Unique DNA

The HMG (high mobility group) box is a DNA-binding domain found in several transcription factors, that can in some cases bend DNA. Some members of this protein family recognize a unique DNA sequence, whereas others bind to a common DNA conformation. 

Development of batch process in 1987, coupled with fluorescent dideoxy-terminator labeling on target DNA, has allowed determination of fluorescence-tagged DNA sequences, separated on high-resolution slab-gels and more recently separated by capillary electrophoresis. Both separation methods are capable of sequencing up to 700 bases for each reaction. The automated DNA sequencer can simultaneously process up to 100 samples at a time within 3 hours and generate data for 100 unique DNA sequences with about 600-700 bases each. 

Tyrosine recombinases of the lambda family also function in eukaryotes. Best known is the FLP (Flip) recombinase, which is encoded by the 2-pm plasmid of Saccharomyces cerevisiae and is thought to function in amplifying the number of plasmid copies.265 The 6.3-kbp plasmid contains a unique DNA sequence that lies between two 599-bp repeats in inverted orientation. Embedded in each repeat is an FLP recombination target (FRT) sequence, which is recognized by the plasmid recombinase. Each FRT segment includes inverted repeats 13 bp in length with an 8-bp spacer between them. As with other integrase systems the... 

Apart from the above applications, PNA is also of interest in its own right. This quite unique DNA mimic has inspired many chemists to search for similar molecules both by making derivatives and analogues of the original PNA structure, but also by searching for novel structural motifs. 

The basic monomers of nucleic acids are nucleotides which are made up of heterocyclic nitrogen-containing compounds, purines and pyrimidines, linked to pentose sugars. There are two types of nucleic acids and these can be distinguished on the basis of the sugar moiety of the molecule, Ribonucleic acids (RNA) contain ribose, while deoxyribonucleic acid (DNA) contains deoxyribose. The bases cytosine (C) adenine (A) and guanine (G) are common in both RNA and DNA. However, RNA molecules contain a unique base, uracil (U), while the unique DNA base is thymidine (T). These differences in the base structure markedly affect the secondary structures of these polymers. The structures of DNA and RNA are outlined in Appendix 5.2. 

Figure 8.17 Schematic diagram for detection of three unique DNA sequences via hybridization of target DNA with magnetic bead-conjugated probe DNA followed by hybridization with three different detection probe DNA-modified semiconductor nanopaiticles, ZnS, CdS, and PbS. Dissolution and electrochemical stripping yielded three well-resolved peaks corresponding to the specific metal, and hence, unique DNA sequences detected.76 (Reprinted with permission from J. Wang et aL, J. Am. Chem. Soc. 2003,125, 3214-3215. Copyright 2003 American Chemical Society.) (See color insert.)...

About 7,000 F2 cultures are required to determine whether the spontaneous rate was at least doubled by the treatment. Obviously, fewer tests cure needed for mutagens that induce very large mutation rates. If a significant increase in recessive-lethal frequency has not been observed in 7,000 tests of the treated group, the treatment is considered to be negative. Finally, it should be stressed that, with 800 different test genes distributed over the X chromosome, unique DNA-mutagen specificities should be detectable. 

Applying short ssDNA strands that selectively interact with a specific part of a molecular device is another method to make the device move. A robust rotary device was developed based on multiple crossover motifs [91]. The motivity of the device was the reversible binding of DNA strands. The central axis consists of a couple of ssDNA sections. The conformation of the two ssDNA strands can readily be switched between a PX conformation and its topoisomer conformation. The ssDNA strand replacement can cause the interconversion between the two conformations, and results in an 180° rotation of the end of one strand. This work showed that a rotary nanomechanical device is capable of being cycled by the addition of strands that direct its structure (Fig. 12a). As an application of the DNA nanodevice, a unique DNA nanomechanical device that enables the positional synthesis of products whose sequences are determined by the state of the device has been... 

Large-scale preparation of unique DNA segments 1 mg DNA (phage, plasmid, virus)... 

Many of the other chapters in this volume deal with evolutionary analyses of specific genes and unique DNA sequences.24-28 There are, however, some evolutionary aspects unique to repeated DNA sequences. The most important of these factors is the amplification dynamics. Sequences become repetitive because there are amplification processes that make extra copies of them. These include retroposition and transposition mechanisms that would explain the majority of interspersed repeated DNA sequences, as well as recombination or replication slippage mechanisms that would probably explain most tandem replications. For any given repeated sequence, various factors may combine to increase or decrease the amplification rate of that sequence at various times in the evolutionary process. Thus, the dynamics of the amplification process could greatly affect the observed evolution of the family. This is particularly important in cross-species comparisons, because the amplification dynamics of a specific repeated DNA family may be altered in one species, relative to another. 

BioWatch is a program using air samplers to test for threat agents. The samplers are located in undisclosed cities and monitor the air 24 hours a day, 7 days a week. LRN BioWatch labs test filters from these samplers. Tests include polymerase chain reaction (PCR). PCR can quickly detect the presence of an agent s unique DNA. 

CDC labs identified the unique DNA sequence of the virus that causes SARS. The LRN developed tests and... 

A method for synthesizing and amplifying a specific DNA sequence based on the use of specific oligonucleotide primers and unique DNA polymerases such as the thermostable DNA polymerase from Thermus aquaticus... 

---