Anti-parallel strand

Very recently the trans- [Pt(NH3)2Cl2] isomer has been shown to promote the formation of some highly unusual multiple strand nucleic acid structures (28). A parallel-stranded DNA duplex, psPtDNA, has been prepared which incorporates a frarcs-Pt(NH3)2+ crosslink. The pla-tinated strands were synthesized through the series of reactions illustrated in Fig. 3. The initial mono-functional G N7 adduct is formed at pH 3.5 by addition of rans-[Pt(NH3)2(H20)Cl]+ to the pyrimidine-rich sequence 5 -d(T4CT4G). After the pH is increased, normal anti-parallel duplex formation occurs upon addition of the complementary purine-rich strand, 5 -d(A4GA4G). This intermediate anti-parallel stranded... 

While RNA molecules do not have the double stranded structure usually found in DNA, in many RNA molecules stem-loop structures are found in which the anti-parallel strands are connected by a 5-7 residue loop. Rather like the P-tum in proteins, this allows the... 

Double helical structures may be constructed from complementary single-stranded polynucleotide chains sharing a common helical axis according to the procedure outlined below. The two strands of the complex are assumed to be regular helices defined by a common set of backbone and glycosyl torsion angles. The data presented here are limited to model poly(dA) poly(dT) double helices stabilized by Watson-Crick base pairs between anti parallel strands. 

Under physiological conditions DNA exists predominantly as a duplex formed between complementary anti-parallel strands of DNA in which the purines of one strand are hydrogen bonded to the pyrimidines of the complementary strand and vice versa to form G C and A T base pairs. The Watson-Crick G C base pairs (Figure 2) possess three hydrogen bonds and the A T base pairs two hydrogen bonds, each hydrogen bond contributing approximately 2 kcal mol to the stabil-... 

This common fold variously contains from four to nine anti-parallel four-stranded beta sheets. These are arrayed radially with a geometry similar to a ship s propeller, each propeller blade being composed of four anti-parallel strands, each slighdy twisted in the same orientation. The height or... 

Diffraction patterns obtained by Davies and Baldwin [12] indicated that poly d(A-T).poly d(A-T) could assume a conformation with axial periodicity about 24.5 A which they named D-DNA. Similar diffraction patterns were obtained from poly d(I-C).poly d(I-C) by Mitsui et al. [46]. They proposed a novel left-handed double helix with anti-parallel strands and Watson-Crick base-pairs. This eightfold helix contained sugars with an unusual pucker and the bases were placed about 2 A behind the helix axis i.e. on the opposite side from the position of the base-pairs in the A form of DNA. Arnott et al. [47] obtained better quality D-form diffraction patterns from poly d(A-T).poly d(A-T) which they analysed using the linked atom least squares technique. They rejected the left-handed model of Mitsui et al. [46] and claimed... 

Anti-parallel stranded quadruplex stacked repeat with a syn-anti-step... 

Figure 7 A series of stacked guanine tetrads with various strand arrangements syn and anti relationships, (a) Parallel stranded quadruplex stacked repeat where all bases have anti-glycosidic torsion angles stacked over a second tetrad containing only anti-glycosidic torsion angles, (b) First step in an anti-parallel stranded quadruplex with a syn-anti-syn-antitetrad stacked arrangement over an adjacent anti-syn-anti-syn tetrad, (c) Second step in an anti-parallel stranded quadruplex with anti-syn-anti-syn tetrad stacked over a syn-anti-syn-anti-tetrad...

Fig. 2 i f -Strand schematic showing ( ), / and t angles where is the angle about the N-Ca bond, / is the angle about the Ca-C bond and x is the angle about the N-Ca-C (peptide) bond, ii and iii p-Sheet schematics showing the H-bond network (dashed lines) between NH and C=0 backbone residues of adjacent parallel and anti-parallel strands (direction shown by arrows)... 

DNA propellers. The a-mitochondriate Giardia is one of the most ancestral eukaryote. It has two telomeric G4 sequences a propeller-type parallel-stranded one with three G-tetrads, and a basket type anti-parallel-stranded one with two G-tetrads. Components of the G-quadruplexes can be readily exchanged by a cut and paste principle the chromosomal ends are kept capped [388]. The giardia genome is packed with retrotransposons (both LTR-, and non-LTR-types). The non-LTR-types are LINEs (long interspersed nuclear elements) with a single ORF... 

To some extent, the structures discussed above resemble turn structures in peptides. A typical peptide turn structure is depicted in Scheme 5.5. Ring constraints by hydrogen bonds define y-turns (7-membered ring) or p-tums (10-membered ring), whereas 13-membered rings are present in a-helices. Before and after the turn, the peptide extends as anti-parallel strands, often in p-sheets... 

Let us understand this with a famous experiment. Decades ago it had become known that the two anti-parallel strands of the DNA duplex were simultaneously replicated. However, how this could be achieved was not imderstood. All known DNA polymerases can only extend the DNA in 5 3 direction. This would mean that only one strand could be replicated at one time. 

The structure of chymotrypsin inhibitor 2 (CI2) is particularly well-characterized, but the crystal structure and NMR solution structure have small but distinct differences. Early NMR results suggested that there is an additional pair of anti-parallel -strands in comparison with the crystal structure. Subsequent experiment and constrained simulation concluded that the difference between these experimental techniques is caused by the refinement methodology used. 

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