Base-paired hairpin

RNA polymerase proceeds along the DNA template, transcribing one of its strands until it reaches a terminator sequence. This sequence encodes a termination signal, which in E. coli is a base-paired hairpin on the newly synthesized RNA molecule (Figure 5.28). This hairpin is formed by base pairing of self-complementary sequences that are rich in G and C. Nascent RNA spontaneously dissociates from RNA polymerase when this hairpin is followed by a string of U residues. 

Weyermann, P. and P.B. Dervan. Recognition of ten base pairs of DNA by head-to-head hairpin dimers. J. Am. 

Figure 35-7. Diagrammatic representation of the secondary structure of a single-stranded RNA molecule in which a stem loop, or "hairpin," has been formed and is dependent upon the intramolecular base pairing. Note that A forms hydrogen bonds with U in RNA.

Rho-dependent transcription termination signals in E coll also appear to have a distinct consensus sequence, as shown in Figure 37—6. The conserved consensus sequence, which is about 40 nucleotide pairs in length, can be seen to contain a hyphenated or interrupted inverted repeat followed by a series of AT base pairs. As transcription proceeds through the hyphenated, inverted repeat, the generated transcript can form the intramolecular hairpin structure, also depicted in Figure 37-6. 

Figure 37-6. The predominant bacterial transcription termination signal contains an inverted, hyphenated repeat (the two boxed areas) followed by a stretch of AT base pairs (top figure). The inverted repeat, when transcribed into RNA, can generate the secondary structure in the RNA transcript shown at the bottom of the figure. Formation of this RNA hairpin causes RNA polymerase to pause and subsequently the p termination factor interacts with the paused polymerase and somehow induces chain termination.

Hairpin A double-helical stretch formed by base pairing between neighboring complementary se-... 

Letsinger and Wu [24] also made the seminal observation that Sa-linked hairpins possessing polyT and polyA arms are strongly fluorescent, whereas the Sa fluorescence is strongly quenched by a neighboring G C base pair. 

The dynamics of photoinduced charge separation, kcs, and charge recombination, kcr (Fig. 2a), have been studied in several families of hairpins containing an Sa linker and a single G C base pair by means of femtosecond time-resolved transient absorption spectroscopy [27, 28]. Both the singlet state and anion radical of Sa have strong transient absorption centered at 575 nm. The difference in the independently determined band shapes for Sa ... 

Values of kcs and kcr for a family of hairpins containing a single G C base pair separated from Sa by one-to-four A T base pairs are summarized in... 

Fig. 4 Free energy dependence of the rate constants for charge separation and charge recombination for hairpins in which two A T base pairs separate the linker acceptor from the nucleobase donor. The dashed line is a fit of the charge separation data to the Marcus-Levitch-Jortner equation...

St /G AG-0.14 V fluorescence quenching stilbene radical anion detected in transient absorption no Gs near injection site or in intervening sequence k = 1012-108 s 1 for 0-4 intervening A-T base-pairs (-3.4-17 A) exponential distance dependence of CT rate constant (3 0.6-0.7 A"1 small variations in k depending on whether G is in the A or T arm of the hairpin... 

---