Self-hairpinning

Rajagopal K, Ozbas B, Pochan DJ et al (2005) Self-assembled hydrogels from beta- hairpin peptides tuning responsiveness and bulk material properties by peptide design. Biopolymers 80 487 87... 

Kretsinger JK, Haines LA, Ozbas B et al (2005) Cytocompatibility of self-assembled ss-hairpin peptide hydrogel surfaces. Biomaterials 26 5177-5186... 

Yucel T, Micklitsch CM, Schneider JP et al (2008) Direct observation of early-time hydrogelation in beta-hairpin peptide self-assembly. Macromolecules 41 5763-5772... 

Rajagopal K, Lamm MS, Haines-Butterick LA et al (2009) Tuning the ph responsiveness of beta-hairpin peptide folding, self-assembly, and hydrogel material formation. Biomacromolecules 10 2619-2625... 

Hule RA, Nagarkar RP, Altunbas A et al (2008) Correlations between structure, material properties and bioproperties in self-assembled beta-hairpin peptide hydrogels. Faraday Discuss 139 251-264... 

Fig. 4. The self-cleaving hairpin motif from the satellite RNA of tobacco ringspot virus (sTobRV). The arrow indicates the cleavage site. The numbers in brackets indicate the nucleotide positions within the sTobRV satellite RNA...

Schneider and Pochan (2002) have described a different system of peptides with alternating polar and hydrophobic residues composed of Val as an amino acid with high -sheet forming propensity and Lys as a modulator of pH-dependent self-assembly. Self-assembly was designed to be triggered by intramolecular folding into a /3-hairpin structure based on the stereochemistry of central Pro residues (Fig. 14.8). 

Figure 14.8 (Left) Primary sequence of peptide MAXI with /8-hairpin promoted intramolecular folding, leading to the reversible formation of self-assembled /8-sheets. (Right) Cryo-TEM image of self-assembled peptide scaffolds. Scale bar = 200 nm. Reprinted from Schneider et al. (2002). Copyright 2002 American Chemical Society.

Figure 14.8 (Left) Primary sequence of peptide MAXI with /3-hairpin promoted intramolecular folding, leading to the reversible formation of self-assembled...

Krishnan-Ghosh Y, Balasubramanian S (2003) Dynamic covalent chemistry on self-templating peptides formation of a disulfide-linked -hairpin mimic. Angew Chem Int Ed 42 2171-2173... 

The bending observed with this and other sequences may be important in the binding of some proteins to DNA A rather common type of DNA sequence is a palindrome. A palindrome is a word, phrase, or sentence that is spelled identically read either forward or backward two examples are ROTATOR and NURSES RUN. The term is applied to regions of DNA with inverted repeats of base sequence having twofold symmetry over two strands of DNA (Fig. 8-20). Such sequences are self-complementary within each strand and therefore have the potential to form hairpin or cruciform (cross-shaped) structures (Fig. 8-21). When the inverted repeat occurs within each individual strand of the DNA, the sequence is called a mirror repeat. Mrror repeats do not have complementary sequences within the same strand and cannot form hairpin or cruciform structures. Sequences of these types are found... 

Most p-independent terminators have two distinguishing features. The first is a region that produces an RNA transcript with self-complementary sequences, permitting the formation of a hairpin structure (see Fig. 8-2la) centered 15 to 20 nucleotides before the projected end of the RNA strand. The second feature is a highly conserved string of three A residues in the template strand that are transcribed into U residues near the 3 end of the hairpin. When a polymerase arrives at a termination site with this structure, it pauses (Fig. 26-7). Formation of the hairpin structure in the RNA disrupts several A=U base pairs in the RNA-DNA hybrid segment and may disrupt important interactions... 

Smaller self-cleaving RNAs have been found among plant viruses and viroids. Many of them have a common catalytic core which can be converted into 30- to 40-nucleotide ribozymes. Only 17 nucleotides and three hydrogen-bonded helical stems are required to form the self-cleaving "hammerhead" domain, which has a structural similarity to the catalytic core of the Tetrahymena ribozyme. The hammerhead ribozymes (Fig. 12-27) represent one form of small ribozyme.793-797 Another is the hairpin ribozyme shown in Fig. 

Fig. 33 Various types of colloid DNA-mediated interactions, either conventional or self-protected - switched off - through intra-particle hybridization, (a, b) Normal, hairpin-free pair of complementary sticky ends, either grafted to separate beads (a) or mixed on the same bead (b). (c, d) Self-complementary sticky ends. Besides self-protective loops as in (b), this sequence can form two hairpin structures the sticky end sequence can fold on itself (1), or it can bind to the backbone (2). (e, f) As in (a), but each of the sticky ends can fold into a protective hairpin. Adapted with permission from [140]...

Fig. 34 Kinetics of association and dissociation for conventional and self-protected interactions, (a) Conventional scheme (Fig. 33a). Red lines and right axis represent temperature as a function of the elapsed time, while symbols and the left axis are the corresponding particle singlet fraction at fast (blue) or slow black) temperature quench. The insets show microscopy images of isolated or aggregated particles, (b) Self-protected scheme (Fig. 33c). Particle singlet fraction as a function of time at fixed temperature profile (red line), but at different overall particle concentrations for dilute colloids, intra-particle hybridization prevents aggregation, while at higher c the interparticle diffusion competes with hairpin formation. Adapted with permission from [140]...

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