material is RNA rather than DNA HI Vs require a host cell to reproduce and the hosts m humans are the T4 lymphocytes which are the cells primarily responsible for inducing the immune system to respond when provoked The HIV penetrates the cell wall of a T4 lymphocyte and deposits both its RNA and an enzyme called reverse transcriptase inside There the reverse transcriptase catalyzes the formation of a DNA strand that is complementary to the viral RNA The transcribed DNA then serves as the template from which the host lymphocyte produces copies of the virus which then leave the host to infect other T4 cells In the course of HIV reproduction the ability of the T4 lymphocyte to reproduce Itself IS compromised As the number of T4 cells decrease so does the body s ability to combat infections... 

Also present in the first test tube is a synthetic analog of ATP in which both the 2 and 3 hydroxyl groups have been replaced by hydrogens This compound is called 2 3 dideoxyadenosme triphosphate (ddATP) Similarly ddTTP is added to the second tube ddGTP to the third and ddCTP to the fourth Each tube also contains a primer The primer is a short section of the complementary DNA strand which has been labeled with a radioactive isotope of phosphorus ( P) When the electrophoresis gel is examined at the end of the experiment the positions of the DNAs formed by chain extension of the primer are located by a technique called autoradiography which detects the particles emitted by the P isotope... 

The solution is then cooled to 60°C allowing new hydrogen bonds to form [Fig ure 28 14(c)] However the reaction mixture contains much larger concentrations of two primer molecules than DNA and the new hydrogen bonds are between the separated DNA strands and the primers rather than between the two strands... 

Dou ble hel ix (Section 28 8) The form in which DNA normally occurs in living systems Two complementary strands of DNA are associated with each other by hydrogen bonds be tween their base pairs and each DNA strand adopts a helical shape... 

As shown in Figure 45.1, the bases appear in complementary pairs, A with T and G with C in this particular example, the sequence for one strand of DNA is A-T-C-G-T- while the other strand is -T-A-G-C-A-. The sequences of the bases attached to the sugar-phosphate backbone direct the production of proteins from amino acids. Along each strand, groups of three bases, called codons, correspond to individual amino acids. For example, in Figure 45.1, the triplet CGT, acting as a codon, would correspond to the amino acid serine. One codon, TAG, indicates where synthesis should begin in the DNA strand, and other codons, such as ATT, indicate where synthesis should stop. 

The linking difference can be considered in terms of changes in the twist, Tiv, and writh, Wr, of the molecule. Twist describes how the DNA strands are coHed around each other writh describes the coiling of the hehcal axis. The change in linking number is related to changes in twist and writh ... 

In another method for sequencing, the DNA is labeled at internal base positions by enzymes which repHcate DNA strands in the presence of specific chain terrninators, thus producing an array of labeled fragments which reflect the sequence of the DNA. The rest of the procedure is the same as described for the chemical cleavage method (22). 

Administration of dipyridamole-AMP to mice 5—25 min after 1 Gy (100 rad) of TBI y-kradiation is also protective, as indicated by plasma thymidine levels and the amount of saline soluble polynucleotides in the thymus (112). Adding dipyridamole-AMP to in vitro kradiated suspensions of thymocytes enhances the rejoining of DNA strand breaks (112). These post-kradiation effects ate presumably mediated by the activation of extraceUulat adenosine receptors. 

The key to hexavalent chromium s mutagenicity and possible carcinogenicity is the abiHty of this oxidation state to penetrate the cell membrane. The Cr(VI) Species promotes DNA strand breaks and initiates DNA—DNA and DNA-protein cross-links both in cell cultures and in vivo (105,112,128—130). The mechanism of this genotoxic interaction may be the intercellular reduction of Cr(VI) in close proximity to the nuclear membrane. When in vitro reductions of hexavalent chromium are performed by glutathione, the formation of Cr(V) and glutathione thiyl radicals are observed, and these are beHeved to be responsible for the formation of the DNA cross-links (112). 

The only sequence-specific hydrogen bonds between TBP side chains and the bases in the minor groove occur at the very center of the TATA box (Figure 9.7). The amide groups of two asparagine side chains donate four hydrogen bonds, two each to adjacent bases on the same DNA strand (Asn 69... 

Adhering to the convention of writing nucleotide sequences in the 5 o direction, what is the nucleotide sequence of the DNA strand that is complementary to d-ATCGCAACTGTCACTA ... 

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