DNA Stem-Loops

The charger transfer resistance f ct for electron transfer from 

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Figure 5 Cross-peaks in homonuclear 2D TOCSY spectra arising due to ROESY effects. Clean TOCSY spectra were acquired with the MLEV-17 spin-lock sequence, (a) Base proton H6-to-methyl correlations in a 27-nt AT-rich DNA stem-loop structure 93 the spectrum was recorded with the 50-ms mixing sequence, (b) and (c) TOCSY spectra acquired for a 31 -nt stem-loop RNA (unpublished data), (b) H5-H6 cross-peaks in pyrimidines and a H1 -H8 cross-peak (boxed) in the syn guanine from the tetraloop UACG the spectrum was recorded with the 30-ms mixing sequence, (c) Sequential H2 -H6/H8 cross-peaks the spectrum was recorded with the 90-ms mixing sequence.

Figure 10 Portions of NOESY spectra and 1D slices through the frequencies of aromatic protons, (a) A 150-ms 2D NOESY spectrum of a 27-nt DNA stem-loop 93 a slice through the frequency of A5H8 is shown, (b) A 200-ms 2D NOESY spectrum of a 34-nt RNA stem-loop 68 a slice through the frequency of C7H6 is shown. Assignments of H5 and H5" protons are tentative. Note that some of the cross-peaks partially overlap with cross-peaks in another slice through the frequency of A8H2. (c) A 150-ms 3D 13C-edited NOESY-HMQC spectrum of the same molecule shown in (b). A slice of the proton and carbon frequencies of H6 and C6 in residue C7 are shown. Note a significantly lower digital resolution in the indirect uj2 dimension in this spectrum compared to the indirect u1 dimension in the 2D NOESY spectrum shown in (b).

The direct detection of DNA via conformational changes of ferrocene-conjugated DNA stem-loop (or hair-pin) structure onto electrode surface induced by the hybridization was also proposed (Fig. 11.1c) [4, 20]. The conformational change induces the displacement of ferrocene molecules from the electrode surface, resulting in a drop in peak redox current measured by cyclic voltametry. The detection limits were 115 fM for 24-base oligonucleotide [20] and 10 pM for 17-base oligonucleotide [4], respectively. Furthermore, the difference between... 

While RNA molecules do not have the double stranded structure usually found in DNA, in many RNA molecules stem-loop structures are found in which the anti-parallel strands are connected by a 5-7 residue loop. Rather like the P-tum in proteins, this allows the... 

The broad peaks B, D, and E are shifted far upfield by reaction with bisulfite (Eq. 5-11) suggesting that they are not hydrogen bonded and are present in the loop of the stem-loop structure. Peaks A, E, F, and G correspond to resonances 64, 7, 67, and 4, respectively, in (A) and represent fluorouracil in the stem structure. From Chu et al.69i Courtesy of Jack Horowitz. (C) A 31P NMR spectrum of a synthetic 14 base-pair DNA segment related to the E. coli lac operator. The palindromic sequence is TCTGAGCGCTCAGA. The numbers refer to the positions from the 5 end. From Schroeder et al.688... 

Figure 7.2 Enzymes acting on DNA breaks. FEN-1, 3 -exonuclease (3 -Exo.), DNA polymerases (DNA pol.) and DNA ligases act on single-strand DNA breaks (SSB). Double-strand DNA breaks (DSB) are also susceptible to FEN-1 and 3 -Exo. PARP-1 is capable of binding to SSB and DSB. In addition, PARP-1 has a binding affinity for RNA stem-loops.

Historically, attenuation was discovered when it was noticed that deletion of a short sequence of DNA between the operator and the first structural gene, trpE, increased the level of transcription. This region was named the attenuator (see Fig. 1) and is the DNA that encodes that part of the leader sequence that forms the transcription terminator stem-loop. 

DNA can be construed as a modification of RNA, and the results of similar selections that start from either a DNA or an RNA pool are informative. Aptamers against reverse transcriptase selected from RNA pools [49] have different sequences and structures compared to those selected from DNA pools [50] the same is true for aptamers against ATP [13,51], The DNA aptamer against thrombin forms a G-quartet [12], whereas the RNA aptamer is predicted to form a stem-loop structure [52],... 

A ribosome display construct (the library in the ribosome display format) can be prepared completely in vitro either by ligation of the DNA library to the spacer region or by assembly PCR of the DNA library and the spacer. All the above-mentioned features, which are important for ribosome display (T7 promoter, ribosome binding site, and stem-loop structure), are then introduced by PCR (Fig. 3). 

Figure 5.19. Stem-Loop Structures. Stem-loop structures may be formed from single-stranded DNA and RNA molecules.

The inverted repeat may be a binding site for a dimeric DNA-binding protein or it may correspond to a stem-loop structure in the encoded RNA. 

Two structures incorporating modified nucleotides include the co-crystal structure of pseudouridine synthase TruB with a T stem-loop of tRNA in which the modification site (U55) is modified with 5-fluorouridine, " and the crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to DNA containing an abasic site. " ... 

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