Hairpin loop mismatch

NMR studies of RNA have greatly benefited from isotope labelling which allows the introduction of C-13 and N-15. A method to generate isotope-labelled DNA for NMR studies has been described.The structure of a series of RNA hairpin loops containing the GNRA consensus sequence has been studied by NMR. The structure of a duplex containing GU mismatches has also been determined. 

Similar to RNA, secondary structure elements of DNA (duplexes, hairpin loops, bulges, mismatches, junctions, and abasic sites) have been identified and characterized by CW EPR methods by several research groups, using both rigid and flexible spin labels [92-94]. 

Figure 7.10. [A) An unlabeled stem-loop structure immobilized on gold electrode opens up in the presence of target DNA, forming a film of matched and mismatched ds-DNA, respectively. (B) Nyquist plots shows in the increase in the chaise transfer resistance of the DNA film after hybridization Ra of hairpin (a], mismatched duplex (b) and matched duplex (c]. Inset shows the modified Randle s equivalent circuit used to fit the electrochemical data. (C] Relationship between ARa and the concentration ofthe target strand showing sensitivity up to lOpM. Y. Wang, C. Li, X. Li, Y. Li, H.-B. Kraatz, Anal. Chem., 2008, 80, 2255-2260. Copyright 2008 American Chemical Society.

Hairpin Loops. The free energy of hairpins is based on the model of Serra and co-workers (16-18). In this model, hairpin stability for loops larger than three nucleotides is independent of sequence with the exception of the first mismatch and closing pair. The free energy for a hairpin loop, AG" l. is ... 

Table I. Stability of Closing Base pair and First Mismatch in Hairpin Loops.

Although it is usual for DNA to rely on helical twists to coil it around there are other mechanisms by which the direction of the duplex can be radically altered. The simplest occurs when one or more bases insert into an otherwise complementary pair of strands. Assuming that all the other bases pair up, this leaves a small loop, or bulge, where the unpaired bases reside. A more extensive internal loop forms when both strands are mismatched in the same region. Hairpins are formed when a self-complementary single strand of DNA folds back on itself to form a duplex. A loop due to unpaired bases remains at the point where the strand reverses. 

The hairpin-DNA transporter (Table 24.1) was 30 bases long (30-mer) and contained a thiol substituent at the 5 end that allowed it to be covalently attached to the inside walls of the Au nanotubes [6]. The first six bases at each end of this molecule are complimentary to each other and form the stem of the hairpin, and the middle 18 bases form the loop (Table 24.1). The permeating DNA molecules were 18-mers that are either perfectly complementary to the bases in the loop, or contain one or more mismatches with the loop (Table 24.1). A second thiol-terminated DNA transporter was investigated (Table 24.1). This DNA transporter was also a 30-mer, and the 18 bases in the middle of the strand were identical to the 18 bases in the loop of the hairpin-DNA transporter. However, this second DNA transporter does not have the complementary stem-forming bases on either end and thus cannot form a hairpin. This linear-DNA transporter was used to test the hypothesis that the hairpin-DNA... 

A nanopore instrument, which can discriminate between individual DNA hairpins that differ by one base pair or one nucleotide, has been demonstrated. RNA and DNA strands produce ionic current signatures when driven through an alpha-hemolysin channel by an applied voltage. This nanopore detector was combined with a support vector machine (S VM) to analyze DNA hairpin molecules on the millisecond time scale. Measurable properties include duplex stem length, base pair mismatches, and loop length. ... 

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