Category: Blog

Article in Nature:

DNA Software was featured in a recent article published in Nature on July 16, 2018 titled “Multiplexed identification, quantification and genotyping of infectious agents using a semiconductor biochip”. To learn more click here

Biology Methods & Protocols:

DNA Software Acknowledged and Referenced in Biology Methods & Protocols paper titled “An array-based melt curve analysis method for the identification and classification of closely related pathogen strains”.

Fall 2019 newsletter

Click here to download a pdf copy of the DNA Software Fall Newsletter

Large Scale Multiplex PCR Panel Design

Large Scale Multiplex PCR Panel Design with >95% Success in Hours, Not Months
John SantaLucia, Ph.D., co-founder and CEO, DNA Software
Abstract: We aim to solve the problem of multiplex PCR design by a three-pronged approach: 1. improved understanding of the mechanism of PCR and the causes of artifacts, 2. improved algorithms for predicting secondary structure and mis-hybridization, and 3. implementation of cloud to address large sequence databases. These approaches vastly improve the success of fully automated multiplex PCR design with larger plex sizes. This enables applications such as targeted enrichment for NGS and infectious disease molecular diagnostics.

DNAS releases PanelPlex

Infectious disease molecular diagnostic(MDx) assays require rapid identification of pathogens and their drug resistance profiles in clinical samples use a highly multiplexed molecular approach. The market pull for such MDx assays has led to the software solution, PanelPlexTM.

Ann Arbor, MI – June 7, 2017.

DNAS releases PanelPlex™ , a cloud based product to solve the four most common problems in multiplex. PanelPlex™ was built in direct response to the molecular diagnostics customers that DNA Software has served over the past two decades. These multiplex problems include lost time in design and time to market, costs related to lengthy design, lack of organizational expertise and the use of sub-optimal tools and freeware. PanelPlex™ is designed to solve the tough problems that are problematic for “freeware”.

There are two options for customers. One is to use the product directly utilizing cloud-computing. The other option is to have DNA Software use the software to do all the design work. Some customers opt for hands-on work, others want a concierge service utilizing DNA Software’s team of professionals.

“We are very excited to offer the most comprehensive software product with exactly the right functionality and user experience for researchers designing panels. PanelPlex™ is the result of 15 years of investigation into the mechanism of PCR and careful experiments to identify the sources of failure of PCR” commented CEO, Dr. John SantaLucia.

About DNAS

About DNA Software Inc.
Over 20 years ago, Dr. John SantaLucia made significant discoveries at a prestigious research university regarding the behavior of DNA and his seminal published work has now been cited over 5000 times. DNA Software, Inc. was founded to commercialize this research for real market applications by the accuracy of predictive models into software algorithms to replace traditional trial and error experimentation. DNA Software (DNAS) has now offered solutions to some of the most difficult problems in DNA Diagnostic Design and Analysis, first in desktop software and now in cloud based applications.

DNA Software receives FastTrack award

ANN ARBOR, MICH. – At its annual meeting, Ann Arbor SPARK presented its annual FastTrack awards to 17 Washtenaw County-based companies that have demonstrated fast growth. Several of the 2016 and 2017 FastTrack award recipients were multiple year winners.

“It’s incredible to see the range of companies that are thriving in our region,” said Paul Krutko, president and CEO of Ann Arbor SPARK. “The achievement of FastTrack companies is truly remarkable: They all maintained year over year growth for three consecutive years. These leading businesses prove that Ann Arbor offers what companies need to be successful.”

Yeo & Yeo CPAs & Business Consultants sponsors the Ann Arbor SPARK FastTrack Awards and verified all of the award applications.

About Ann Arbor SPARK

Ann Arbor SPARK, a non-profit organization, is advancing the region by encouraging and supporting business acceleration, attraction and retention. The organization identifies and meets the needs of business at every stage, from start-ups to large organizations. Ann Arbor SPARK collaborates with business, academic, government, and community investor partners including the University of Michigan, Eastern Michigan University, Washtenaw Community College, Washtenaw County,

DNAS cited in Science Advances

Early identification of pathogens is essential for limiting development of therapy-resistant pathogens and mitigating infectious disease outbreaks. Most bacterial detection schemes use target-specific probes to differentiate pathogen species, creating time and cost inefficiencies in identifying newly discovered organisms. We present a novel universal microbial diagnostics (UMD) platform to screen for microbial organisms in an infectious sample, using a small number of random DNA probes that are agnostic to the target DNA sequences. Our platform leverages the theory of sparse signal recovery (compressive sensing) to identify the composition of a microbial sample that potentially contains novel or mutant species. We validated the UMD platform in vitro using five random probes to recover 11 pathogenic bacteria. We further demonstrated in silico that UMD can be generalized to screen for common human pathogens in different taxonomy levels. UMD’s unorthodox sensing approach opens the door to more efficient and universal molecular diagnostics.

Rice University group publishes on universal microbial diagnostics (UMD) recently in Science Advances

Increase Accuracy of Assure-CNV

A world class agricultural company compared the capabilities of Assure-CNV to their current workflow. This customer found Assure-CNV increased accuracy with 12 standard deviations versus the 8 provided by their traditional method. Their standard workflow also required several days to organize the data for statistical analysis, whereas Assure-CNV accurately called 100% of the samples within a few minutes. As a high throughput lab running millions of samples, Assure CNV provided a significant improvement in accuracy while reducing time and cost compared to their previous method. The Assure-CNV product was found to help the determination of transgene copy number and event sorting and ultimately impacting the confidence of the seed zygosity calls that will be made downstream.

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Better Antisense Design Without the Trial and Error:  Problems we Solve

Most researchers use naïve strategies to design antisense oligonucleotides.  However, to maximize assay sensitivity and specificity one must consider probe and target sequence and their respective and combined chemistries.  That is why DNA Software has built the Antisense Architect design and simulation platform for the rational design of Antisense Oligonucleotide Analogs.  Three problems that we solve are the proper evaluation of Target Accessibility and sensitivity, the minimization off-target effects that elicit immune responses and often cell death, and we have the necessary thermodynamic libraries to predict the proper use of Chemical Modifications to prevent enzymatic digestion.

Target Accessibility:  The Conventional Approach to Duplex Formation

The naïve way to design Antisense Oligonucleotides is to only consider the two-state model of probe hybridization which describes the probe and its hybridization to its complement.  Target accessibility and tail folding are not accounted for, therefore this is an incomplete model of what is really happening in the system which leads to a lack of sensitivity due to target and probe secondary structure and negates the effect of bimolecular mishybridization reactions.

Competing Secondary Structure-False-Negative Assays

The platform for each of our DNA Software products is based on the multi-state equilibrium model which accounts for the energetic cost of target and probe secondary structure through coupled equilibria, which ultimately increases assay sensitivity.  This means that the Antisense Architect will evaluate and thermodynamically score your desired design sites, and if given an entire target, it will identify all thermodynamically accessible sites.

Off-Target Effects:  Using ThermoBLAST to Predict Crosshybridization and Mishybridization

Many researchers use NCBI BLAST for their oligonucleotide design because its free, but even free has its associated costs because BLAST is the wrong tool for determining selectivity.  BLAST was meant to determine common evolutionary ancestry through sequence similarity, however sequence similarity does not equal thermodynamic stability as BLAST does not account for thermodynamic contributions of basepairing and mismatches, target bulges and dangling ends and different oligo backbone chemistries.  DNA Software’s products take all of the aforementioned thermodynamic contributions into account in both the design and simulation of Antisense oligonucleotide analogs, which results in a more accurate prediction of oligonucleotide mishybridization and crosshybridization.

Chemical Modification:   Packages are Customizable

It is well documented that the key to preventing the enzymatic digestion of Antisense oligonucleotides, or in some cases immune stimulation, lays in the chemical substitution of the probe backbone or 2’ sugar moieties. What is not well documented is the thermodynamic libraries required for rational design that takes into account the thermodynamic contributions of the modifications listed that predict probe secondary structure and the energy of hybridization and ultimately the melting temperature, or Tm.  Depending on the modifieds used the Tm could differ by as much as +/- 10 degrees celcius, which may have an unwanted and undefined effect on your assay if you are not able to simulate the use of modifieds in design. DNA Software has determined the thermodynamic effects of the listed modifieds and is prepared to build an Antisense Architect Platform that is specific to your research needs and requirements.

DNA Software’s Antisense Architect

The recurring issues of Target accessibility, Probe design, Off-target effects and the proper use of chemical modifications are solved in the Antisense Architect which uses design heuristics that allows for the rational design of Antisense oligonucleotides.  Some heuristics that are used in design include the evaluation of secondary structure and sequence composition and complexity of targets and probes.  We will discuss the design heuristics in more detail when we review the design results of our demo.

Antisense Architect: 4 easy steps

The Antisense Architect use a design wizard format to collect necessary input from the user for the design of highly sensitive and selective Antisense probes in four easy steps:

-Choose the background RefSeq of interest and the target

-Choose target design region

-Choose desired probe chemistry and hybridization conditions

-Run the job and get results.

And now…the Antisense Architect Demo!

Real Cost of Multiplex

This conversation is consistent with our feedback from customers throughout the years.   Building a successful multiplex is hard, expensive and time-consuming.  Often times we work with customers after they’ve already tried “going it alone”.  We unfortunately are not surprised when they decide to engage the help of DNA Software only after some difficult or challenging circumstances, and we hear “that approach didn’t work” or “that team member is no longer with us” quite often.

We recently spoke with a customer who was sharing with us the trials and tribulations of developing a multiplex PCR assay with multiple experimental iterations, at least a half dozen.  When we starting asking clarifying questions, and we were surprised to learn the answers.   We asked, “how long have you been working on this multiplex”?  Our customer replied, “well this particular assay has been approximately six months but some similar assays have taken over a year.”  When we asked “how many people do you have dedicated to this project”, we discovered that these projects typically require up to 3 FTE and 6-12 months is a common time requirement.  We quickly calculated the real cost at one quarter to one half million dollars without the certainty of success.

We acknowledge that free PCR design software works in some instances for easy and non-trivial design, but that is not what our ideal customer looks like.  Our ideal customer understands the challenges of design and they understand that they themselves lack the necessary expertise to execute a large scale multiplex design themselves. Our customers have often become aware that they need better tools and expertise to solve their most challenging multiplexes and that they don’t have a “resident thermodynamics expert” on staff.  Thankfully, our software will solve these challenging problems for you.  DNA Software will work with you to thoroughly understand the nuances of your system and deliver a customized solution that creates success in your bottom line.