Team:OUC-China/Project/DesignMaking/Background
From 2012.igem.org
Zhangpeiran (Talk | contribs) |
|||
(18 intermediate revisions not shown) | |||
Line 8: | Line 8: | ||
<style> | <style> | ||
+ | #back-top { | ||
+ | position: fixed; | ||
+ | bottom: 60px; | ||
+ | margin-left: 1160px; | ||
+ | } | ||
+ | #back-top a { | ||
+ | width:85px; | ||
+ | display: block; | ||
+ | text-align: center; | ||
+ | font: 11px/100% Arial, Helvetica, sans-serif; | ||
+ | text-transform: uppercase; | ||
+ | text-decoration: none; | ||
+ | color: #bbb; | ||
+ | -webkit-transition: 1s; | ||
+ | -moz-transition: 1s; | ||
+ | transition: 1s; | ||
+ | } | ||
+ | #back-top a:hover { | ||
+ | color: #000; | ||
+ | } | ||
+ | #back-top span { | ||
+ | width: 85px; | ||
+ | height: 85px; | ||
+ | display: block; | ||
+ | margin-bottom: 7px; | ||
+ | background: #B9B7B7 url(https://static.igem.org/mediawiki/2012/5/5e/Ouc-2012-up-arrow.png) no-repeat center center; | ||
+ | -webkit-border-radius: 15px; | ||
+ | -moz-border-radius: 15px; | ||
+ | border-radius: 15px; | ||
+ | -webkit-transition: 1s; | ||
+ | -moz-transition: 1s; | ||
+ | transition: 1s; | ||
+ | } | ||
+ | #back-top a:hover span { | ||
+ | background-color: #777; | ||
+ | } | ||
+ | .mini-riboon{ | ||
+ | position: relative; | ||
+ | z-index:0; | ||
+ | left: 1001px; | ||
+ | top: 90px; | ||
+ | width: 106px; | ||
+ | height: 45px; | ||
+ | } | ||
*{ | *{ | ||
margin:0; | margin:0; | ||
Line 19: | Line 63: | ||
padding:0; | padding:0; | ||
margin:0; | margin:0; | ||
- | overflow-x: | + | overflow-x:auto; |
font: 500 12px/1.625 "Helvetica Neue", Helvetica, Arial, sans-serif; | font: 500 12px/1.625 "Helvetica Neue", Helvetica, Arial, sans-serif; | ||
+ | } | ||
+ | #top-section{ | ||
+ | width:99%; | ||
} | } | ||
#page{ | #page{ | ||
Line 139: | Line 186: | ||
text-align:center; | text-align:center; | ||
margin-top:25px; | margin-top:25px; | ||
- | margin-left: | + | margin-left:10px; |
+ | width:800px; | ||
} | } | ||
Line 149: | Line 197: | ||
margin-bottom:-10px; | margin-bottom:-10px; | ||
background-color:#1487DF; | background-color:#1487DF; | ||
- | border | + | border:none; |
- | + | padding-left:0; | |
- | + | padding-right:0; | |
} | } | ||
#footer a | #footer a | ||
Line 186: | Line 234: | ||
</div> | </div> | ||
<ul class="menu"> | <ul class="menu"> | ||
- | <li> <a href=" | + | <li> <a href="https://2012.igem.org/Team:OUC-China">Index</a> </li> |
- | <li> <a href=" | + | <li> <a href="https://2012.igem.org/Team:OUC-China/Project/Overview">Project</a> </li> |
- | <li> <a href=" | + | <li> <a href="https://2012.igem.org/Team:OUC-China/Modeling/Overview">Modeling</a> </li> |
- | <li> <a href=" | + | <li> <a href="https://2012.igem.org/Team:OUC-China/HumanPractice/Overview">Human Practice</a> </li> |
- | <li> <a href=" | + | <li> <a href="https://2012.igem.org/Team:OUC-China/Team/members">Team</a> </li> |
- | <li> <a href=" | + | <li> <a href="https://2012.igem.org/Team:OUC-China/Parts">Parts</a> </li> |
- | <li> <a href=" | + | <li> <a href="https://2012.igem.org/Team:OUC-China/Safety">Safety</a> </li> |
- | <li> <a href=" | + | <li> <a href="https://2012.igem.org/Team:OUC-China/labnote">Note</a> </li> |
</ul> | </ul> | ||
</div> | </div> | ||
Line 199: | Line 247: | ||
<ul class="submenu"> | <ul class="submenu"> | ||
<li> | <li> | ||
- | <a href=""> | + | <a href="https://2012.igem.org/Team:OUC-China"> |
- | <img src="" /> | + | <img src="https://static.igem.org/mediawiki/2012/a/af/Projectoverview.jpg" /> |
- | + | Home | |
</a> | </a> | ||
</li> | </li> | ||
<li> | <li> | ||
- | <a href=""> | + | <a href="https://2012.igem.org/Team:OUC-China#hmo"> |
- | <img src="" /> | + | <img src="https://static.igem.org/mediawiki/2012/4/49/Humanpracticeoverview.jpg" /> |
- | + | HumanPractice index | |
</a> | </a> | ||
</li> | </li> | ||
<li> | <li> | ||
- | <a href=""> | + | <a href="https://2012.igem.org/Team:OUC-China/Judgingform"> |
- | <img src="" /> | + | <img src="https://static.igem.org/mediawiki/2012/6/6e/Juding-form.jpg" /> |
- | + | JudgingForm | |
</a> | </a> | ||
</li> | </li> | ||
<li> | <li> | ||
- | <a href=""> | + | <a href="https://2012.igem.org/Team:OUC-China/contactus"> |
- | <img src="" /> | + | <img src="https://static.igem.org/mediawiki/2012/1/1e/Contact-us.jpg" /> |
+ | Contact Us | ||
+ | </a> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <ul class="submenu"> | ||
+ | <li> | ||
+ | <a href="https://2012.igem.org/Team:OUC-China/Project/Overview"> | ||
+ | <img src="https://static.igem.org/mediawiki/2012/5/59/Ouc-nav-project-overview.jpg" /> | ||
+ | Project Overview | ||
+ | </a> | ||
+ | </li> | ||
+ | <li> | ||
+ | <a href="https://2012.igem.org/Team:OUC-China/Project/Sensor/AbstractandBackground"> | ||
+ | <img src="https://static.igem.org/mediawiki/2012/1/15/Ouc-nav-project-secsor.jpg" /> | ||
+ | Sensor | ||
+ | </a> | ||
+ | </li> | ||
+ | <li> | ||
+ | <a href="https://2012.igem.org/Team:OUC-China/Project/DesignMaking/Abstract"> | ||
+ | <img src="https://static.igem.org/mediawiki/2012/3/34/Ouc-nav-device.jpg" /> | ||
+ | Decision-making Device | ||
+ | </a> | ||
+ | </li> | ||
+ | <li> | ||
+ | <a href="https://2012.igem.org/Team:OUC-China/Project/GVP/GasandBackground"> | ||
+ | <img src="https://static.igem.org/mediawiki/2012/5/57/Ouc-nav-project-gvp.jpg" /> | ||
+ | Gas vesicle | ||
</a> | </a> | ||
</li> | </li> | ||
Line 225: | Line 300: | ||
<ul class="submenu"> | <ul class="submenu"> | ||
<li> | <li> | ||
- | <a href=""> | + | <a href="https://2012.igem.org/Team:OUC-China/Modeling/ODEModel"> |
- | <img src="" /> | + | <img src="https://static.igem.org/mediawiki/2012/f/f6/Ouc-nav-modeling-ode.jpg" /> |
- | + | ODEModel | |
</a> | </a> | ||
</li> | </li> | ||
<li> | <li> | ||
- | <a href=""> | + | <a href="https://2012.igem.org/Team:OUC-China/Modeling/ParameterSensitivityAnalysis"> |
- | <img src="" /> | + | <img src="https://static.igem.org/mediawiki/2012/c/cf/Ouc-nav-modeling-sensertitive.jpg" /> |
- | + | Parameter Sensitivity Analysis | |
</a> | </a> | ||
</li> | </li> | ||
<li> | <li> | ||
- | <a href=""> | + | <a href="https://2012.igem.org/Team:OUC-China/Modeling/ParameterSweep"> |
- | <img src="" /> | + | <img src="https://static.igem.org/mediawiki/2012/0/07/Ouc-nav-modeling-sweep.jpg" /> |
- | + | Parameter Sweep | |
</a> | </a> | ||
</li> | </li> | ||
<li> | <li> | ||
- | <a href=""> | + | <a href="https://2012.igem.org/Team:OUC-China/Modeling/NoiseAnalysis"> |
- | <img src="" /> | + | <img src="https://static.igem.org/mediawiki/2012/0/04/Ouc-nav-modeling-noise.jpg" /> |
- | + | Noise Analysis | |
</a> | </a> | ||
</li> | </li> | ||
Line 251: | Line 326: | ||
<ul class="submenu"> | <ul class="submenu"> | ||
<li> | <li> | ||
- | <a href=""> | + | <a href="https://2012.igem.org/Team:OUC-China/HumanPractice/Overview"> |
- | <img src="" /> | + | <img src="https://static.igem.org/mediawiki/2012/6/61/Ouc-nav-humanoverview.jpg" /> |
- | + | HumanPractice Overview | |
</a> | </a> | ||
</li> | </li> | ||
<li> | <li> | ||
- | <a href=""> | + | <a href="https://2012.igem.org/Team:OUC-China/HumanPractice/Communication"> |
- | <img src="" /> | + | <img src="https://static.igem.org/mediawiki/2012/c/cc/Ouc-nav-Communication.jpg" /> |
- | + | Meeting and Academic Communication | |
</a> | </a> | ||
</li> | </li> | ||
<li> | <li> | ||
- | <a href=""> | + | <a href="https://2012.igem.org/Team:OUC-China/HumanPractice/Camps"> |
- | <img src="" /> | + | <img src="https://static.igem.org/mediawiki/2012/8/8d/Ouc-nav-humcamp.jpg" /> |
- | + | Camps, Class and Lectures | |
</a> | </a> | ||
</li> | </li> | ||
<li> | <li> | ||
- | <a href=""> | + | <a href="https://2012.igem.org/Team:OUC-China/HumanPractice/SpecialHM"> |
- | <img src="" /> | + | <img src="https://static.igem.org/mediawiki/2012/b/b7/Ouc-nav-hmspcial.jpg" /> |
- | + | Special HP | |
</a> | </a> | ||
</li> | </li> | ||
Line 277: | Line 352: | ||
<ul class="submenu"> | <ul class="submenu"> | ||
<li> | <li> | ||
- | <a href=""> | + | <a href="https://2012.igem.org/Team:OUC-China/Team/members"> |
- | <img src="" /> | + | <img src="https://static.igem.org/mediawiki/2012/6/6d/Ouc-nav-team.jpg" /> |
- | + | Team Members | |
</a> | </a> | ||
</li> | </li> | ||
<li> | <li> | ||
- | <a href=""> | + | <a href="https://2012.igem.org/Team:OUC-China/Team/instructor"> |
- | <img src="" /> | + | <img src="https://static.igem.org/mediawiki/2012/3/35/Ouc-nav-instructor.jpg" /> |
- | + | Instructors | |
</a> | </a> | ||
</li> | </li> | ||
<li> | <li> | ||
- | <a href=""> | + | <a href="https://2012.igem.org/Team:OUC-China/Team/AcknowledgementandCooperation"> |
- | <img src="" /> | + | <img src="https://static.igem.org/mediawiki/2012/a/a6/Ouc-nav-co.jpg" /> |
- | + | Acknowledgement&Cooperation | |
</a> | </a> | ||
</li> | </li> | ||
<li> | <li> | ||
- | <a href=""> | + | <a href="https://2012.igem.org/Team:OUC-China/Team/Lab"> |
- | <img src="" /> | + | <img src="https://static.igem.org/mediawiki/2012/a/a7/Ouc-nav-lab.jpg" /> |
- | + | Lab | |
+ | </a> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <ul class="submenu"> | ||
+ | <li> | ||
+ | <a href="https://2012.igem.org/Team:OUC-China/Parts"> | ||
+ | <img src="https://static.igem.org/mediawiki/2012/f/f9/Ouc-nav-parts.jpg" /> | ||
+ | Parts | ||
+ | </a> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <ul class="submenu"> | ||
+ | <li> | ||
+ | <a href="https://2012.igem.org/Team:OUC-China/Safety"> | ||
+ | <img src="https://static.igem.org/mediawiki/2012/5/5d/Ouc-nav-safety.jpg" /> | ||
+ | Safety | ||
+ | </a> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <ul class="submenu"> | ||
+ | <li> | ||
+ | <a href="https://2012.igem.org/Team:OUC-China/labnote"> | ||
+ | <img src="https://static.igem.org/mediawiki/2012/8/8b/Ouc-nav-labnote.jpg" /> | ||
+ | Labnote | ||
+ | </a> | ||
+ | </li> | ||
+ | <li> | ||
+ | <a href="https://skydrive.live.com/redir?resid=6A13E80E2A176A23!249&authkey=!AGsNOi9excznIt8"> | ||
+ | <img src="https://static.igem.org/mediawiki/2012/4/4e/Ouc-nav-modelingnote.jpg" /> | ||
+ | Modeling Note | ||
+ | </a> | ||
+ | </li> | ||
+ | <li> | ||
+ | <a href="https://2012.igem.org/Team:OUC-China/protocol"> | ||
+ | <img src="https://static.igem.org/mediawiki/2012/7/7d/Ouc-pro.png" /> | ||
+ | Protocols | ||
</a> | </a> | ||
</li> | </li> | ||
Line 315: | Line 426: | ||
</ul> | </ul> | ||
</div> | </div> | ||
- | </div> | + | </div> |
+ | <div class="mini-riboon"><img src="https://static.igem.org/mediawiki/2012/0/03/Ouc-mini-ribbon-decision-making.png"></div> | ||
<div class="article-list"> | <div class="article-list"> | ||
<div class="start"></div> | <div class="start"></div> | ||
<div class="list-box"> | <div class="list-box"> | ||
<div class="list-text"> | <div class="list-text"> | ||
- | <h1>Background</h1> | + | <h1 style="border:none;">Background</h1> |
<p> Precise control of gene expression is at the core of any genetic engineering-dependent discipline. | <p> Precise control of gene expression is at the core of any genetic engineering-dependent discipline. | ||
<br/> | <br/> | ||
Line 350: | Line 462: | ||
<br/> | <br/> | ||
<br/> | <br/> | ||
- | <p | + | <p><strong>Approaches artificial sRNA in synbio</strong><span></span>However, active artificial sRNAs reperssion stem or orthogonal seed region can be screened from error-prone libraries,in which natural sRNA scaffolds are fused to a randomized antisense domain. |
<br/> | <br/> | ||
- | + | <a><img style=" margin-left: 200px;" src="https://static.igem.org/mediawiki/2012/8/8d/Ouc-project-designmaking-background2.jpg" /></a> | |
- | <a><img style=" | + | <br/> |
+ | <p style="font-size:90%; ">Fig. Heat map of percentage repression profile of 23 RNA-IN mutants in presence of 23 antisense RNA-OUT mutants</p> | ||
<br/> | <br/> | ||
<br/> | <br/> | ||
Line 369: | Line 482: | ||
<br/> | <br/> | ||
<br/> | <br/> | ||
- | < | + | |
+ | <a><img style=" margin-left:150px;" src="https://static.igem.org/mediawiki/2012/6/67/Ouc-project-designmaking-background4.jpg" /></a> | ||
+ | <br/> | ||
<br/> | <br/> | ||
+ | <p style="font-size:90%; text-align:center;">Fig. (A)The strength of sRNA repression decreases as the target transcription increases. | ||
<br/> | <br/> | ||
(B)Steady-state solution of a model for protein | (B)Steady-state solution of a model for protein | ||
regulators, where the strength of repression is | regulators, where the strength of repression is | ||
independent of target transcription rate. | independent of target transcription rate. | ||
- | |||
<br/> | <br/> | ||
(C)Temporal behavior in a single stochastic simulation of the expression of two model genes, regulated by sRNA(blue line) and protein regulators(red) respectively.Parameter set is given in reference | (C)Temporal behavior in a single stochastic simulation of the expression of two model genes, regulated by sRNA(blue line) and protein regulators(red) respectively.Parameter set is given in reference | ||
</p> | </p> | ||
- | |||
<br/> | <br/> | ||
<br/> | <br/> | ||
Line 388: | Line 502: | ||
<a><img style="margin-left:20px;" src="https://static.igem.org/mediawiki/2012/5/5c/Ouc-project-designmaking-background5.jpg"></a> | <a><img style="margin-left:20px;" src="https://static.igem.org/mediawiki/2012/5/5c/Ouc-project-designmaking-background5.jpg"></a> | ||
<br/> | <br/> | ||
- | <a><img style="margin-left: | + | <a><img style="margin-left:40px;" src="https://static.igem.org/mediawiki/2012/c/c8/Ouc-diyrna.png"></a> |
<br/> | <br/> | ||
<h2>What is <i>spot42</i>?</h2> | <h2>What is <i>spot42</i>?</h2> | ||
Line 410: | Line 524: | ||
<br/> | <br/> | ||
<br/> | <br/> | ||
- | <p | + | <p><i>spot42</i> have a weak Hfq binding site (whereas galK weaker),an endogenous terminator(unclear efficiency,maybe weak),and the multitarget repression stem-loop.</p> |
- | + | ||
<br/> | <br/> | ||
<br/> | <br/> | ||
- | < | + | |
+ | <a><img style="margin-left:170px;" src="https://static.igem.org/mediawiki/2012/e/ef/Ouc-project-designmaking-ackground9.jpg" /></a> | ||
+ | <p style=" text-align:center; font-size:90%;">Fig. <i>spot42</i> modular structure. | ||
5’→3’:Repression stemloop, Hfq binding stem,terminator stem.</p> | 5’→3’:Repression stemloop, Hfq binding stem,terminator stem.</p> | ||
- | |||
<br/> | <br/> | ||
<br/> | <br/> | ||
<h2>How about <i>dsrA</i>?</h2> | <h2>How about <i>dsrA</i>?</h2> | ||
- | <p | + | <p><i>dsrA</i> is an 87-nt untranslated RNA that regulates both the global transcriptional silencer and nucleoid protein H-NS and the stationary phase and stress response sigma factor <i>rpos</i> (ss). |
Both <i>dsrA</i> and <i>rpos</i> have strong Hfq binding site. | Both <i>dsrA</i> and <i>rpos</i> have strong Hfq binding site. | ||
<br/> | <br/> | ||
<br/> | <br/> | ||
</p> | </p> | ||
- | < | + | |
- | + | <a><img style="margin-left:180px;" src="https://static.igem.org/mediawiki/2012/7/79/Ouc-project-designmaking-background10.jpg" /></a> | |
+ | <p style="text-align:center; font-size:90%;">Fig. Models for <i>dsrA</i> riboregulation. | ||
+ | |||
<br/>At the top, <i>dsrA</i> forms RNA:RNA interactions with target transcripts. | <br/>At the top, <i>dsrA</i> forms RNA:RNA interactions with target transcripts. | ||
- | + | ||
<br/>On the left (-) is a model for translational repression of hns. | <br/>On the left (-) is a model for translational repression of hns. | ||
- | + | ||
<br/>On the right (+) is a model for translational activation of <i>rpos</i> | <br/>On the right (+) is a model for translational activation of <i>rpos</i> | ||
</p> | </p> | ||
- | |||
<br/> | <br/> | ||
<br/> | <br/> | ||
Line 467: | Line 582: | ||
</div> | </div> | ||
</div> | </div> | ||
+ | <p id="back-top"> | ||
+ | <a href="#top"><span></span>Back to Top</a> | ||
+ | </p> | ||
</body> | </body> | ||
+ | <script> | ||
+ | $(document).ready(function(){ | ||
+ | // hide #back-top first | ||
+ | $("#back-top").hide(); | ||
+ | |||
+ | // fade in #back-top | ||
+ | $(function () { | ||
+ | $(window).scroll(function () { | ||
+ | if ($(this).scrollTop() > 100) { | ||
+ | $('#back-top').fadeIn(); | ||
+ | } else { | ||
+ | $('#back-top').fadeOut(); | ||
+ | } | ||
+ | }); | ||
+ | |||
+ | // scroll body to 0px on click | ||
+ | $('#back-top a').click(function () { | ||
+ | $('body,html').animate({ | ||
+ | scrollTop: 0 | ||
+ | }, 800); | ||
+ | return false; | ||
+ | }); | ||
+ | }); | ||
+ | }); | ||
+ | </script> | ||
<script src="http://www.google-analytics.com/urchin.js" type="text/javascript"> | <script src="http://www.google-analytics.com/urchin.js" type="text/javascript"> | ||
</script> | </script> |
Latest revision as of 01:38, 27 October 2012
![](https://static.igem.org/mediawiki/2012/0/03/Ouc-mini-ribbon-decision-making.png)
Background
Precise control of gene expression is at the core of any genetic engineering-dependent discipline.
What is small RNA?
Definition & MechanismOBacteria employ a range of RNA regulators collectively termed small RNAs (sRNAs) to help
respond to changes in the environment.They have important functions as genetic regulators in prokaryotes. sRNAs act post-transcriptionally through complementary pairing with target mRNAs to regulate protein expression.The subsequent effects of trans-ecoded complementary pairing on 5’ UTR include repression(through blocking RBS like spot42-galk::mRNA) and activation(through unlocking inert secondary structures near RBS like dsrA-rpos::mRNA).
Fig. Small RNA regulation mechanisms.
Modular achitecture Almost all the trans-encoded small RNAs consist of repression stem-loops,a RNA chaperone binding site and a endogenous terminator(unclear termination efficiency),even a few RNase recognition sites on vital functional domain.
The repression stem-loop initializes complementary pairing through several nucleotides motif called seed region,which has been proven crucial in small RNA regulation.
RNase recognition site is conincident with RNA chaperone binding site in some cases,thus the chaperone Hfq protects small RNA from degradation.
RNA chaperoneRNA chaperone,that is the hexameric Escherichia coli Hfq,is involved in riboregulation of target mRNAs by many small trans-encoded RNAs.Hfq is a highly abundant protein 20000~40000 copies,always plays a significant role in sRNA regulation by binding to RNA.It binds to sRNA and mRNA respectively, then hfq-RNA complexes binds to each other,increasing the local concentration for pairing,accelerating strand-exchange,altering RNA structures for initiation,protect sRNA from degradation and exposure of seed region.Hfq molecular titration experiments have convinced us that the essential status of hfq in sRNA regulation
Fig. Variable requirement for Hfq in sRNA-mediated gene regulations in bacteria.
How is current study going on?
Unfortunately, analogous technology for use in bacteria that is as reliable and efficient as mammalian RNAi has remained elusive due to its complicated mechanism,but many more indepth researches have shed some light on rational designation of bacterial small RNA.
Approaches artificial sRNA in synbioHowever, active artificial sRNAs reperssion stem or orthogonal seed region can be screened from error-prone libraries,in which natural sRNA scaffolds are fused to a randomized antisense domain.
Fig. Heat map of percentage repression profile of 23 RNA-IN mutants in presence of 23 antisense RNA-OUT mutants
What’s in sRNA topology?
On the other hand,ongoing characterization of base pairing sRNAs in bacteria has started for several years to reveal the modular architecture and how these sRNAs participate in global regulatory networks. These networks can be broken down into smaller regulatory circuits that have characteristic behaviors and functions.
Fig. Overview of regulatory circuits in which sRNAs are found in E. coli and Salmonella.
Quantitative simulation
Now, the precise control of sRNA has been quantitatively understood preliminaryily.A threshold-linear response with a tunable threshold, a robust noise resistance characteristic, and a built-in capability for hierarchical cross-talk, the outstanding nature of riboregulator makes it more popular in synthetic biology.
Fig. (A)The strength of sRNA repression decreases as the target transcription increases.
(B)Steady-state solution of a model for protein
regulators, where the strength of repression is
independent of target transcription rate.
(C)Temporal behavior in a single stochastic simulation of the expression of two model genes, regulated by sRNA(blue line) and protein regulators(red) respectively.Parameter set is given in reference
Why choose small RNA as information processing medium?
Advantage of Ribo/Protein regulators:
What is spot42?
spot42 is a multitarget small RNA that mediates the discoordinate expression of the E.coli galactose operon and other sugar metabolic pathway,such as galK,nanC,ytfJ,srlA,which are the 5’ leader sequence of the corresponding metabolic enzymes.
Take galK for example,spot42 causes translation repression by base pairing to RBS in the 5’ leader sequence,then block the recognition of the antiSD sequence on 30S subunit.
It’s a very strong pairing(up to 20bases),but it only causes 2.6 fold repression according to Johannes H. Urban and Jo¨ rg Vogel,for it doesn’t result in the degradation of the RNA complex by RNaseE(ssRNA degradation) and RNaseIII(dsRNA degradation),both of them are major enzymes that causes RNA degradation in vivo.spot42-galK complex degrades in a slow and presently unclear way. The base pairing is initiated by the recognition of seed region,which plays a significant role in the repression efficiency
Fig. Basepairing between spot42 and galK
Hfq binds to the AU-rich domain of spot42,and footprinting experiments has shown that spot42.It is essential to most of small RNAs in E.coli,extremely enchances the repression efficiency.
Fig. Repression efficiency of many known sRNA in WT,RNase deficient strain,RNA chaperone deficient strain
spot42 have a weak Hfq binding site (whereas galK weaker),an endogenous terminator(unclear efficiency,maybe weak),and the multitarget repression stem-loop.
![](https://static.igem.org/mediawiki/2012/e/ef/Ouc-project-designmaking-ackground9.jpg)
Fig. spot42 modular structure. 5’→3’:Repression stemloop, Hfq binding stem,terminator stem.
How about dsrA?
dsrA is an 87-nt untranslated RNA that regulates both the global transcriptional silencer and nucleoid protein H-NS and the stationary phase and stress response sigma factor rpos (ss).
Both dsrA and rpos have strong Hfq binding site.
![](https://static.igem.org/mediawiki/2012/7/79/Ouc-project-designmaking-background10.jpg)
Fig. Models for dsrA riboregulation.
At the top, dsrA forms RNA:RNA interactions with target transcripts.
On the left (-) is a model for translational repression of hns.
On the right (+) is a model for translational activation of rpos