Deoxynucleotide residues

DNA supercoiling provides conformational potential energy for DNA tertiary structure formation such as the development of DNA cruciform structures (Figure 1.77). Supercoiling also leads to the creation of DNA triple helix (DNA triplex) structures, which form when an oligodeoxynucleotide chain, with an appropriately complementary deoxynucleotide residue... 

Calculation The molecular weight of a dAMP residue in DNA is 313 and that for dCMP is 275 so a round number for a deoxynucleotide residue is 300. Since the E. coli genome consists of 4.6 x 10 bp, the molecular... 

DNA polymerases normally use 3 -deoxynucleotide triphosphates as substrates for polymerization. Given an adequate concentration of substrate, DNA polymerase synthesizes a long strand of new DNA complementary to the substrate. The use of this reaction for sequencing DNA depends on the inclusion of a single 2/3 -dideoxynucleoside triphosphate (ddNTP) in each of four polymerization reactions. The dideoxynucleotides ate incorporated normally in the chain in response to a complementary residue in the template. Because no 3 -OH is available for further extension, polymerization is... 

F. H. Westheimer (1987) has provided a detailed survey of the multifarious ways in which phosphorus derivatives function in living systems (Table 4.7). The particular importance of phosphorus becomes clear when we remember that the daily turnover of adenosine triphosphate (ATP) in the metabolic processes of each human being amounts to several kilograms Phosphate residues bond two nucleotides or deoxynucleotides in the form of a diester, thus making possible the formation of RNA and DNA the phosphate always contains an ionic moiety, the negative charge of which stabilizes the diester towards hydrolysis and prevents transfer of these molecules across the lipid membrane. 

Deoxynucleotides for DNA synthesis are made at the nucleoside diphosphate level and then have to be phosphorylated up to the triphosphate using a kinase and ATP. The reducing equivalents for the reaction come from a small protein, thioredoxin, that contains an active site with two cysteine residues. Upon reduction of the ribose to the 2 -deoxyri-bose, the thioredoxin is oxidized to the disulfide. The thioredoxin(SS) made during the reaction is recycled by reduction with NADPH by the enzyme thioredoxin reductase. 

Dong, Q., Copeland, W. C., and Wang, T. S. (1993). Mutational studies of human DNA polymerase a Identification of residues critical for deoxynucleotide binding and misinsertion fidelity of DNA synthesis. / Biol. Chem. 268, 24163-24174. 

Fig. 3.7. Principle of the partial ribosubstitution method of Barnes (1978). iC, rA, inserted ribocytidine and riboadenine residues N, any deoxynucleotide.

Figure 7. Schematic representation of the hydrogen bond interaction of the deoxynucleotide sequence C-T-T-A-A-G with Argl45, Arg200 and Glul44 residues of the a and 3 subunits of Eco RI endonuclease. (Reproduced with permission from Ref. 13. Copyright 1986 American Association for the Advancement of Science.)...

Figure 1. a. Amino acid residues of RNase A that compose the subsites for binding phospho-ryl groups (PO, PI, and P2) and bases (Bl, B2, and B3) of single-stranded nucleic acids, b. Fluorescein-labeled deoxynucleotides used to assess binding to the Bl subsite. 

In the assay outlined earlier, apoptotic cells are detected because of lowered signal intensity resulting from DNA degradation. The finding that apoptosis involves a specific form of DNA degradation allows one to detect these unique events with a specific labeling procedure. With the aid of terminal deoxynucleotide transferase, fluorescently labeled dUTP residues are... 

In DNA and RNA, the chain of phosphodiester links and sugar rings is known as the phosphodiester backbone the bases may be regarded in both cases almost as side-chains . By convention, DNA or RNA chains begin at the 5 -end (i.e., where carbon atom C-5 of the terminal residue is not involved in a phosphodiester link) and terminate at the 3 -end (where carbon atom C-3 is not involved in a phosphodiester link). Each chain is therefore said to run by convention from S to S (5 —>-3 ). Several shorthand conventions are used to describe the sequences of deoxynucleotide or nucleotide residues in DNA and RNA respectively. These include the Fischer, linear alphabetic and condensed alphabetic conventions that draw upon the letter codes for bases and deoxynucleosides or nucleosides as described previously (Figure 1.59). 

Figure 1.63 Illustration of conformational preferences of the conformational angle y subtended about the D—C bond. Each deoxynucleotide (or nucleotide) residue adopts either a +sc or ap conformation. The former is usually preferred but for exceptional circumstances.

DNA (Table 1.2) (Figure 1.74). The helbc sense of Z-form DNA is now left handed and the backbones of the two poly deoxynucleotide chains map out a zigzag spiral path. This results from the tendency of deoxyguanosine nucleotide residues to distort so that their 2 -deoxy-/3-D-ribofuranose rings adopt a C -endo instead of C -endo twist conformation (Figure 1.71). However, in addition, the guanine bases move to a syn conformation (positioned over the top of their attached furanose rings), instead of the more usual anti conformation... 

Nucleic acids can play roles farbeyond merely harbouring the coding information for proteins. Single-stranded nucleic acids can fold into intricate structures capable of molecular recognition and even catalysis. Three-dimensional structures are specified by the primary structure, namely the deoxynucleotide (or nucleotide, for RNA) sequence (5 - 3, by analogy to the situation in which the amino-acid residue sequence determines the three-dimensional structures of polypeptides. In nature, transfer RNAs (tRNAs) use their three-dimensional shape for molecular recognition, while some ribosomal RNAs (rRNAs) are able to catalyse crucial steps even within the protein synthetic pathways themselves. 

The original PROBE assay has been replaced now by a bead-free, homogeneous assay called the MassExtend (hME) assay. Before the primer extension reaction, shrimp alkaline phosphatase (SAP) is added to the PCR product. This dephosphorylates any residual deoxynucleotides that otherwise would inter-... 

---