Maximum expected accuracy structural neighbors of an RNA secondary structure

Since RNA molecules regulate genes and control alternative splicing by allostery, it is important to develop algorithms to predict RNA conformational switches. Some tools, such as paRNAss, RNAshapes and RNAbor, can be used to predict potential conformational switches; nevertheless, no existent tool can detect general (i.e., not family specific) entire riboswitches (both aptamer and expression platform) with accuracy. Thus, the development of additional algorithms to detect conformational switches seems important, especially since the difference in free energy between the two metastable secondary structures may be as large as 15-20 kcal/mol. It has recently emerged that RNA secondary structure can be more accurately predicted by computing the maximum expected accuracy (MEA) structure, rather than the minimum free energy (MFE) structure.


Source code for RNAborMEA can be downloaded from or

Apps Collections for Synthetic Biology


Synthetic biology which is inspired by “plug-and-play” concept is supported by standardized biobricks and also computational tools for analysis and optimization [1]. Here are bio-apps collections for you. Personally Tinkercell and UNAFold are mostly used.

Circuit design and simulation
Circuit optimization
DNA and RNA design
 Gene Designer
 Vienna RNA package∼ivo/RNA/
 Vienna RNA web servers
 Zinc Finger Tools
Protein design
 Autodock 4.2
 HEX 5.1∼ritchied/hex/
Integrated workflows


Suggested pages listing useful bio-apps maybe you will like in synthetic biology research:

  1. WikiGenes Toolbox ( As a free on-line tutorial edited by people all around the world, WikiGenes has spirits of Linux: open-source, sharing, interest, so is WikiGenes-Synthetic-Biology page. It enables you fast-learn what is synthetic life.
  2. OpenWetWare (
  3. JCVI ( This page is from J. Craig Venter Institute.


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[1] Marchisio, M. A., & Stelling, J. (2009). Computational design tools for synthetic biology. Current Opinion in Biotechnology, 20(4), 479-485. Retrieved from

microRNAs quantitative assay with Splinted Ligation

Do you still use Northern Blot to quantitate microRNAs expression? Here I recommend Splinted Ligation Assay[1,2], though this method is an old story (published in 2007).


Detection of miRNAs using splinted ligation. Schematic depiction of the assay process. As described in the text, the assay involves: (1) Labeling of the ligation oligonucleotide; (2) concurrent annealing of the ligation oligonucleotide and miRNA to a bridge oligonucleotide; (3) linking of the ligation oligonucleotide to the miRNA by DNA ligase; (4) removal of labeled phosphate from unligated oligonucleotide; and (5) fractionation on a denaturing gel.

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[1] Maroney, P. a, Chamnongpol, S., Souret, F., & Nilsen, T. W. (2007). A rapid, quantitative assay for direct detection of microRNAs and other small RNAs using splinted ligation. RNA (New York, N.Y.), 13(6), 930-6. doi:10.1261/rna.518107

[2] Maroney, P. A., Chamnongpol, S., Souret, F., & Nilsen, T. W. (2008). Direct detection of small RNAs using splinted ligation. Nat. Protocols, 3(2), 279-287. Nature Publishing Group. Retrieved from