Bacteriophage base sequences

Sanger determines the complete base sequence of DNA in bacteriophage < )X174. 

Bacteriophage repressor proteins provide excellent examples of sequence-specific interactions between the side chains of a protein and bases lining the floor of the major groove of B-DNA. As we shall see, to fit the protein s recognition module into this groove it has to be made even wider in other words, the B-DNA has to be distorted. 

Figure 8.15 Sequence-specific protein-DNA interactions provide a general recognition signal for operator regions in 434 bacteriophage, (a) In this complex between 434 repressor fragment and a synthetic DNA there are two glutamine residues (28 and 29) at the beginning of the recognition helix in the helix-turn-helix motif that provide such interactions with the first three base pairs of the operator region.

Figure 16.19 Schematic drawing illustrating the structure and sequence of the RNA fragment that is recognized and bound by the coat protein of bacteriophage MS2. The RNA fragment forms a base-paired stem with a bulge at base -10 and a loop of four bases. Bases that form sequence-specific Interactions with the coat protein are red. (Adapted from a diagram provided by L. Llljas.)...

All earlier studies [155-158] reported the complexation of berberine with calf thymus DNA and suggested by a mechanism of intercalation. Maiti and coworkers [159-162] demonstrated first the base- and sequence-specificity of berberine from studies with several naturally occurring DNAs (Clostridium perfringenes, cholera bacteriophage 02, calf thymus, Escherichia coli, Micrococcus lysodeikticus) and synthetic DNAs ((poly(dG-dC) poly(dG-dC), poly(dG)-poly(dC), poly(dA-dT) poly(dA-dT), poly(dA)-poly(dT)) using various physicochemical techniques. Several aspects of the interaction were reported ... 

An alternative to repeated cloning of PCR products is a recombination-based approach developed by Liu et al. (1998) to permit the cloning of a PCR product into a plasmid and the rapid conversion of the plasmid to a number of different expression systems without the necessity of cloning the PCR product multiple, independent times. The method, termed the univector plasmid-fusion system (UPS), involves the insertion of the PCR product into a particular type of plasmid, called the univector, which can then be placed under the control of a variety of promoters or fused in-frame to various tag sequences. The system is based upon plasmid fusion using the Cre-lox site-specific recombination system of bacteriophage PI (Sternberg et al., 1981). The Cre enzyme is a site-specific recombinase that catalyzes recombination between two 34 base pair (bp) loxP sequences and is involved in the resolution of dimers formed during replication of the... 

In E. coli cells, DNA replication starts at a specific site called oriC. The oriC locus contains only 245 base pairs. Similar sequences are responsible for initiating the synthesis of plasmid and bacteriophage DNA. The oriC nucleotide sequence binds several units of the tetrameric form of the dnaA protein. This protein is named for the gene that encodes it. The dnaB and dnaC proteins then bind to the complex. As a result of binding these proteins, a portion of the helical DNA is unwound. This forces the rest of the DNA into a left-handed double helix that wraps around the proteins to give a structure... 

Figure 5-53 (A) JH NMR spectrum of a 17 base-pair DNA segment from the operator sequence OR3 from bacteriophage X in D20 at 37°C. (B) Combined COSY above the diagonal and NOESY (below the diagonal) spectra. C5H and C6H J coupling is established from cross-peaks in box d for cytosines and in box a for thymines. Two unresolved cross-peaks give rise to the more intense spots marked by arrows. Box b contains cross-peaks from scalar coupling of the two H2 protons to the HT protons of the deoxyribose rings. Most of the aromatic proton resonances could be assigned using the NOE cross-peaks in box f. For further details see Wemmer et al.676 See also Bax and Lerner.672 Courtesy of B. Reid.

Good evidence for the occurrence of the first type of mutation exists at least in bacteriophage of the T series, which infect Escherichia coli. The deletion or addition of a single base pair into a DNA chain of a gene should be expected to cause considerable difficulties in the translation of the code in the derived niRNA. into an amino acid sequence For example, if the mRNA of ihe nonmulant strain has the sequence ... 

The polymerase chain reaction is the prevalent method for DNA amplification. Much effort has been made to integrate PCR chambers on microchips to carry out amplifications of DNA molecules prior to their analysis. For instance, PCR was first achieved on a Si-based reaction chamber (25 or 50 pL) integrated with a polysilicon thin-film (2500-A-thick) heater for the amplification of the GAG gene sequence (142 bp) of HIV (cloned in bacteriophage M13) [997]. 

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