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MELTING, a flexible platform to predict the melting temperatures of nucleic acids

Marine Dumousseau, Nicolas Rodriguez, Nick Juty, Nicolas Novère
2012 BMC Bioinformatics  
MELTING is a free open source software which computes the enthalpy, entropy and melting temperature of nucleic acids.  ...  Computing accurate nucleic acid melting temperatures has become a crucial step for the efficiency and the optimisation of numerous molecular biology techniques such as in situ hybridization, PCR, antigene  ...  Competing interests The authors declare that they have no competing interests. Authors contributions  ... 
doi:10.1186/1471-2105-13-101 pmid:22591039 pmcid:PMC3733425 fatcat:go5la6rttra5tggtaarvumccs4

PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling

Cyrille Pauthenier, Jean-Loup Faulon
2014 Nucleic Acids Research  
It integrates the most up-to-date melting temperature algorithms validated with experimental data, and cross validated with other computational tools.  ...  We generated a library of primers for the extraction and cloning of 61 genes from yeast DNA genomic extract using default parameters.  ...  This is a problem for any primer design tool, because the composition in monovalent and divalent ions is crucial to predict the melting temperature of the primer accurately.  ... 
doi:10.1093/nar/gku393 pmid:24829457 pmcid:PMC4086104 fatcat:p5i7g5qxnzg3bd2ziawcripljy

Thermodynamics of DNA Hybridization from Atomistic Simulations [article]

Gul Zerze, Frank Stillinger, Pablo Debenedetti
2020 bioRxiv   pre-print
We show that the melting temperatures estimated from our atomistic simulations follow an order consistent with the predictions from melting experiments and those from the nearest neighbor model, for a  ...  Here, we describe an order parameter-based advanced sampling technique to calculate the free energy surface of hybridization and estimate the melting temperature of DNA oligomers at the atomistic resolution  ...  We note that the predictive capability of our simulations is limited by the predictive capability of underlying potential energy function (CHARMM36 nucleic acids).  ... 
doi:10.1101/2020.08.05.238485 fatcat:4qymgvd6nvcxlmyolzssbw4qba

chipD: a web tool to design oligonucleotide probes for high-density tiling arrays

Y. S. Dufour, G. E. Wesenberg, A. J. Tritt, J. D. Glasner, N. T. Perna, J. C. Mitchell, T. J. Donohue
2010 Nucleic Acids Research  
The server implements a probe selection algorithm that takes as an input, in addition to the target sequences, a set of parameters that allow probe design to be tailored to specific applications, protocols  ...  The output provides in a text format, the list of probe sequences with their genomic locations, targeted strands and hybridization characteristics. chipD has been used successfully to design tiling arrays  ...  ACKNOWLEDGEMENTS We thank Madeline Fisher for her help in editing the article.  ... 
doi:10.1093/nar/gkq517 pmid:20529880 pmcid:PMC2896189 fatcat:mtlgxzkmyfhahmg6igzke6xgyy

A robust PCR primer design platform applied to the detection of Acidobacteria Group 1 in soil

Jason D. Gans, John Dunbar, Stephanie A. Eichorst, La Verne Gallegos-Graves, Murray Wolinsky, Cheryl R. Kuske
2012 Nucleic Acids Research  
We validated the specificity of the top three assays, collectively predicted to detect 42% of the Acidobacteria Group 1 sequences, by PCR amplification and sequencing of DNA from soil.  ...  We solved this problem by developing a software platform that enables PCR-assay design at an unprecedented scale.  ...  for a robust, flexible design platform like ProSig.  ... 
doi:10.1093/nar/gks238 pmid:22434885 pmcid:PMC3384349 fatcat:n6hlv56l65c63ivpwwbcpzswni

Establishment of a Flexible Real-Time Polymerase Chain Reaction-Based Platform for Detecting Prevalent Deafness Mutations Associated with Variable Degree of Sensorineural Hearing Loss in Koreans

Kyu-Hee Han, Ah Reum Kim, Min Young Kim, Soyeon Ahn, Seung-Ha Oh, Ju Hun Song, Byung Yoon Choi, Dror Sharon
2016 PLoS ONE  
However, most of these platforms do not offer the flexibility to add or remove target mutations, thereby limiting their wider use in a field that requires frequent updates.  ...  PCR-based method using the MeltingArray technique and peptide nucleic acid probes.  ...  In this study, we employed MeltingArray technology (SeaSun Biomaterials, Daejeon, Korea), a peptide nucleic acid (PNA) probe-based fluorescence melting-curve analysis system that can be used in a conventional  ... 
doi:10.1371/journal.pone.0161756 pmid:27583405 pmcid:PMC5008798 fatcat:hef54lxq5raffkftyzfrpi2one

Evaluation of Gel-Pad Oligonucleotide Microarray Technology by Using Artificial Neural Networks

A. Pozhitkov, B. Chernov, G. Yershov, P. A. Noble
2005 Applied and Environmental Microbiology  
Past studies have suggested that thermal dissociation analysis of nucleic acids hybridized to DNA microarrays would improve discrimination among duplex types by scanning through a broad range of stringency  ...  Experimental variability and deviation from ideal melt behavior were shown to be attributable primarily to a method of local background subtraction that was very sensitive to displacement of the grid frames  ...  This work was supported by grant 1U01DE014955-01 from NIH/ NIDCR to H.S. and P.A.N. and grant R-82945801 from EPA-CEER-GOM to P.A.N. Funding through DARPA provided the gel pad microarrays.  ... 
doi:10.1128/aem.71.12.8663-8676.2005 pmid:16332861 pmcid:PMC1317365 fatcat:ufqkumgzgfehfgucrkdht3uutm

Oligonucleotide microarrays in microbial diagnostics

L BODROSSY, A SESSITSCH
2004 Current Opinion in Microbiology  
Oligonucleotide microarrays offer a fast, high-throughput alternative for the parallel detection of microbes from virtually any sample.  ...  The past two years have witnessed a rapid increase of research in this field. Many alternative techniques were developed and validated as seen in 'proof-of-concept' articles.  ...  Nancy Stralis-Pavese and Alexandra Weilharter are acknowledged for their contribution to the abovementioned work.  ... 
doi:10.1016/j.mib.2004.04.005 pmid:15196491 fatcat:yjohzad4nfejjncodab7knb5ue

Oligonucleotide microarrays in microbial diagnostics

L BODROSSY
2004 Current Opinion in Microbiology  
Oligonucleotide microarrays offer a fast, high-throughput alternative for the parallel detection of microbes from virtually any sample.  ...  The past two years have witnessed a rapid increase of research in this field. Many alternative techniques were developed and validated as seen in 'proof-of-concept' articles.  ...  Nancy Stralis-Pavese and Alexandra Weilharter are acknowledged for their contribution to the abovementioned work.  ... 
doi:10.1016/s1369-5274(04)00043-8 fatcat:ju33ql4o6jbdpjjhfk3t7uevma

Entropy-Driven One-Step Formation of Phi29 pRNA 3WJ from Three RNA Fragments

Daniel W. Binzel, Emil F. Khisamutdinov, Peixuan Guo
2014 Biochemistry  
It seems that the three fragments can lead to the formation of the 3WJ complex efficiently within a rapid time.  ...  A low dissociation constant (apparent K D ) of 11.4 nM was determined for RNA, inclusion of 2′-F pyrimidines strengthened the K D to 4.5 nM, and substitution of DNA weakened it to 47.7 nM.  ...  T m 's were calculated by finding the temperature at which 50% of the nucleic acids were in trimer formation compared to the total concentration of the bands observed. 3WJ T m s were used to calculate  ... 
doi:10.1021/bi4017022 pmid:24694349 pmcid:PMC4004221 fatcat:uldq3fvnlfa33aio2h5pmydpye

An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations

John C Tan, Becky A Miller, Asako Tan, Jigar J Patel, Ian H Cheeseman, Tim JC Anderson, Magnus Manske, Gareth Maslen, Dominic P Kwiatkowski, Michael T Ferdig
2011 Genome Biology  
The microarray and workflow presented can be used to identify CNVs and SNPs with 95% accuracy in a single hybridization, in field samples containing up to 92% human DNA contamination.  ...  We show that sample preparation and hybridization conditions mitigate the effects of host DNA contamination in field samples.  ...  Acknowledgements This work was supported by the National Institutes of Health (AI072517, AI075145 to MTF; AI075145 to TJA).  ... 
doi:10.1186/gb-2011-12-4-r35 pmid:21477297 pmcid:PMC3218861 fatcat:gvkcq426djcrveieegvwnshsyq

Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection

Dominik Nörz, Moritz Grunwald, Hui Ting Tang, Flaminia Olearo, Thomas Günther, Alexis Robitaille, Nicole Fischer, Adam Grundhoff, Martin Aepfelbacher, Susanne Pfefferle, Marc Lütgehetmann
2021 Diagnostics  
Conclusion: The recurrence of SNP locations and flexibility of methodology presented in this study allows for rapid adaptation to current and future variants.  ...  acid)-probe design to maximize mismatch discrimination.  ...  We further thank Heinz-Hubert Feucht of Aesculabor Hamburg GmbH for providing nucleic acid extracts of remnant clinical samples.  ... 
doi:10.3390/diagnostics11101818 pmid:34679517 fatcat:owtzjs3cdre6dgu5i247tignym

FilmArray, an Automated Nested Multiplex PCR System for Multi-Pathogen Detection: Development and Application to Respiratory Tract Infection

Mark A. Poritz, Anne J. Blaschke, Carrie L. Byington, Lindsay Meyers, Kody Nilsson, David E. Jones, Stephanie A. Thatcher, Thomas Robbins, Beth Lingenfelter, Elizabeth Amiott, Amy Herbener, Judy Daly (+4 others)
2011 PLoS ONE  
An unprocessed biologic/clinical sample is subjected to nucleic acid purification, reverse transcription, a high-order nested multiplex polymerase chain reaction and amplicon melt curve analysis.  ...  Biochemical reactions are enclosed in a disposable pouch, minimizing the PCR contamination risk. FilmArray has the potential to detect greater than 100 different nucleic acid targets at one time.  ...  We thank the beta and clinical trials sites for the FilmArray data used for melt detection tuning and validation. Author Contributions  ... 
doi:10.1371/journal.pone.0026047 pmid:22039434 pmcid:PMC3198457 fatcat:s6gdfp6bv5hidmjnha5ancvune

Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch

Catherine D. Eichhorn, Jun Feng, Krishna C. Suddala, Nils G. Walter, Charles L. Brooks, Hashim M. Al-Hashimi
2011 Nucleic Acids Research  
An A-to-C mutation within the polyadenine tract alters the observed dynamics consistent with the introduction of a dynamic kink.  ...  NMR carbon spin relaxation data and residual dipolar coupling measurements reveal a flexible yet stacked core adopting an A-form-like conformation, with the level of order decreasing toward the terminal  ...  To our knowledge, these are the first RDC measurements reported on a single-stranded nucleic acid.  ... 
doi:10.1093/nar/gkr833 pmid:22009676 pmcid:PMC3273816 fatcat:speggalkkrfblgjo3yfzytje7i

A Simple, Inexpensive Device for Nucleic Acid Amplification without Electricity—Toward Instrument-Free Molecular Diagnostics in Low-Resource Settings

Paul LaBarre, Kenneth R. Hawkins, Jay Gerlach, Jared Wilmoth, Andrew Beddoe, Jered Singleton, David Boyle, Bernhard Weigl, Eng Eong Ooi
2011 PLoS ONE  
We assess the heater's equivalence to commercially available PCR instruments through the characterization of the temperature profiles produced, and a minimal method comparison.  ...  Molecular assays targeted to nucleic acid (NA) markers are becoming increasingly important to medical diagnostics.  ...  Acknowledgments The authors wish to thank all of their colleagues at PATH for their valuable input and criticism.  ... 
doi:10.1371/journal.pone.0019738 pmid:21573065 pmcid:PMC3090398 fatcat:c7ayclktorc6ddqep2fv7oichy
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