Frequently Asked Questions

Q. What is siRNAmod?

siRNAmod is a manually curated database for experimentally validated chemically modified siRNA involving 128 different types chemical modifications with different permutations and combinations, targeting various genes.the total number of chemically modified siRNA sequences reported is with 4894 aditionally 435 sequences are provided which are non-modified sequences but used in various studies.

Q. How to find information about the unique siRNA modifications of siRNAmod?

We have provided list of unique chemicals modifications in the databse, which on clicking display the structural information of the modification.

Q. What is the importance of siRNAmod database to scientific community?

Since, “siRNAmod” will be useful for people working on siRNA-based techniques as well as chemists working in the field of improving the siRNA-based techniques. It is also useful in identifying the modifications for further research. Therefore, in order to make these chemical modifications quickly accessible in the form of a comprehensive database, we have developed siRNAmod.

Q. How many total entries are there in siRNAmod of siRNA?

siRNAmod contains total of 4894 experimentally validated chemically modified   siRNAs. In addition some non chemical modifications like mismatch, mutations, wobble base pairs, Asymmetric siRNA, cut (internally segmented siRNA) category (425 entries in all) is also provided in form of table.

Q. What are the fields of siRNAmod?

These are as follows: -

(i) Modification name (sense/antisense), (ii) Position of modification (iii) Different types of modification, (iv) Overall Number of modifications, (v) Modification component (sugar, base, phosphate), (vi) Chemical information as SMILE along with Inchel, structure and other information about the modification as natural or non-natural siRNA sequence, (vii) siRNA sequence, (viii) Biological activity, (ix) Target gene, (x) siRNA concentration used, (xi) Experiment to heck activity, (xii) Cell line or Organism, (xiii) Melting temperature, (xiv) Reference title, (xv) PMID and siRNAmodID.

Q. In what type experimentation of chemical modifications of siRNA is done?

Both in vivo and in vitro are used in chemical modification of siRNA in siRNAmod. In vivo, C57BL/6 mice is used while for in vitro HeLa, HEK293, H1299 cells, COS7 cells, PC12 Cells, Vero cells, HEK 293, HCT116 cells, NIH-3T3-MDR cells, Hepa1-6 cells, SH-SY5Y cells,MiaPaca II cells,Rhabdomyosarcoma cells, Huh7 cells are used.

Q. What components are used in chemical modifications of siRNA in siRNAmod?

All three components are used in siRNAmod. They are Sugar, Base and Phosphate.

Q. How are different chemical modfications on siRNA represented in database?

Firstly the siRNA is divided into sense and antisense strands and their respective modifications defined. Secondly the different chemical modfications on same siNRA are separated by asterisk (*) mark e.g in SM4840 two chemical modifications in sense strand represented as "2,4-bridged nucleic acid* DeoxyThymidine" and their corresponding positions defined as "1,2,3,4,5 * 23,24". I.e. 2,4-bridged nucleic acid is present at positions 1,2,3,4,5 and DeoxyThymidine at 23,24 positions.

Q. How to use search option in siRNAmod?

User can enter the query/keyword after clicking "Search" web page on menu bar. The keyword can be searched in the all fields like siRNAmod Id, PMID,SMILIE of chemical, Name of siRNA in paper of sense/antisense strand, Sequence of sense/antisense strand, Modification (sense/antisense), Type of modification of sense/antisense, Position of modification of sense/antisense, Biological activity, Target gene, siRNA concentration used, Cell or Organism used, Transfection method, there is also facility that user can select some out of all fields to search that keyword in those fields only.

Q. What is the use of siRNAmod tool?

The siRNAmod tool searches the siRNA sequence in the database similar to the siRNA sequence provided by the user and searches whether that siRNA sequence have been already reported in the literature or not.

There are two tools in siRNAmod to help user analyze their sequence. These are:

1) siRNAmodBlast: To blast user provided siRNA to the siRNAmod in the database.

2) siRNAmod Map: To mapsiRNAmod siRNA on your siRNA/shRNA or nucleotide sequence.

3) Structure search: To search the structure of chemical modification user can draw structure and then find it in siRNAmod database.

Q. How to download data from siRNAmod? 

Data is freely available to download from siRNAmod under the downloads section in the menu bar. User can download entire database in excel format depending upon their requirement.

Q. What and how is efficacy designated in siRNAmod?

The efficacy is the potency of the chemically modified siRNA to silence the particular gene. It is given as biological activity in database and is defined in terms of percentage of gene silenced (e.g. 90 percentage of target mRNA inhibition) or IC50 of a particular siRNA. In some cases it is also mentioned via quantitative way as high or increased (as defined by the paper).

Q. How is efficacy, biological activity and mRNA (target gene) inhibition related to each other?

These three are interlinked. Efficacy is the ability of the chemically modified siRNA to inhibit the target gene translation, which inturn is its biological activity i.e. the activity of inhibting target gene/mRNA in biological context (cells).

Q. What is updation status of database and how user will contact to add any modification?

The database is updated till May 2015. Further it will be updated 6 monthly. There is web page provided for upadtion of the database in which user can provide information about any modification if it happens to be missing in the databse or any other related information.

Q. Is this database freely available?

Yes, this database is freely available through this url: