ModifiedsTM Nucleic Acid Software
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What are Modified Nucleotides?
DNA and RNA are polymers of repeating nucleotide subunits. A nucleotide, which is comprised of a base (G, C, A, or T/U), nucleoside (sugar), and backbone (phosphate), can be chemically modified to alter the physical properties of a nucleic acid sequence. Such modified nucleotides (e.g. LNA, 2’-O-Methyl, 5-Methyl-C, etc.) are commonly incorporated into oligonucleotides to improve the sensitivity and specificity of genotyping assays for difficult targets or to improve efficacy of siRNAs and antisense RNAs. Example modified nucleotides and their applications are further described below.
Software for Modeling Modified Oligonucleotides:
DNA Software, Inc.’s unique ModifiedsTM module enables you to accurately:
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predict secondary structure of oligos and targets with modified nucleotides
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design and optimize hybridization-based experiments that include modified nucleotides
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scan modified oligos against large genome databases to detect false positives and off-target effects
Currently Available Modified Nucleotides in the ModifiedsTM Module:
| Modified Nucleotide Type |
Function |
| LNA |
Stability and specificity |
| PNA |
Stability and reduced degradation |
| Morpholino |
Antisense efficacy |
| Phosphorothioate |
Antisence efficacy |
| 2'-O-methyl-RNA |
siRNA efficacy, reduced degradation |
| rT in RNA |
Stability |
| Deoxyinosine |
Universal base |
| Deoxyuridine |
Reduced PCR contamination, Methylation specific assays |
| 5-methyl-C in DNA |
Methylation specific assays |
| isoC-isoG |
Expanded alphabet, zip codes |
The best way to learn how ModifiedsTM can assist your work and to see representative case studies is to schedule a live web demo specifically tailored to your research interests.
ModifiedsTM In Silico Predictions Match Experimental Results:
The ModifiedsTM module is powered by the industry’s largest database of thermodynamic parameters, which were derived in DNA Software’s own wet lab. DNA Software has validated the ModifiedsTM module’s exceptionally accurate in silico predictions with over 1000 measurements of the thermodynamics of duplexes with modified nucleotides. Example comparisons of DNA Software's in silico predictions versus experimental results are as follows.
DNA Software is continuing to derive new thermodynamic parameters for many more modified nucleotides, which will be added to the ModifiedsTM module. In addition, DNA Software can create a custom software module for a customer’s own proprietary modified nucleotides.
Product Options:
The ModifiedsTM module is offered in three different product formats. It is available as an additional module that integrates into (1) Visual OMPTM for assay development, (2) ThermoBLASTTM for genome scanning, or (3) OMP Developer EditionTM or ThermoBLAST Developer EditionTM for high-throughput, command line applications.
ModifiedsTM Support & Training