Line 1,970: | Line 1,970: | ||
<div class="col"> | <div class="col"> | ||
Our tRNA primer designer is a web tool for potential users of our mutagenesis system to design their own tRNA primers according to their experimental setups. Here we provide a step-by-step guide to using this software.<br /><br /> | Our tRNA primer designer is a web tool for potential users of our mutagenesis system to design their own tRNA primers according to their experimental setups. Here we provide a step-by-step guide to using this software.<br /><br /> | ||
− | Step 1. Input a DNA sequence that you want to mutate. The last 18 nucleotides of the sequence are selected to be PBS. Note that this sequence should be longer than 18 nucleotides. Besides, it shouldn't contain any characters other than A/T/C/G | + | Step 1. Select the type of reverse transcriptase (RT) that you want to use based on your experimental design. Note that this software only allows you to choose from MMLV RT/ HIV-1 RT/ RSV RT.<br /><br /> |
− | + | Step 2. Input a DNA sequence that you want to mutate. The last 17/18 nucleotides (nt) of the sequence are selected to be PBS, depending on the type of RT that you have chosen in <b><i>Step 1</i></b>. The length of PBS is 18nt if MMLV RT/ HIV-1 RT is selected, and is 17nt if RSV RT is selected. Note that this sequence should be longer than 17/18 nucleotides based on your selected RT. Besides, it shouldn't contain any characters other than A/T/C/G.<br /><br /> | |
Step3. Click on the "DESIGN FOR ME!!!" button and see the result. The result is composed of two parts. The first part shows you the secondary structure of the template tRNA that you will be using as well as the designed tRNA primer. The fragment that can be annealed to PBS of the input DNA sequence is shown in red. The second part will give you the DNA sequence encoding the tRNA primer that satisfies your need. You can just copy it and use it elsewhere. | Step3. Click on the "DESIGN FOR ME!!!" button and see the result. The result is composed of two parts. The first part shows you the secondary structure of the template tRNA that you will be using as well as the designed tRNA primer. The fragment that can be annealed to PBS of the input DNA sequence is shown in red. The second part will give you the DNA sequence encoding the tRNA primer that satisfies your need. You can just copy it and use it elsewhere. | ||
</div> | </div> | ||
Line 1,985: | Line 1,985: | ||
<div class="col"> | <div class="col"> | ||
<ul class="paraUl" style="list-style:none;"> | <ul class="paraUl" style="list-style:none;"> | ||
− | <li>[1] | + | <li>[1]. Peters G , Dahlberg J E . RNA-directed DNA synthesis in Moloney murine leukemia virus: interaction between the primer tRNA and the genome RNA.[J]. Journal of Virology, 1979, 31(2):398-407.</li> |
− | <li>[2] | + | <li>[2]. Kulpa, D. Determination of the site of first strand transfer during Moloney murine leukemia virus reverse transcription and identification of strand transfer-associated reverse transcriptase errors[J]. EMBO (European Molecular Biology Organization) Journal, 1997, 16(4):856-865.</li> |
− | <li>[3] | + | <li>[3]. Palmer M T , Kirkman R , Kosloff B R , et al. tRNA Isoacceptor Preference prior to Retrovirus Gag-Pol Junction Links Primer Selection and Viral Translation[J]. Journal of Virology, 2007, 81(9):4397-4404.</li> |
− | <li>[4] | + | <li>[4]. Kinouchi M , Kurokawa K . [Special Issue: Fact Databases and Freewares] tRNAfinder: A Software System To Find All tRNA Genes in the DNA Sequence Based on the Cloverleaf Secondary Structure[J]. Journal of Computer Aided Chemistry, 2006, 7:116-124.</li> |
− | <li>[5] | + | <li>[5]. Lund, Anders H. et al. “Mutated primer binding sites interacting with different tRNAs allow efficient murine leukemia virus replication.” Journal of virology, 67 12 (1993): 7125-30.</li> |
</ul> | </ul> | ||
</div> | </div> |
Revision as of 04:34, 16 October 2019