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MELTING, a flexible platform to predict the melting temperatures of nucleic acids
2012
BMC Bioinformatics
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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
2014
Nucleic Acids Research
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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]
2020
bioRxiv
pre-print
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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
2010
Nucleic Acids Research
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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
2012
Nucleic Acids Research
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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
2016
PLoS ONE
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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
2005
Applied and Environmental Microbiology
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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
2004
Current Opinion in Microbiology
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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
2004
Current Opinion in Microbiology
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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
2014
Biochemistry
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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
2011
Genome Biology
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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
2021
Diagnostics
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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
2011
PLoS ONE
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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
2011
Nucleic Acids Research
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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
2011
PLoS ONE
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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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