Base pairing DNA sequencing

Sequence tagged site (STS) Short (200-500 base pairs) DNA sequence that has been identified and located as a single occurrence in the human genome. Detectable by polymerase chain reaction, STSs are useful for localizing and mapping of sequence data reported from different laboratories (see also expressed sequence tags). 

The fur gene and its product were first identified, and have been best characterized, in E. coli, but homologs have also been found in a wide variety of other organisms [2, 8]. The relationships between metal binding, protein conformation and DNA binding remain very poorly understood. Fur binds ferrous iron, and the Fur-Fe + complex interacts with a characteristic, approximately 20-base pair, DNA sequence (the iron box ) in the promoter regions of Fur-repressed genes. Thus Fur, which is rich in histidine and cysteine residues, is an iron-responsive repressor of transcription. Other divalent metal cations, especially Mn + and Co +, mimic the effect of iron on Fur in both in vivo and in vitro experiments [8, 22, 23]. 

Certain deoxyribonucleases cleave any sequence of single-strand DNA to yield nucleoside monophosphates these enzymes do not hydrolyze base-paired DNA sequences. What products would you expect when you incubate a solution containing a singlestrand specific deoxyribonuclease and the follotving oligodeoxyribonucleotide ... 

Figure 3 A Swiss 3D-Image of the crystal structure of the coli catabolite gene activator protein (CAP) complexed with a 30-base pair DNA sequence (PDB IDCODE ICGP] shows that the DNA is bent by 90° ...

Figure 9.19 Nucleotide sequence of the 21-base pair DNA fragment cocrystalUzed with the DNA-binding domain of p53. The p53 binds in a sequence-specific manner to the shaded region.

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.

The broad peaks B, D, and E are shifted far upfield by reaction with bisulfite (Eq. 5-11) suggesting that they are not hydrogen bonded and are present in the loop of the stem-loop structure. Peaks A, E, F, and G correspond to resonances 64, 7, 67, and 4, respectively, in (A) and represent fluorouracil in the stem structure. From Chu et al.69i Courtesy of Jack Horowitz. (C) A 31P NMR spectrum of a synthetic 14 base-pair DNA segment related to the E. coli lac operator. The palindromic sequence is TCTGAGCGCTCAGA. The numbers refer to the positions from the 5 end. From Schroeder et al.688... 

Ames developed strains of bacteria that had carefully selected lethal mutations. In a test system the bacteria could survive only when its mutation had been corrected by experiencing another mutation caused by the tested material. This correction could be accomplished by causing a point mutation or frameshift mutations . Point mutations are base-pair substitutions, that is, a base change in DNA of at least one DNA base pair. In a reverse mutation test, this change in base pairs may occur at the site of the original mutation, or at a secondary site in the bacterial genome. Frameshift mutations are the addition or deletion of one or more base pairs in the DNA. Since amino acids are encoded by triplets of base pairs in sequence, any addition or deletion of 1 or 2 base pairs will dramatically alter the expressed protein from that point on. The Ames system employs strains of Salmonella typhimurium and Escherichia coli that require amino acids (histidine or tryptophan, respectively) to detect such reverse point and frameshift mutations. The reverse mutation allows the S. typhimurium or E. coli strains to restore the functional capability of the bacteria to be able to synthesize the specific amino acid on their own, independent of amino acid content in the medium. 

A nucleosome core particle is formed by a 146 base pairs DNA fragment wrapped 1.65 times around the histone octamer (formed by two copies of H2A, H2B, H3 and H4 histones). NCP are connected by regions of naked DNA called linkers. The nucleotide sequences of the 146 bp DNA fragments involved in nucleosomes are polymorphic. The regions of contact between DNA and the core of histones are distributed along DNA with a periodicity of around 10.4 bp, which is the number of base pairs per helical turn of DNA in the nucleosome. 

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