DNA antisense strand

Unlike what happens in DNA replication, where both strands are copied, only one of the two DNA strands is transcribed into mRNA. The DNA strand that contains the gene is often called the sense strand, or coding strand, and the DNA strand that gets transcribed to give RNA is called the antisense strand, or noncoding strand. Because the sense strand and the antisense strand in DNA are complementary, and because the DNA antisense strand and the newly formed RNA strand are also complementary, the RNA molecule produced during transcription is a copy of the DNA sense strand. That is, the complement of the complement is the same as the original. The only difference is that the RNA molecule has a U everywhere the DNA sense strand has a T. 

When you see a sequence written with only one strand shown, the 5 end is written on the left. Usually this sequence is also identical to that of the RNA that would be made from this piece of DNA when transcribed left to right. The DNA strand that has the same sequence (except U for T) as the RNA that is made from it is called the sense strand. The sense strand has the same sequence as the mRNA. The antisense strand serves as the template for RNA polymerase. 

RNA polymerase uses the antisense strand of DNA as a template. RNA is synthesized in the 5 to 3 direction. 

RNA polymerase makes a copy of the sense strand of the DNA using the antisense strand as a template (Fig. 5-8). The sequence of the primary transcript is the same as that of the sense strand of the DNA. RNA polymerase needs no primer—only a template. Either of the two DNA strands can serve as the template strand. Which DNA strand is used as the tern-... 

Unlike the DNApolymerase reaction, RNApolymerases catalyze the transcription of only one of the two DNA strands. The two DNA strands are termed the sense strand and the antisense strand. It is the antisense strand that is transcribed by the RNA polymerases. Thus, the base sequence of the newly synthesized RNA strand is identical to the sense strand of the DNA template, except of conrse that U replaces T. 

F ig U re 1 3.1 A schematic view of RNA chain elongation catalyzed by an RNApolymerase. In the region being transcribed, the DNA double helix is unwound by about a turn to permit the DNAs sense strand to form a short segment of DNA-RNA hybrid double helix. That forms the transcription bubble. Note that the DNA bases in the bubble on the antisense strand are now exposed to the enzyme and are useable as a template for chain elongation. The RNApolymerase works its way down the DNA molecule until it encounters a stop signal. (Reproduced from D. Voet and J. G. Voet, Biochemistry, 3rd, edn, 2004 Donald and Judith G Voet. Reprinted with permission of John Wiley and Sons, Inc.)... 

The PCR is a three-step cyclic process that repeatedly duplicates a specific DNA sequence, contained between two oligonucleotide sequences called primers (154,155). The two primers form the ends of the sequence of DNA to be amplified and are normally referred to as the forward and reverse primers. The forward primer is complementary to the sense strand of the DNA template and is extended 5 to 3 along the DNA by DNA polymerase enzyme (Fig. 27). The reverse primer is complementary to the antisense strand of the DNA template and is normally situated 200-500 base pairs downstream from the forward primer, although much longer sequences (up to 50 kbase) can now be amplified by PCR. The process employs a thermostable DNA polymerase enzyme (such as the Taq polymerase from Thermus aqualicus BM) extracted from bacteria found in hot water sources, such as thermal pools or deep-water vents. These enzymes are not destroyed by repeated incubation at 94 °C, the temperature at which all double stranded DNA denatures or melts to its two separate strands (155). 

The term (XG + Xc) is the sum of the mole fractions of guanine and cytidine in the antisense strand. The mole fraction of any nucleobase is equal to the number of nucleotides containing that base divided by the total number of nucleotides in the oligonucleotide strand. [M+] is the molar concentration of monovalent cations. In a typical mammalian cell, [K + ] is 140 mM, and [Na+ ] is 10 mM. L is the length of the duplex in base pairs. Based on Equation 6.2 and the assumption that phosphorothioate oligonucleotides behave as regular DNA, fomivirsen (6.17) would have a predicted Tm of 59 °C. Equation 6.1 predicts 64 °C. More complex forms of Equation 6.2 with increased accuracy appear regularly in the literature.8... 

The mRNA is known as the sense strand because it is the portion of the DNA that is ultimately translated by the cell into proteins. An antisense strand is the other, complementary strand in DNAs double helix structure—or any nucleic acid that is complementary to, and can pair exactly with, at least part of a sense strand. 

Each RNA polymerase transcribes only one strand, the antisense (—) strand, of a double-stranded DNA template, directed by a promoter. Synthesis occurs 5 — 3 and does not require a primer. 

During transcription of information from DNA into mRNA, the two complimentary strands of the DNA partly uncoil. The sense strand separates from the antisense strand. The antisense strand of DNA is used as a template for transcribing enzymes that assemble mRNA (transcription), which, in the process produces a copy of the sense strand. Then, mRNA migrates into the cell, where other cellular structures called ribosomes read the encoded information, its mRNA s base sequence, and in so doing, string together amino acids to form a specific protein. This process is called translation. ... 

The sequence of nucleotides within the single-stranded mRNA is assembled according to the complementary-base-pairing (Chap. 7) instructions from one of the strands of duplex DNA, which contains the gene. The DNA strand that bears the same sequence as the mRNA (except for T instead of U) is called the coding strand or sense strand. The other strand of DNA which acts as the template for transcription is called the template or antisense strand. Some textbooks do not define sense" and antisense in the way described here, and for this reason it may be preferable to use coding and template when referring to a particular strand. 

Figure 2 Base stacking provided by the correlations in nucleotide sequences is the major mechanism of DNA thermostability. Upper row. Real amino acid sequence and original codon bias. Middle row. The effect of codon interface is removed through the reshuffling of protein sequences while retaining the actual codons used for each amino acid. Bottom row. Codon bias in natural protein sequences is removed by using synonymous codons with equal probabilities. ApG and CpT pairs in the sense strand and ApG pairs in the antisense strand of DNA are underlined if they are located inside one codon. For example (upper row), the first ApG pair in the sense strand is in the Lys codon, whereas the second ApG pair is on the border between the codons of Leu and Val.

The first nucleotide (the start site) of a transcribed DNA sequence is denoted as +1 and the second one as +2 the nucleotide preceding the start site is denoted as -1. These designations refer to the coding strand of DNA. Recall that the sequence of the template strand of DNA is the complement of that of the RNA transcript (see Figure 5.26). In contrast, the coding strand of DNA has the same sequence as that of the RNA transcript except for thymine (T) in place of uracil (U). The coding strand is also known as the sense (+) strand, and the template strand as the antisense (-) strand. 

The strand that is written is the one that is identical to the RNA transcript, thus the antisense strand of the DNA is always selected for presentation. 

Nucleotide incorporation is determined by base pairing with the template strand of the DNA. The template is the DNA strand, also called the sense strand, that is copied by the RNA polymerase into a complementary strand of RNA called the transcript. The DNA strand that is not copied is know as the antisense strand. Note that while the RNA chain grows in a 5 to 3 direction the polymerase migrates along the sense strand in a 3 to 5 direction. Thus, the 5 to 3 ribonucleotide sequence of the RNA transcript is identical to the 5 to 3 antisense DNA strand with uracil in place of thymidine. 

Unlike what happens in DNA replication, where both strands are copied, only one of the two DNA strands is transcribed into mRNA. The strand that contains the gene is called the coding strand, or sense strand, and the strand that gets transcribed is called the template strand, or antisense strand. Since the template strand and the coding strand are... 

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