Strands sense

Fig. 6. Metal-crosslinking in antisense and antigene technology. The recognition of the target (sense) strand by the antisense strand is rapid and is followed by a slower irreversible metal crosslinking. 

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. 

In addition to the known transcript (APOE SI) that translates into APOE, there are three additional transcripts in mice. Two of these transcripts, APOE S2 and APOE S3, which are predicted to be TM proteins, are transcribed from the sense strand. APOE SI is transcribed from the antisense strand and is complementary to exon 4 of APOE... 

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.)... 

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. 

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. 

Structural studies on Ago proteins revealed that the so-called MID domain binds the 5 end of the guide strand (39,40). Because of its central localization in the Ago protein, this domain has been named MID domain. Crystal co-structures and Kj measurements of the MID domain in combination with all four nucleotides at the 5 end revealed that uridine (U) binds with the highest affinity to the MID domain, adenosine (A) with a slightly reduced affinity, and cytosine (C) and guanosine (G) with more than tenfold less affinity (41). Therefore, siRNA guide (antisense) strands should ideally contain a U or A at the 5 end. C and G should be avoided. For the passenger (sense) strand 5 end, C and G should be selected in order to minimize strand incorporation (Fig. la). Based on our own unpublished data the nucleotide specificity is not only a tool to manipulate strand selection but siRNA strands with U or A at the 5 end show also a higher absolute affinity for Ago proteins and therefore are more likely to be potent siRNAs (see Notes 2 and 3). 

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. 

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). 

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. 

RNA polymerases, enzymes that are able to read the base pair information written in the DNA sequence. RNA polymerases use one strand of double-stranded DNA as a template to create the anti-sense strand represented by the developing RNA molecule. 

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.)...

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. 

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. ... 

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