Secondary structure base paired helices

This type of hydrogen bonds includes the N-H 0=C interactions which are the most predominant hydrogen bonds in fibrous and globular proteins. Because they are responsible for the formation of the commonly occurring secondary structure elements a-helix, -pleated sheet and / -turn, a large body of much less accurate data is available from protein crystal structures which will be analyzed in Part III, Chap. 19. The N-H 0=C type hydrogen bond is also the most common in the purine and pyrimidine crystal structures (Thble 7.14), and is one of the two important bonds in the base pairing of the nucleic acids. 

These observations, together with those on supercoiled DNAs relaxed by intercalating dyes and by topoisomerase I, indicate that complete conversion from the prevalent secondary structures in supercoiled DNAs to the normal B-helix must be severely hindered kinetically. It is also clear that the free energies per base pair of the secondary structure states a and b must be nearly identical in order for these states to be interconverted by such a small environmental perturbation. 

A constant number of chromosomes is present in each cell. The somatic cells (i.e. not sperm or egg) are described as diploid because they contain two complete sets of chromosomes. There are 23 pairs of chromosomes in each cell, 22 pairs of somatic chromosomes (one of each pair derived from each parent) and one pair of sex chromosomes, either two Xs in the female or an X and Y in the male. Together, the 23 chromosomes contain about two metres of linear DNA or about three billion pairs of nucleotides. The linear structure of bases in DNA strands is called the primary structure of the chromosome. The secondary structure is the double heUx, in which the two complementary strands of DNA twist about each other. One turn of the helix is called a pitch and consists of ten nucleotides. 

As with proteins, the nucleic acid polymers can denature, and they have secondary structure. In DNA, two nucleic acid polymer chains are twisted together with their bases facing inward to form a double helix. In doing so, the bases shield their hydrophobic components from the solvent, and they form hydrogen bonds in one of only two specific patterns, called base pairs. Adenine hydrogen bonds only with thymine (or uracil in RNA), and guanine pairs only with cytosine. Essentially every base is part of a base pair in DNA, but only some of the bases in RNA are paired. The double-helix structure... 

Figure 29-2 (A) Secondary structure model for the 1542-residue E. coli 16S rRNA based on comparative sequence analysis.733 Dots indicate G U or A G pairs dashes indicate G C or A U pairs. Strongly implied tertiary interactions are shown by solid green lines. Helix numbering according to Brimacombe. Courtesy of Robin Gutell. (B) Simplified schematic drawing of type often used. (C) Positions of the A, P, and E sites on the 30S ribosomal subunit from Carter et al7° (D) Stereoscopic view of the three-dimensional fold of the 16S RNA from Thermus thermophilus as revealed by X-ray structural analysis at 0.3 nm resolution. Features labeled are the head (H), beak (Be), neck (N), platform (P), shoulder (Sh), spur (Sp), and body (Bo). (E-H) Selected parts of the 16S RNA. In (E) and (F) the helices are numbered as in (A). (F) and (H) are stereoscopic views. The decoding site...

Recently, a quite different model has been proposed that accounts for the appearance of many kinds of mutations, including base pair substitutions, additions and deletions, and small chromosomal mutations of the type that would usually be classified as gene mutations. The model accounts for frequent palindromic sequences (more exactly, imperfect palindromes or quasipalindromes) in DNA that can predispose to alternative DNA structures (e.g., clover leaves) that differ from the usual double helix. The alternative or "secondary" structures can then be acted on by any of a variety of DNA-processing enzymes in ways that may ultimately lead to mutations. The details of these processes are only now becoming manifest, but the general model clearly explains many hitherto mysterious mutational phenomena.371... 

Elongation is the function of the RNA polymerase core enzyme. RNA polymerase moves along the template, locally unzipping the DNA double helix. This allows a transient base pairing between the incoming nucleotide and newly-synthesized RNA and the DNA template strand. As it is made, the RNA transcript forms secondary structure... 

Most of the DNA in nature has the double helical secondary structure. The hydrogen bonds between the base pairs provide the stability of the double helix. Under certain conditions the hydrogen bonds are broken. During the replication process itself, this happens and parts of the double helix unfold. Under other conditions, the whole molecule unfolds, becomes single stranded, and assumes a random coil conformation. This can happen in denaturation processes aided by heat, extreme acidic or basic conditions, etc. Such a transformation is often referred to as helix-to-coil transition. There are a number of techniques that can monitor such a transition. One of the most sensitive is the measurement of viscosity of DNA solutions. 

Just as main-chain NH 0=C hydrogen bonds are important for the stabilization of the a-helix and / -pleated sheet secondary structures of the proteins, the Watson-Crick hydrogen bonds between the bases, which are the side-chains of the nucleic acids, are fundamental to the stabilization of the double helix secondary structure. In the tertiary structure of tRNA and of the much larger ribosomal RNA s, both Watson-Crick and non-Watson-Crick base pairs and base triplets play a role. These are also found in the two-, three-, and four-stranded helices of synthetic polynucleotides (Sect. 20.5, see Part II, Chap. 16). 

NMR was used to solve the structure of an oligonucleotide from the helix III sequence of Xenopus oocyte 5S rRNA. The structure includes two unpaired adenosine residues flanked by G C base pairs which is required for binding of ribosomal protein L5. The adenosine residues are located in the minor groove stacked onto the 3 guanine bases. The major groove is widened at the site of the adenosines, and the helix is substantially bent. E-motifs are secondary struc-... 

Similarly to proteins, both DNA and RNA have a secondary and a tertiary structure. The secondary structure of DNA shows two chains running in opposite directions, coiled in a left-handed (double) helix about the same axis. All the bases are inside the helix, and the sugar phosphate backbone is on the outside (see e.g. [1]). The chains are held together by hydrogen bonds between the bases with adenine always paired with thymine and guanine paired with cytosine. The base pairing in DNA is shown below ... 

---