DNA hairpin loops

Mao, Y., Luo, C., Ouyang, Q. (2003). Studies of temperature-dependent electronic transduction on DNA hairpin loop sensor. Nucleic Acids Res 31, el08. 

Bormet, G, Krichevsky, O, and Libchalter, A, Kinetics of conformational fluctuations in DNA hairpin-loops. Proceedings of the National Academy of Sciences of the United States of America 95(1998)8602-8606. 

Wallace, MI, Ying, LM, Balasubramanian, S, and Klenerman, D, Fret fluctuation spectroscopy Exploring the conformational dynamics of a DNA hairpin loop. Journal of Physical Chemistry B104 (2000) 11551-11555. 

Ying, LM, Wallace, MI, and Klenerman, D, Two-state model of conformational fluctuation in a DNA hairpin- loop. Chemical Physics Letters 334 (2001) 145-150. 

Figure 5.1 Sketch of the DNA molecular beacon. The five bases at the two ends of the beacon are complementary to each other. The size of the loop and its content are varied. The beacon flips between open and closed states with the characteristic rates and k+.Thefluorophore(F)and the quencher (Q) are covalently linked to the two arms of the beacon. In the open state the beacon fluoresces, in the closed state the fluorescence is quenched. Reprinted with permission from Bonnet etal., Kinetics of conformational fluctuations in DNA hairpin-loops. Proceedings of the National Academy of Sciences of the United States of America 95 (1998) 8602-8606. Copyright 1998 NationalAcademy of Sciences, USA.

In this manner, the kinetics of the two-state system were determined and are shown in Figure 5.2. Figure 5.2(a) shows the autocorrelation of the fluorescence for the 6G labelled DNA hairpin loop and the control sample, which in this case was a DNA hairpin loop with a 6G label and no quencher. The 6G fluorescence is assumed to be unaffected by the dynamics of the DNA in the control sample. Similarly, the difference in diffusion properties for this moderately lower mass molecule is assumed negligible in the control. The ratio of the two curves in... 

In 2009, Hansen et al. have proposed another DTS-based library synthesis approach, in which three-way DNA hairpin-looped Junctions assist the library... 

Increments were calculated at 1 M NaCl, except for DNA internal loops which are calculated at 0.5 M NaQ and DNA hairpin loops which arc calculated at 0.2 M NaCI. 

Kannan, S., Zacharias, M. (2007a). Folding of a DNA Hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulations. Biophysical Journal, 93, 3218. 

Rho-independent termination occurs when the newly formed RNA folds back on itself to form a GC-rich hairpin loop closely followed by 6-8 U residues. These two structural features of the newly synthesized RNA promote dissociation of the RNA from the DNA template. This is the type of terminator shown in Figure 1-3-4. 

UG pairs provide a very small amount of stabilization to an RNA double helix, while the presence of unpaired bases has a destabilizing effect. The most stable hairpin loops contain four or five bases. Depending upon whether the loop is "closed" by CG or AU, the helix is destabilized by 20-30 kj/mol. "Bulge loops," which protrude from one side of a helix, have a smaller destabilizing effect. An example of the way in which Table 5-2 can be used to estimate the energies of formation of a loop in a straight-chain RNA is illustrated in Fig. 5-9. Similar analysis of base pairing in DNA can also be done.53 55... 

A few recent NMR investigations of polynucleotides include studies of triple-helical DNA,689 Holliday junctions,290 double-stranded oligonucleotides containing adducts of carcinogens,690 691 of hairpin loops with sheared A A and G G pairs,692 and of proton exchange in both imino and amino groups.693... 

To place a dye at internal positions without breaking the RNA backbone, the Pan lab developed a method that involves replacing nonessential hairpin loops within RNA sequences with larger loops with specific sequences that are hybridized to labeled DNA oligos (Smith et al., 2005). These modifications had little effect on structure, as assayed by chemical footprinting, or catalytic efficiency of the catalytic domain ofRNase P. The same method was successfully employed for studying ribosome dynamics (Dorywalska et al., 2005). 

The structures of RNA molecules consist of a single polymer chain of nucleotides with the same bases as DNA, with the exception of thymine, which is replaced by uracil, which forms a complementary base pair with adenine (Figure 1.33(a)). These chains often form single stranded hairpin loops separated by short sections of a distorted double helix formed by hydrogen bonded complementary base pairs (Figure 1.33(b)). 

M. McCullagh et al., Effect of loop distortion on the stability and structural dynamics of DNA hairpin and dumbbell conjugates. J. Phys. Chem. B 112, 11415-11421 (2008)... 

---