Helix-Slipping - Revision history

Dajordan at 19:28, 8 December 2007

2007-12-08T19:28:13Z

Dajordan at 21:53, 6 December 2007

2007-12-06T21:53:35Z

Dajordan at 21:53, 6 December 2007

2007-12-06T21:53:14Z

Dajordan at 21:49, 6 December 2007

2007-12-06T21:49:42Z

Dajordan at 21:48, 6 December 2007

2007-12-06T21:48:19Z

Dajordan at 21:47, 6 December 2007

2007-12-06T21:47:06Z

Dajordan at 21:35, 6 December 2007

2007-12-06T21:35:46Z

Dajordan: /* Links */

2007-12-06T18:08:28Z

‎Links

Dajordan at 12:09, 20 November 2007

2007-11-20T12:09:22Z

Dajordan at 12:09, 20 November 2007

2007-11-20T12:09:05Z

← Older revision		Revision as of 19:28, 8 December 2007
Line 1:		Line 1:
−	Helix-slipping uses a sequence that forms an imperfectly paired double-stranded stem that is flexible in its nucleotide base-pairing through a "slip-structure" mechanism. It does not allow for rational design and results in disruption or restoration of the hammerhead ribozyme in response to changes in the aptamer.	+	Helix-slipping uses a sequence that forms an imperfectly paired double-stranded stem that is flexible in its nucleotide base-pairing through a "slip-structure" mechanism (Win and Smolke, 2007). It does not allow for rational design and results in disruption or restoration of the hammerhead ribozyme in response to changes in the aptamer.
	Helix-slipping only results in OFF switches due to this lack of rational design. However, it works in much the same way that the ON switch does in strand-displacement because when the ligand binds to the aptamer, the catalytic core is restored and the ribozyme can self-cleave, preventing gene expression (Figure 4A). In addition, because helix-slipping uses random aptamers created by directed evolution, the level of repression can vary from aptamer to aptamer (Figure 4B).		Helix-slipping only results in OFF switches due to this lack of rational design. However, it works in much the same way that the ON switch does in strand-displacement because when the ligand binds to the aptamer, the catalytic core is restored and the ribozyme can self-cleave, preventing gene expression (Figure 4A). In addition, because helix-slipping uses random aptamers created by directed evolution, the level of repression can vary from aptamer to aptamer (Figure 4B).

@@ Line 1: / Line 1: @@
 Helix-slipping uses a sequence that forms an imperfectly paired double-stranded stem that is flexible in its nucleotide base-pairing through a "slip-structure" mechanism. It does not allow for rational design and results in disruption or restoration of the hammerhead ribozyme in response to changes in the aptamer.
-Helix-slipping only results in OFF switches due to this lack of rational design. However, it works in much the same way that the ON switch does in strand-displacement because when the ligand binds to the aptamer, the catalytic core is restored and the ribozyme can self-cleave, preventing gene expression (Figure 4A). In addition, because helix-slipping uses random aptamers created by [[Directed evolution]], the level of repression can vary from aptamer to aptamer (Figure 4B).
+Helix-slipping only results in OFF switches due to this lack of rational design. However, it works in much the same way that the ON switch does in strand-displacement because when the ligand binds to the aptamer, the catalytic core is restored and the ribozyme can self-cleave, preventing gene expression (Figure 4A). In addition, because helix-slipping uses random aptamers created by directed evolution, the level of repression can vary from aptamer to aptamer (Figure 4B).
 http://www.pnas.org/content/vol104/issue36/images/large/zpq0340773700003.jpeg

@@ Line 1: / Line 1: @@
 Helix-slipping uses a sequence that forms an imperfectly paired double-stranded stem that is flexible in its nucleotide base-pairing through a "slip-structure" mechanism. It does not allow for rational design and results in disruption or restoration of the hammerhead ribozyme in response to changes in the aptamer.
-Helix-slipping only results in OFF switches due to this lack of rational design.
+Helix-slipping only results in OFF switches due to this lack of rational design. However, it works in much the same way that the ON switch does in strand-displacement because when the ligand binds to the aptamer, the catalytic core is restored and the ribozyme can self-cleave, preventing gene expression (Figure 4A). In addition, because helix-slipping uses random aptamers created by [[Directed evolution]], the level of repression can vary from aptamer to aptamer (Figure 4B).
 http://www.pnas.org/content/vol104/issue36/images/large/zpq0340773700003.jpeg

@@ Line 1: / Line 1: @@
 Helix-slipping uses a sequence that forms an imperfectly paired double-stranded stem that is flexible in its nucleotide base-pairing through a "slip-structure" mechanism. It does not allow for rational design and results in disruption or restoration of the hammerhead ribozyme in response to changes in the aptamer.
-Helix-slipping only results in ON switches.
+Helix-slipping only results in OFF switches due to this lack of rational design.
 http://www.pnas.org/content/vol104/issue36/images/large/zpq0340773700003.jpeg

@@ Line 4: / Line 4: @@
 http://www.pnas.org/content/vol104/issue36/images/large/zpq0340773700003.jpeg
-Figure 4. "Regulatory properties of the strand-displacement information transmission mechanism. The color scheme corresponds to that used in Fig. 1 with the following exceptions: switching strand, red; competing strand, green. (A) Gene expression ON ribozyme switch platform, L2bulge1. (B) Gene expression OFF ribozyme switch platform, L2bulgeOff1. (C and D) The theophylline-dependent gene-regulatory behavior of L2bulge1 (ON switch) (C), L2bulgeOff1 (OFF switch) (D), and L2Theo (nonswitch control). Gene-expression levels are reported in fold as defined in SI Text and were normalized to the expression levels in the absence of effector." (Win and Smolke, 2007). ''Image Permission Pending.''
+Figure 4. "Regulatory properties of the helix-slipping information transmission mechanism. The color scheme corresponds to that used in Fig. 1 with the following exception: communication module sequence, orange. (A) Gene expression OFF ribozyme switch platform based on helix slipping, L2cm4. The base stem of the aptamer was replaced with a communication module. (B) Regulatory activities of helix-slipping-based ribozyme switches. Gene-regulatory effects of the OFF switches at 5 mM theophylline are reported in fold repression relative to expression levels in the absence of effector. The corresponding communication module sequences are indicated. Gene expression levels are reported as described in Fig. 2." (Win and Smolke, 2007). ''Image Permission Pending.''
 == Links ==

← Older revision		Revision as of 21:35, 6 December 2007
Line 3:		Line 3:

	http://www.pnas.org/content/vol104/issue36/images/large/zpq0340773700003.jpeg		http://www.pnas.org/content/vol104/issue36/images/large/zpq0340773700003.jpeg
		+
		+	Figure 4. "Regulatory properties of the strand-displacement information transmission mechanism. The color scheme corresponds to that used in Fig. 1 with the following exceptions: switching strand, red; competing strand, green. (A) Gene expression ON ribozyme switch platform, L2bulge1. (B) Gene expression OFF ribozyme switch platform, L2bulgeOff1. (C and D) The theophylline-dependent gene-regulatory behavior of L2bulge1 (ON switch) (C), L2bulgeOff1 (OFF switch) (D), and L2Theo (nonswitch control). Gene-expression levels are reported in fold as defined in SI Text and were normalized to the expression levels in the absence of effector." (Win and Smolke, 2007). ''Image Permission Pending.''

	== Links ==		== Links ==

← Older revision		Revision as of 18:08, 6 December 2007
Line 7:		Line 7:
	[[Ribozyme Switch]]		[[Ribozyme Switch]]

−	[~~[Applications of Ribozymes in Synthetic Systems~~ - ~~Danielle Jordan]~~]	+	== '''[http://gcat.davidson.edu/GcatWiki/index.php/Applications_of_Ribozymes_in_Synthetic_Systems_-_Danielle_Jordan Main Page]''' ==

← Older revision		Revision as of 12:09, 20 November 2007
Line 1:		Line 1:
	Helix-slipping uses a sequence that forms an imperfectly paired double-stranded stem that is flexible in its nucleotide base-pairing through a "slip-structure" mechanism. It does not allow for rational design and results in disruption or restoration of the hammerhead ribozyme in response to changes in the aptamer.		Helix-slipping uses a sequence that forms an imperfectly paired double-stranded stem that is flexible in its nucleotide base-pairing through a "slip-structure" mechanism. It does not allow for rational design and results in disruption or restoration of the hammerhead ribozyme in response to changes in the aptamer.
		+

	http://www.pnas.org/content/vol104/issue36/images/large/zpq0340773700003.jpeg		http://www.pnas.org/content/vol104/issue36/images/large/zpq0340773700003.jpeg