Antiparallel complementary strand

DNA synthesis is catalysed by DNA polymerases and requires the precursor dNTPs (dATP, dGTP, dCTP and dTTP, each of these existing as Mg2+ complexes), a template (i.e. the dsDNA being copied) and a primer (an initial deoxyribose 3 -OH to enable the reaction to insert the first new nucleotide). The reaction proceeds in a 5 to 3 direction, that is, at the end of the synthesis there is a vacant deoxyribose 3 -OH. The fidelity of the replication process is based on the incoming nucleotides base pairing with the correct base on the antiparallel template. DNA synthesis is semi-conservative (i.e. the newly synthesized strand partners its antiparallel complementary strand) and is bidirectional (because both original strands are replicated). 

DNA is composed of two antiparallel complementary strands, which build a double helix. Pairing of the bases, which grant stability to the helix, takes place via hydrogen bonds. The base pairs (bp) are A-T (two bonds) and G-C (three bonds), and constitute the inner side of the double helix (Scheme 1). The backbone of the helix is composed of the sugar-phosphate chain. Another important contribution to the stability of the helix comes from the base stacking of the aromatic rings of the... 

The two complementary strands of the DNA double helix run in antiparallel directions (Fig. 4-1). The phosphodiester connection between individual deoxynucleotides is directional. It connects the 5 -hydroxyl group of one nucleotide with the 3 -hydroxyl group of the next nucleotide. Think of it as an arrow. If the top strand sequence is written with the 5 end on the left (this is the conventional way), the bottom strand will have a complementary sequence, and the phosphate backbone will run in the opposite direction the 3 end will be on the left. The antiparallel direc-... 

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... 

In the present example we have examined the sequence in mRNA. In the DNA there are two strands. One is the coding strand (also called the nontranscribing or nontranscribed strand), which has a sequence that corresponds to that in the mRNA and the one that is given in Fig. 5-4. The second antiparallel and complementary strand can be called the template strand or the noncoding, transcribing, or transcribed strand.372 The mRNA that is formed is sometimes referred to as a sense strand. The complementary mRNA, which corresponds in sequence to the noncoding strand of DNA, is usually called antisense RNA. 

Fig. 8 Schematic representation of DNA junctions and crossover tiles. Motif 1 is a branched DNA junction with three arms and motif 2 with four arms. Every terminal in the arm is an unpaired ssDNA. The ssDNA acts as sticky ends , which may pair with another complementary strand. The two motifs 3 and 4 are two different antiparallel double-crossover molecules containing an even number of half-helical turns between branch points (DAE) or an odd number (DAO). They are more stable and thus usually applied. Oligonucleotide strands are individually represented with different colors...

Antiparallel strands of DNA. DNA usually consists of two complementary strands, with all the base pairs hydrogen bonded together. The two strands are antiparallel, running in opposite directions. (In these drawings of DNA, ribose means /3-D-2-deoxyribofuranoside.)... 

Natural DNA (B DNA) contains two complementary antiparallel polynucleotide strands wound together into a regular right-handed double helix with the bases on the In-... 

To study the UAG3T UAG3T quadruplexes kinetics, the authors performed different types of experiments. Addition of an excess of the complementary strand induces a time-dependent formation of the duplex, whose kinetics are related to quadruplex unfolding. A single exponential function perfectly fits the data for each form. At temperature below 40°C, the parallel quadruplex unfolds faster than the antiparallel one. As the antiparallel quadruplex has slightly higher activation energy of dissociation (Eob = +43 kcal moN v.s. +34 kcal mol for the parallel form), kinetic stability is reversed above 40°C. At 37°C, the lifetimes of the two quadruplexes are very close, around 2 h. To study their kinetics of... 

The two chains in the double helix are antiparallel (one goes 5 to 3 whereas the complementary strand goes 3 to 5 ). 

As concluded by Watson and Crick, the two complementary strands of DNA run in opposite directions. On one strand, the 5 -carbon of the sugar is above the 3 -car-bon (Fig. 12.8). This strand is said to run in a 5 to 3 direction. On the other strand, the 3 -carbon is above the 5 -carbon. This strand is said to run in a 3 to 5 direction. Thus, the strands are antiparallel (that is, they run in opposite directions.) This concept of directionality of nucleic acid strands is essential for understanding the mechanisms of replication and transcription. 

By convention, when polynucleotide sequences are written, left to right means 5 —> 3. Since complementary strands are antiparallel, if one wishes to write the complementary sequence without specifically labeling the ends, the order of the bases must be reversed. 

Similarly to B-DNA, the A form can be adopted by an arbitrary sequence of nucleotides. Like in B-DNA, in A-DNA the two complementary strands are antiparallel and form right-handed helices. DNA undergoes transition from the B to A form under dehydration conditions (reviewed by Ivanov and Krylov, 1992 [34]). In A-DNA, the base pairs are planar but their planes make a considerable angle with the axis of the double helix. In doing so, the base pairs shift from the center of the duplex forming an empty channel in the center. 

Z-DNA (Fig. 2b) presents the most striking example of how different from the B form the DNA double helix can be (Wang et. al., 1979 [87]). Although in Z-DNA the complementary strands are antiparallel like in B-DNA, unlike in B-DNA, they form left-handed, rather than right-handed, helices. There are many other dramatic differences between Z- and B-DNA (reviewed by Dickerson, 1992 [15]). 

The complementary strands in a DNA duplex can be parallel. Such parallel-stranded (ps) DNA is formed most readily if both strands carry only adenines and thymines and their sequence excludes formation of the ordinary antiparallel duplex (reviewed by Rippe and Jovin, 1992 [58]). If these requirements are met, the parallel duplex is formed under quite normal conditions. It is right-handed, but the AT pairs are not the usual, Watson-Crick ones, but rather the so-called reverse Watson-Crick. 

Imagine a single DNA strand containing a section with the following base sequence 5 -GCArrGGC-3. What is the base sequence of the complementary strand (The two strands of DNA will come together in an antiparallel fashion that is, 5 -TAG-3 will bind to 3 -ATC-5. )... 

In 1953, James D. Watson and Francis C. Crick used X-ray diffraction patterns of DNA fibers to determine the molecular structure and conformation of DNA. They found that DNA contains two complementary polynucleotide chains held together by hydrogen bonds between the paired bases. Figure 23-26 shows a portion of the double strand of DNA, with each base paired with its complement. The two strands are antiparallel One strand is arranged 3 5 from left to right, while the other runs in the opposite direction, 5 3 from left to right... 

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