1
|
Fulghum B, Tanker SH, White RA. DeGenPrime provides robust primer design and optimization unlocking the biosphere. BIOINFORMATICS ADVANCES 2024; 4:vbae044. [PMID: 38590916 PMCID: PMC11001487 DOI: 10.1093/bioadv/vbae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/19/2024] [Accepted: 03/12/2024] [Indexed: 04/10/2024]
Abstract
Motivation Polymerase chain reaction (PCR) is the world's most important molecular diagnostic with applications ranging from medicine to ecology. PCR can fail because of poor primer design. The nearest-neighbor thermodynamic properties, picking conserved regions, and filtration via penalty of oligonucleotides form the basis for good primer design. Results DeGenPrime is a console-based high-quality PCR primer design tool that can utilize MSA formats and degenerate bases expanding the target range for a single primer set. Our software utilizes thermodynamic properties, filtration metrics, penalty scoring, and conserved region finding of any proposed primer. It has degeneracy, repeated k-mers, relative GC content, and temperature range filters. Minimal penalty scoring is included according to secondary structure self-dimerization metrics, GC clamping, tri- and tetra-loop hairpins, and internal repetition. We compared PrimerDesign-M, DegePrime, ConsensusPrimer, and DeGenPrime on acceptable primer yield. PrimerDesign-M, DegePrime, and ConsensusPrimer provided 0%, 11%, and 17% yield, respectively, for the alternative iron nitrogenase (anfD) gene target. DeGenPrime successfully identified quality primers within the conserved regions of the T4-like phage major capsid protein (g23), conserved regions of molybdenum-based nitrogenase (nif), and its alternatives vanadium (vnf) and iron (anf) nitrogenase. DeGenPrime provides a universal and scalable primer design tool for the entire tree of life. Availability and implementation DeGenPrime is written in C++ and distributed under a BSD-3-Clause license. The source code for DeGenPrime is freely available on www.github.com/raw-lab/degenprime.
Collapse
Affiliation(s)
- Bryan Fulghum
- Department of Bioinformatics and Genomics, North Carolina Research Campus (NCRC), The University of North Carolina at Charlotte, Kannapolis, NC 28081, United States
- Department of Bioinformatics and Genomics, Computational Intelligence to Predict Health and Environmental Risks (CIPHER) Research Center, The University of North Carolina at Charlotte, Charlotte, NC 28223, United States
| | - Sophie H Tanker
- Department of Bioinformatics and Genomics, North Carolina Research Campus (NCRC), The University of North Carolina at Charlotte, Kannapolis, NC 28081, United States
- Department of Bioinformatics and Genomics, Computational Intelligence to Predict Health and Environmental Risks (CIPHER) Research Center, The University of North Carolina at Charlotte, Charlotte, NC 28223, United States
| | - Richard Allen White
- Department of Bioinformatics and Genomics, North Carolina Research Campus (NCRC), The University of North Carolina at Charlotte, Kannapolis, NC 28081, United States
- Department of Bioinformatics and Genomics, Computational Intelligence to Predict Health and Environmental Risks (CIPHER) Research Center, The University of North Carolina at Charlotte, Charlotte, NC 28223, United States
| |
Collapse
|
2
|
Jiang W, Yue S, He S, Chen C, Liu S, Jiang H, Tong H, Liu X, Wang J, Zhang F, Sun H, Li M, Wang C. New design of probe and central-homo primer pairs to improve TaqMan™ PCR accuracy for HBV detection. J Virol Methods 2018; 254:25-30. [PMID: 29407210 DOI: 10.1016/j.jviromet.2018.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 01/03/2023]
Abstract
Quantitative PCR (qPCR) assay using TaqMan™ probe was widely used in the detection of different nucleic acids. However, this technology has several drawbacks, including false negative results caused by primer-dimer (PD) and false positive issues due to primer-probe aggregations. Here, we designed a modified TaqMan™-Molecular Beacon probe by adding an antisense base and a new type of primer pair named central-homo primer pairs bearing 5-10 bases homologous sequence on the 3' end. Using the HBV qPCR assay as a proof of concept, the new design significantly improved the accuracy of the TaqMan™ qPCR assay for HBV detection. Application of the central-homo primer pair led to significantly delayed Ct values by 5-10 cycles compared with conventional primer design. The modified probe containing an antisense base did not produce any detectable signal in repeating primer-probe aggregation experiments. Furthermore, the use of the central-homo primer pair and the non-competitive internal control could solve the false negative problem caused by PD formation. We validated this customized duplex qPCR system using 208 clinical samples collected from patients in clinic showing accuracy was higher than that of the conventional qPCR method.
Collapse
Affiliation(s)
- Wencan Jiang
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China; College of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Suwen Yue
- Beijing Tag Array Molecular Test Co., Ltd, Beijing 100085, People's Republic of China
| | - Shang He
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Chen Chen
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Shanshan Liu
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China; College of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Hong Jiang
- Beijing Tag Array Molecular Test Co., Ltd, Beijing 100085, People's Republic of China
| | - Hongli Tong
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Xiaoting Liu
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Jianan Wang
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China; College of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Fan Zhang
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Huizhen Sun
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Mianyang Li
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Chengbin Wang
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China.
| |
Collapse
|
3
|
Caparco AA, Bommarius AS, Champion JA. Effect of peptide linker length and composition on immobilization and catalysis of leucine zipper‐enzyme fusion proteins. AIChE J 2018. [DOI: 10.1002/aic.16150] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Adam A. Caparco
- School of Chemical and Biomolecular Engineering, Petit Institute for Bioengineering and BioscienceGeorgia Institute of TechnologyAtlanta GA 30332
| | - Andreas S. Bommarius
- School of Chemical and Biomolecular Engineering, Petit Institute for Bioengineering and BioscienceGeorgia Institute of TechnologyAtlanta GA 30332
| | - Julie A. Champion
- School of Chemical and Biomolecular Engineering, Petit Institute for Bioengineering and BioscienceGeorgia Institute of TechnologyAtlanta GA 30332
| |
Collapse
|
4
|
Durney BC, Crihfield CL, Holland LA. Capillary electrophoresis applied to DNA: determining and harnessing sequence and structure to advance bioanalyses (2009-2014). Anal Bioanal Chem 2015; 407:6923-38. [PMID: 25935677 PMCID: PMC4551542 DOI: 10.1007/s00216-015-8703-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/09/2015] [Accepted: 04/13/2015] [Indexed: 12/17/2022]
Abstract
This review of capillary electrophoresis methods for DNA analyses covers critical advances from 2009 to 2014, referencing 184 citations. Separation mechanisms based on free-zone capillary electrophoresis, Ogston sieving, and reptation are described. Two prevalent gel matrices for gel-facilitated sieving, which are linear polyacrylamide and polydimethylacrylamide, are compared in terms of performance, cost, viscosity, and passivation of electroosmotic flow. The role of capillary electrophoresis in the discovery, design, and characterization of DNA aptamers for molecular recognition is discussed. Expanding and emerging techniques in the field are also highlighted.
Collapse
Affiliation(s)
- Brandon C Durney
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | | | | |
Collapse
|
5
|
Yoon H, Leitner T. PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes. Bioinformatics 2014; 31:1472-4. [PMID: 25524896 DOI: 10.1093/bioinformatics/btu832] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 12/11/2014] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Analyses of entire viral genomes or mtDNA requires comprehensive design of many primers across their genomes. Furthermore, simultaneous optimization of several DNA primer design criteria may improve overall experimental efficiency and downstream bioinformatic processing. To achieve these goals, we developed PrimerDesign-M. It includes several options for multiple-primer design, allowing researchers to efficiently design walking primers that cover long DNA targets, such as entire HIV-1 genomes, and that optimizes primers simultaneously informed by genetic diversity in multiple alignments and experimental design constraints given by the user. PrimerDesign-M can also design primers that include DNA barcodes and minimize primer dimerization. PrimerDesign-M finds optimal primers for highly variable DNA targets and facilitates design flexibility by suggesting alternative designs to adapt to experimental conditions. AVAILABILITY AND IMPLEMENTATION PrimerDesign-M is available as a webtool at http://www.hiv.lanl.gov/content/sequence/PRIMER_DESIGN/primer_design.html CONTACT tkl@lanl.gov or seq-info@lanl.gov.
Collapse
Affiliation(s)
- Hyejin Yoon
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| |
Collapse
|
6
|
Pan Y, Karns K, Herr AE. Microfluidic electrophoretic mobility shift assays for quantitative biochemical analysis. Electrophoresis 2014; 35:2078-90. [PMID: 24591076 DOI: 10.1002/elps.201300500] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 01/31/2014] [Accepted: 02/09/2014] [Indexed: 02/02/2023]
Abstract
Electrophoretic mobility shift assays (EMSAs) play an important role in analytical chemistry, quantitative bioscience, and point-of-care diagnostics. Emerging microfluidic lab-on-a-chip technologies bring high throughput and multiplexed analysis to affinity-based electrophoretic separations, greatly advancing the performance of traditional EMSAs. This review elaborates on the relevant theoretical basis for EMSAs, surveys microfluidic-based EMSA applications in molecular conformation analyses, immunoassays, affinity assays and genomics, and outlines challenges and potential future improvements needed from this powerful assay.
Collapse
Affiliation(s)
- Yuchen Pan
- Graduate Program in Bioengineering, University of California San Francisco and University of California Berkeley, CA, USA
| | | | | |
Collapse
|
7
|
Brodin J, Krishnamoorthy M, Athreya G, Fischer W, Hraber P, Gleasner C, Green L, Korber B, Leitner T. A multiple-alignment based primer design algorithm for genetically highly variable DNA targets. BMC Bioinformatics 2013; 14:255. [PMID: 23965160 PMCID: PMC3765731 DOI: 10.1186/1471-2105-14-255] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 08/20/2013] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to population diversity and primer localization in relatively conserved regions, in addition to recognized constraints typically considered in primer design. RESULTS Design constraints include degenerate sites to maximize population coverage, matching of melting temperatures, optimizing de novo sequence length, finding optimal bio-barcodes to allow efficient downstream analyses, and minimizing risk of dimerization. To facilitate primer design addressing these and other constraints, we created a novel computer program (PrimerDesign) that automates this complex procedure. We show its powers and limitations and give examples of successful designs for the analysis of HIV-1 populations. CONCLUSIONS PrimerDesign is useful for researchers who want to design DNA primers and probes for analyzing highly variable DNA populations. It can be used to design primers for PCR, RT-PCR, Sanger sequencing, next-generation sequencing, and other experimental protocols targeting highly variable DNA samples.
Collapse
Affiliation(s)
- Johanna Brodin
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|