DNA strand pairing

In the transcription process the two DNA strands are separated and the antisense DNA strand paired with its complementary RNA bases by enzymes called RNA polymerases to produce mRNA that encodes the same sequence of bases as the sense DNA strand. The only difference between the DNA and RNA sequences is that the saccharide section of the nucleoside is ribose rather than deoxyribose and uracil takes the place of thymine. The effects of these changes are that the hydrophobic 5-methyl group of thymine has been removed to generate uracil and a 2 -hydroxy group is present in the linking saccharide (Table 2.4). 

FIGURE 25-9 Nick translation. In this process, an RNA or DNA strand paired to a DNA template is simultaneously degraded by the 5 —>3 exonuclease activity of DNA polymerase I and replaced by the polymerase activity of the same enzyme. These activities have a role in both DNA repair and the removal of RNA primers during replication (both described later). The strand of nucleic acid to be removed (either DNA or RNA) is shown in green, the replacement strand in red. DNA synthesis begins at a nick (a broken phosphodiester bond, leaving a free 3 hydroxyl and a free 5 phosphate). Polymerase I extends the nontemplate DNA strand and moves the nick along the DNA—a process called nick translation. A nick remains where DNA polymerase I dissociates, and is later sealed by another enzyme. 

Figure 22.17 outlines the de novo and salvage synthetic pathways to thymine nucleotides. dUTP, an intermediate in the de novo pathways that begins with UDP, is readily recognized by DNA polymerases and can be incorporated into DNA in place of dXTP. The uracil from a dUMP residue in a DNA strand pairs with adenine (like thymine from a dXMP residue would), so there is no loss of or change in information in the DNA. However, dUMP residues can also arise from spontaneous deamination of dCMP. When this DNA is replicated, a mutation at the site will result because cytosine is meant to pair with guanine, not adenine. 

Figure 1.8 Two approaches of DNA-templated self-assembly (a) self-assembled DNA strands A (blue cross shape) carrying nanoparticle B pair with another self-assembled DNA strands A to form a 2-D nanogrid with nanoparticles (adapted from [38] with permission) (b) Complimentary DNA strands pair into nanogrids and functional materials incorporate with the nanogrid later (bl), forming arrays of nanomaterials (b2) (adapted from [37] with permission).

Each pair contains one purine and one pyrimidine base This makes the A T and G C pairs approximately the same size and ensures a consistent distance between the two DNA strands... 

Figure 28 4 supplements Figure 28 3 by showing portions of two DNA strands arranged side by side with the base pairs m the middle... 

Dou ble hel ix (Section 28 8) The form in which DNA normally occurs in living systems Two complementary strands of DNA are associated with each other by hydrogen bonds be tween their base pairs and each DNA strand adopts a helical shape... 

As shown in Figure 45.1, the bases appear in complementary pairs, A with T and G with C in this particular example, the sequence for one strand of DNA is A-T-C-G-T- while the other strand is -T-A-G-C-A-. The sequences of the bases attached to the sugar-phosphate backbone direct the production of proteins from amino acids. Along each strand, groups of three bases, called codons, correspond to individual amino acids. For example, in Figure 45.1, the triplet CGT, acting as a codon, would correspond to the amino acid serine. One codon, TAG, indicates where synthesis should begin in the DNA strand, and other codons, such as ATT, indicate where synthesis should stop. 

The renaturation rate of DNA is an excellent indicator of the sequence complexity of DNA. For example, bacteriophage T4 DNA contains about 2 X 10 nucleotide pairs, whereas Escherichia coli DNA possesses 4.64 X 10 . E. coli DNA is considerably more complex in that it encodes more information. Expressed another way, for any given amount of DNA (in grams), the sequences represented in an E. coli sample are more heterogeneous, that is, more dissimilar from one another, than those in an equal weight of phage T4 DNA. Therefore, it will take the E. coli DNA strands longer to find their complementary partners and reanneal. This situation can be analyzed quantitatively. 

Lee et al. [60] investigated the adhesion of a single pair of DNA strands. They identified two types of forces interchain forces associated with Watson-Crick base pairing between complementary strands, and intrachain forces associated with the elasticity of single strands. For studying interchain interactions, complementary oligomers (ACTG)s and... 

The DNA double heUx illustrates the contribution of multiple forces to the structure of biomolecules. While each individual DNA strand is held together by covalent bonds, the two strands of the helix are held together exclusively by noncovalent interactions. These noncovalent interactions include hydrogen bonds between nucleotide bases (Watson-Crick base pairing) and van der Waals interactions between the stacked purine and pyrimidine bases. The hehx presents the charged phosphate groups and polar ribose sugars of... 

Figure 36-22. Mismatch repair of DNA. This mechanism corrects a single mismatch base pair (eg, C to A rather than T to A) or a short region of unpaired DNA. The defective region is recognized by an endonuclease that makes a single-strand cut at an adjacent methylated GATC sequence. The DNA strand is removed through the mutation, replaced, and religated.

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