Complementary DNAs

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]. 

Also present in the first test tube is a synthetic analog of ATP in which both the 2 and 3 hydroxyl groups have been replaced by hydrogens This compound is called 2 3 dideoxyadenosme triphosphate (ddATP) Similarly ddTTP is added to the second tube ddGTP to the third and ddCTP to the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 phosphorodithioates DNA derivatives have been shown to bind specifically to complementary DNA or ENA sequences to form stable adducts. Because they are also highly resistant to degradation by cellular exonucleases, these derivatives can be useful both for appHcations in research and as therapeutic dmgs. Phosphorodithioate DNA has been shown to stimulate Rnase H activity in nuclear cell extracts and is a potent inhibitor of HIV type-1 reverse transcriptase (56). 

The methylphosphonates differ from the phosphodiesters and phosphorothiolates in that the methyl derivatives are uncharged and are thus less water soluble. Moreover, compared to the naturally occurring phosphodiesters, the methylphosphonates form slightly less stable duplexes with complementary DNA and RNA sequences. This effect has been ascribed to the iaevitable chiraUty problem that is, if one isomer biads less well, the overall binding is decreased. Methylphosphonates can enter cell membranes by a passive mechanism and are completely resistant to nucleases. 

Fig. 4. Steps in making a cDNA library. Cellular mRNA is used as a template to make a complementary DNA. This cDNA is then ligated to a plasmid,...

Eor example, the technique of Southern blotting was developed (68) for use with agarose gel electrophoresis of DNA fragments. Southern blots are designed to detect specific sequences of DNA. After electrophoresis is complete, the DNA is denatured and the single stranded DNA transferred to the specially prepared nitrocellulose paper. The nitrocellulose is then incubated with radioactive RNA or DNA complementary to those DNA sequences of interest. After the nitrocellulose has been sufftciendy incubated with the radioactive complementary DNA, autoradiography is used to identify the fragments of interest. 

M Schena, D Shalon, RW Davis, PO Brown. Quantitative monitoring of gene expression patterns with a complementary DNA microaiTay. Science 270 467-470, 1995. 

Differential display is a method for identifying differentially expressed genes, using anchored oligo-dT, random oligonucleotide primers and polymerase chain reaction on reverse-transcribed RNA from different cell populations. The amplified complementary DNAs are displayed and comparisons are drawn between the different cell populations. 

Rebmann G. Hertig C. Bull J. Mauch F. Dudler R. (1991) Complementary DNA cloning and sequence analysis of a pathogen-induced putative peroxidase from rice / / Plant Mol. Biol. V. 16. P. 329-331. 

An abasic peptide (Ac-Gys -Lys-(Ser-Ala-Ala-Lys)4-Ser-Gly-Lys-NH2) with unmodified Ser residues was synthesized and used as a control. No induced cooperative binding to. TAjGsAsT) was observed in the UV melting curve with this abasic peptide. This indicated that the cooperative melting between aPNA and its complementary DNA was not merely a reflection of nonspecific interactions be-... 

The schematic model of the film deposited by the technique is shown in Figure 45. A single-stranded DNA layer is sandwiched between two aliphatic amine monolayers. Thus, the technique can be useful for our objectives, for it allows depisition of single-stranded DNA on practically any substrate and does not demand a large quantity of DNA, since only one monolayer will be deposited. Nevertheless, there is a question of whether DNA in such a structure will hybridize. In fact, the film contains a single-stfanded DNA monolayer between two amine monolayers, and it is questionable whether the upper amine monolayer will prevent hybridization with complementary DNA stfands. 

Nambiar S, Mirmohammadsadegh A, Doroudi R, Gustrau A, Marini A, Boeder G, et al. Signaling networks in cutaneous melanoma metastasis identified by complementary DNA microarrays. Arch Dermatol 2005 141 165-73. 

Southern blot A method for transferring DNA from an agarose gel to nitrocellulose filter, on which the DNA can be detected by a suitable probe (eg, complementary DNA or RNA). 

A cloned complementary DNA to a neurotoxin precursor RNA extracted from the venom glands of Laticauda semifasciata was isolated and its nucleotide sequence was identified 11). The cloning of neurotoxin should aid the understanding of structure—function relationship eventually. 

Lee K.-H., Wells R.G. and Reed R. (1987). Isolation of an olfactory complementary DNA similarity to retinol-binding protein suggests a role in olfaction. Science 253, 1053-1066. 

No cross-linking was observed when noncomplementary rather than complementary DNA was added to the mixture, and thus interstrand transfer of QM appears to be effective only from within a hybridized complex. Despite the obvious complications of annealing DNA that is constrained by capture of both QM equivalents of QMP11, such a species is suggested since both QM sites require protection from irreversible reaction over the many hours in which the cross-linking activity is preserved. 

Murphy PM, Tiffany HL. Cloning of complementary DNA encoding a functional human interleukin-8 receptor. Science 1991 253 1280-1283. 

---