DNA sense strand

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.)... 

Figure 2.2 Transcription, mRNA processing, and translation. DNA sense strand is designated by bold lines, hnRNA and mRNA by thinner lines. Exons are shown as rectangles and introns as the intervening spaces between exons. (From An Introduction to Biochemical Toxicology, 3rd edition, E. Hodgson and R. C. Smart, eds., Wiley, 2001.)...

A cloning vector is also cut with the same pair of restriction endonucleases downstream of the promoter element (p) (see Figure 3.5). In cloning vector, pDNA sense strand is dark grey complementary strand is in light grey. In heterologous DNA, sense strand is in red complementary strand is in yellow. 

Nowadays, sequencing is performed with a single DNA polymerisation reaction containing all four ddNTPs differentially labelled with four different types of fluorescent label specific for each ddNTP (see Chapter 4) (Figure 3.13). The complete set of individual DNA sense strand products can now be resolved by capillary electrophoresis (CE, see Chapter 7) so that each successive fluorescent label resolved and identified from the beginning of the elution run (shorter strands run faster) is able to correlate with and identify the deoxynucleoside residue sequence of sense strand DNA starting from the primer. Read lengths are now typically from 400 to 800 deoxynucleoside residues from the primer. 

Gene expression involves a few distinct and well-regulated steps. The first major step of gene expression involves transcription of a messenger RNA (mRNA) which is a RNA sequence complementary to the anti-sense deoxyribonucleic acid (DNA) strands, or, in other words, identical in sequence to the DNA sense strand, composing the gene. 

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. 

What amino acid sequence is coded by the following segment of a DNA sense strand ... 

The mRNA produced during translation is a copy of the DNA sense strand, with each T replaced by U. Thus, the mRNA has the sequence... 

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. 

When writing protein sequences, you write the amino terminus on the left. If you have to use the genetic code tables to figure out a protein sequence from the DNA sequence, it is not necessary to write down the complementary RNA sequence first it s the same as that of the sense strand (the one on top) with the Ts replaced by Us. 

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-... 

To transcribe information from DNA to mRNA, one strand of the DNA is used as a template. This is called the anticoding, or template, strand and the sequence of mRNA is complementary to that of the template DNA strand (Fig. A2.8) (i.e., C->G, G->C, T->A, and A U note that T is replaced by U in mRNA). The other DNA strand, which has the same base sequence as the mRNA, is called the coding, or sense, strand. There are 64 (4 x 4 x 4) possible triplet codes of the four bases 61 are used for coding amino acids and three for termination signals. As there are 20 amino acids for the 61 codes, some triplets code for the same amino acid. A table of the genetic code is presented in Exhibit A2.2. 

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. 

For some years, it was considered that a gene was simply a contiguous sequence of bases within the DNA molecule (i.e. within the sense strand of DNA). In 1977, however, it was shown that this assumption, i.e. that there is a strict one-to-one relationship between the nucleotide sequence of a gene and the amino acid sequence of a polypeptide that it encodes, was not necessarily valid. 

The fourth endpoint is DNA repair. One can determine whether DNA has been damaged in a chemical sense by measuring, by any of several techniques, whether certain characteristic changes in DNA, mainly strand breakage or resynthesis, take place after treatment. 

Figure 1 shows the standard code in DNA language (i. e., as a sequence of triplets in the sense strand of DNA, read in the 5 3 direction see p. 84), represented as a circular diagram. The scheme is read from the inside to the outside. For example, the triplet CAT codes for the amino acid histidine. With the exception of the exchange of U for T, the DNA codons are identical to those of mRNA. 

Only one of the two DNA strands is transcribed into RNA and is called the sense strand. The DNA is unwound in order to make the sense strand available for base pairing. As the transcriptional complex moves along the DNA template extending the RNA chain, a region of local unwinding moves with it. Termination of transcription involves the ability of RNA polymerase II to recognize the sequences that indicate that the end of the gene has arrived and no further bases should be added to the RNA chain. 

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