Nontemplate strand

The two complementary DNA strands have different roles in transcription. The strand that serves as template for RNA synthesis is called the template strand. The DNA strand complementary to the template, the nontemplate strand, or coding strand, is identical in base sequence to the RNA transcribed from the gene,... 

FIGURE 26-2 Template and nontemplate (coding) DNA strands. The two complementary strands of DNA are defined by their function in transcription. The RNA transcript is synthesized on the template strand and is identical in sequence (with U in place ofT) to the nontemplate strand, or coding strand. 

FIGURE 26-5 Typical E. coli promoters recognized by an RNA polymerase holoenzyme containing a70. Sequences of the nontemplate strand are shown, read in the 5 —>3 direction, as is the convention for representations of this kind. The sequences vary from one promoter to the next, but comparisons of many promoters reveal similarities, particularly in the —10 and -35 regions. The sequence element UP, not present in all E. coli promoters, is shown in the P1 promoter for the highly expressed rRNA gene rrnB. UP elements, generally occur-... 

Diverse Functions of TFIIH In eukaryotes, the repair of damaged DNA (see Table 25-5) is more efficient within genes that are actively being transcribed than for other damaged DNA, and the template strand is repaired somewhat more efficiently than the nontemplate strand. These remarkable observations are explained by the alternative roles of the TFIIH subunits. Not only does TFIIH participate in the formation of the closed complex during assembly of a transcription complex (as described above), but some of its subunits are also essential components of the separate nucleotide-excision repair complex (see Fig. 25-24). 

Coding versus Template Strands The RNA genome of phage Q/3 is the nontemplate or coding strand, and when introduced into the cell it functions as an mRNA. Suppose the RNA replicase of phage Q/3 synthesized primarily template-strand RNA and uniquely incorporated this, rather than nontemplate strands, into the viral particles. What would be the fate of the template strands when they entered a new cell What enzyme would such a template-strand virus need to include in the viral particles for successful invasion of a host cell ... 

Figure 11.7 Structure of a transcribing RNA Pol II stalled at a CPD lesion, (a) RNA Pol II (gray) is shown with a template strand (dark blue), nontemplate strand (light blue), and growing mRNA strand (yellow). The translocation of the CPD lesion (red) on the template strand into the active site (active site metal is shown in magenta) is blocked by the bridge helix (purple). Tyr836,...

P.W. (1995) T7 RNA polymerase bypass of large gaps on the template strand reveals a ditical role of the nontemplate strand in elongation. Cell, 82, 577-585. 

Since RNA synthesis uses only one of the two strands of DNA for a template, it is important to identify which strand is being "read." By convention, the template strand has the complementary sequence of the RNA product (with the exception of thymine in place of uracil) and the nontemplate strand has the same sequence as the RNA. The nontemplate strand is also called the coding strand because the sequence of this strand can be used to decipher the primary amino-acid sequence of an encoded protein (see Chapter 26). 

FIGURE 2 Footp rinting results of RNA polymerase binding to the lac promoter (see Fig. 26-5). In this experiment, the 5 end of the nontemplate strand was radioactively labeled. Lane C is a control in which the labeled DNA fragments were cleaved with a chemical reagent that produces a more uniform banding pattern. 

Double-stranded DNA consists of a coding strand and a template strand (Fig. 14.3) The DNA template strand is the strand that is actually used by RNA polymerase during the process of transcription. It is complementary and antiparallel both to the coding (nontemplate) strand of the DNA and to the RNA transcript produced from the template. Thus, the coding strand of the DNA is identical in base sequence and direction to the RNA b anscript, except, of course, that wherever this DNA strand contains a T, the RNA transcript contains a U. By convention, the... 

The strand that the RNA polymerase uses as a template for its RNA is called the template strand, the noncoding strand, the antisense strand, and the (-) strand. The other strand, whose sequence matches the RNA produced except for the T-U change, is called the nontemplate strand, the coding strand, the sense strand, and the (+) strand. 

See Figure 11.1. The top DNA strand is the nontemplate strand because it is not used to create the RNA. It is called the coding strand because it has the same sequence as the RNA produced, except for the change of T for U. It is called the sense strand because its sequence would give the correct... 

Because the Pol II core alone is sufficient to maintain the transcription bubble and the DNA-RNA hybrid during RNA chain elongation, there must be exposed elements on the enzyme surface that keep the nucleic acid strands apart. Protein elements are needed to separate the DNA strands downstream of the active site and to separate the RNA from the DNA template strand at the upstream end of the hybrid. On the basis of their location with respect to nucleic acids, several Pol II structural elements are predicted to maintain the bubble and the hybrid. These proposals are currently tested by site-directed mutagenesis. Separation of the DNA strands at the downstream edge of the bubble may be attributed to binding of the DNA template strand by switch regions 1 and 2 and to blocking of the path of the nontemplate strand by fork loop 2. In the Pol II-TFIIS complex structure, fork loop 2 is ordered and restricts the cleft to a diameter of 15 A, consistent with the proposal that this loop removes the DNA nontemplate strand from the template strand before the active site. 

Ramiro, A. R., Stavropoulos, P., Jankovic, M., and Nussenzweig, M. C. (2003). Transcription enhances AID-mediated cytidine deamination by exposing single-stranded DNA on the nontemplate strand. Nat. Immunol. 4, 452-456. 

The transcription on dsDNA template is arrested when T7 RNA Pol encounters modified bases, e.g., psoralen adduct or cyclobutane pyrimidine dimer, on the template strand but not on the nontemplate strand (19). 

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