Duplex antiparallel

Extrapolation of the molecular structure of an a-maltohexaose duplex com-plexed with triiodide in single crystals leads to a left-handed, 8-fold, antiparallel double-helix for amylose.90 The pitch of this idealized helix is 18.6 A, so h is only 2.33 A. Although this model is no contender to the fiber data, in terms of biosynthesis, it is doubtful that the native amylose helix favors antiparallel chains. 

Fig. 30. — Packing arrangement of 4-fold antiparallel double helices of potassium hyaluronate (32). (a) Stereo view of a unit cell approximately normal to the line of separation of the two helices. The two chains in each duplex, drawn in open and filled bonds for distinction, are linked by not only direct hydrogen bonds, but also water bridges. Inter double-helix hydrogen bonds are mediated between hydroxymethyl and iV-acetyl groups. Potassium ions (crossed circles) at special positions have only a passive role in the association of hyaluronate chains.

Earlier studies using thermal denaturation analysis and spectrophotomet-ric titration with TxA T and CxC-C" containing DNA triplexes showed that coralyne binds strongly to these triplexes by intercalation and does not exhibit a significant sequence-selectivity [222]. In a later study by Morau Allen et al. [217], employing DNase footprinting, thermal denaturation analysis, UV-visible spectrophotometric titrations, circular dichroism and NMR spectroscopy, showed that coralyne is fully intercalated into TxA T triplex DNA whereas in C GxC triplex, it is partially intercalated due to electrostatic repulsion between the cationic alkaloid and the protonated cytosine [217]. Kepler et al. [223] demonstrated that coralyne intercalated to parallel triplex DNA but did not intercalate to antiparallel triplex DNA. Recently Hud and coworkers [219,224] demonstrated that duplex poly(dA) poly(dT) is trans-... 

Fig. 4. Possible homo-dimers of psPtDNA (A) antiparallel duplex, (B) parallel duplex, (C) quadruplex. Adapted from Ref. (28).

C2 Z = 4 Dx = 1.41 R = 0.102 for 4,115 intensities. The structure is a 3 2 complex of proflavine and CpG. The asymmetrical unit contains one CpG molecule, 1.5 proflavine molecules, 0.5 sulfate ion, and 11 5 water molecules. Two CpG molecules form an antiparallel, Watson-Crick, miniature duplex, with a proflavine intercalated between the base pairs through the wide groove. The double helix has exact (crystallographic), two-fold symmetry, and the crystallographic, two-fold axis passes through the C-9-N-10 vector of the intercalated proflavine. A second and a third molecule of proflavine are stacked on top of the C - G pairs ... 

Figure 20.15 Diagram of a small portion of the DNA duplex to illustrate antiparallel nature of the two DNA strands. The bonds = between bases are the hydrogen bonds. The prime ( ) is necessary since the atoms in the base are numbered as are the atoms in the sugar. Numbers in the latter are therefore distinguished by a superscript prime on the pertinent carbon atom. The numbers in this diagram are indicated on only one ribose to keep its diagram in the simplest form.

Using the pitch, symmetry, monomer geometries and other stereochemical constraints, a number of types of molecular model can be constructed. Typical dilemmas are whether the molecular helix is left- or right-handed, whether the molecule is a single helix or coaxial double-helix (and in the later case whether the two chains in the duplex are parallel or antiparallel), or whether, if there are two or more molecules in the unit cell, the molecules are parallel or antiparallel. Solution of a structure therefore involves refinement and adjudication All candidate models are refined until the fit with the measured x-ray amplitudes or steric factors allows one model to be declared significantly superior to the others by some standard statistical test. 

The complementary antiparallel strands of DNA follow the pairing rules proposed by Watson and Crick. The base-paired antiparallel strands differ in base composition the left strand has the composition A3 T2 G, the right, A2 T3 G3 C,. They also differ in sequence when each chain is read in the 5 — 3 direction. Note the base equivalences A = T and G = C in the duplex. 

When the two strands of the DNA double helix are separated, each can serve as a template for the replication of a new complementary strand. This produces two daughter molecules, each of which contains two DISA strands with an antiparallel orientation (see Figure 29.3). This process is called semiconservative replication because, although the parental duplex is separated into two halves (and, therefore, is not "conserved" as an entity), each of the individual parental strands remains intact in one of the two new duplexes (Figure 29.8). The enzymes involved in the DlsA replication process are template-directed polymerases that can synthesize the complementary sequence of each strand with extraordinary fidelity. The reactions described in this section were first known fiom... 

Figure 5-28 (A) Abbreviated reaction sequence for formation of a four-way Holliday junction between two homologous DNA duplexes. In step a strands are cut and rejoined with movement of the strands to a roughly antiparallel orientation. The resulting structure is thought to resemble that shown below the four-stranded representation.

The duplex is a right-handed double helix with 10 bases per turn. The diameter of the helix is 20 A (2 nm) and the pitch is 34 A (3.4 nm). The sugar-phosphate backbone is on the outside of the helix, and the two antiparallel chains are connected by the hydrogen-bonded bases. The DNA in prokaryotes and eukaryotes is generally found in the duplex form, although there are some single-stranded DNA viruses. DNA is a very robust molecule in comparison with many proteins. The simple double-helical secondary structure is readily reassembled after denaturation, unlike the complex tertiary protein structures that can denature... 

Continuous synthesis on both strands of the replication fork would require synthesis in the 5 —> 3 direction on one strand and in the 3 —> 5 direction on the other because of the antiparallel nature of the DNA duplex (fig. 26.5a). Continuous synthesis on both strands seems unlikely since the only known enzymes that catalyze DNA synthesis add bases... 

One such example would be the antiparallel association of d(GGAATCG) with d(CGATTCC) to form the duplex... 

Because the glycosyl links and the associated sugar-phosphate backbone are related, in the Watson-Crick duplex, by a pseudodyad perpendicular to the helix axis, the two strands are oriented antiparallel. They are parallel in the Hoogsteen duplex because the glycosyl links are related by rotation about the helix axis. 

Antiparallel Strand Alignment Duplex Grooves and Recognition Nonplanar Geometry Protein-induced Base-pair Deformations Summary... 

Alexander Rich and his associates discovered a third type of DNA helix when they solved the structure of dCGCGCG. They found that this hexanucleotide forms a duplex of antiparallel strands held together by Watson-Crick base-pairing, as expected. What was surprising, however, was that this double helix was left-handed, in contrast with the right-handed screw sense of the A and B helices. Furthermore, the phosphates in the backbone zigzagged hence, they called this new form Z-DNA (Figure 27.10). 

Both strands of parental DNA serve as templates for the synthesis of new DNA. The site ofDNA synthesis is called the replication fork because the complex formed by the newly synthesized daughter strands arising from the parental duplex resembles a two-pronged fork. Recall that the two strands are antiparallel that is, they run in opposite directions. As shovm in Figure 27.3. both daughter strands appear to grow in the same direction on cursory examination. However, all... 

The base pairing properties of the a- and p-anomers of the imidazo[l,2-a]-1,3,5-triazine nucleoside (96) have been described. Both anomers are more stable than duplexes with dG, though the a-anomer is most stable. When the p-anomer alternates with dG, antiparallel duplexes (aps) are observed, but parallel duplexes (ps) are formed with the a-anomer. A reversal of the chain orientation (ps- aps) occurs when the P-anomer pairs with 2 -deoxyisoguanosine. 

An X-ray crystallography structure of the duplex from d(ATA UAT) and d( ATAT AT) demonstrates that an alternative to the classical B-DNA double helix is possible. This sequence is found not only in TATA boxes, but also in other regulatory regions of DNA. The structure is not related to those found in triplexes or to parallel DNA duplexes, though its conformational parameters are very similar to those of B-form DNA. Bases of the two antiparallel strands form Hoogsteen pairs, with adenines in the syn conformation. 

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