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Emonet SF, Grard G, Brisbarre NM, Moureau GN, Temmam S, Charrel RN, de Lamballerie X. Long PCR Product Sequencing (LoPPS): a shotgun-based approach to sequence long PCR products. Nat Protoc 2007; 2:340-6. [PMID: 17406595 DOI: 10.1038/nprot.2006.453] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Here we describe a practical procedure for sequencing long PCR products. The method relies on ultrasonic shearing of PCR products, resulting in fragments 700-1,000 nt long. Termini are subsequently repaired to obtain blunt ends and 3' A-overhangs are added before TA cloning. A predetermined number of clones are sequenced using an insert-independent primer to obtain an overlapping contig covering the full length of the PCR product. This method is cost effective and enables the complete sequencing of any large PCR product in a high-throughput format. Processing of amplified DNA requires 3 h handling time prior to the ligation step, and the clone library is available 2 d later. The complete sequence information is obtained approximately 5 d after the PCR step, depending on the sequencing procedure adopted.
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Affiliation(s)
- Sébastien F Emonet
- Unité des Virus Emergents (EA3292, IFR48, IRD UR034), Faculté de Médecine, 27 boulevard Jean Moulin, 13005 Marseille, France
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Loakes D, Hill F, Brown DM, Ball S, Reeve MA, Robinson PS. 5′-Tailed Octanucleotide Primers for Cycle Sequencing. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319908044634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- D. Loakes
- a Medical Research Council, Laboratory of Molecular Biology , Hills Road, Cambridge , CB2 2QH , UK
| | - F. Hill
- a Medical Research Council, Laboratory of Molecular Biology , Hills Road, Cambridge , CB2 2QH , UK
| | - D. M. Brown
- a Medical Research Council, Laboratory of Molecular Biology , Hills Road, Cambridge , CB2 2QH , UK
| | - S. Ball
- b Nycomed Amersham plc, Amersham Laboratories , White Lion Road, Amersham, Buckinghamshire , HP7 9LL , UK
| | - M. A. Reeve
- b Nycomed Amersham plc, Amersham Laboratories , White Lion Road, Amersham, Buckinghamshire , HP7 9LL , UK
| | - P. S. Robinson
- b Nycomed Amersham plc, Amersham Laboratories , White Lion Road, Amersham, Buckinghamshire , HP7 9LL , UK
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Abstract
BACKGROUND There is a need for DNA sequencing methods that are faster, more accurate, and less expensive than existing techniques. Here we present a new method for DNA analysis by means of indexer walking. METHODS For DNA sequencing by indexer walking, we ligated double-stranded synthetic oligonucleotides (indexers) to DNA fragments that were produced by type IIS restriction endonucleases, which generate nonidentical 4-nucleotide 5' overhangs. The subsequent amplification (30 thermal cycles) of indexed DNA provided a template for automated DNA sequencing with fluorescent dideoxy terminators. The data gathered in the first sequencing reaction permitted further movement into the unknown nucleotide sequence by digestion of analyzed DNA with selected type IIS restriction endonuclease followed by ligation of the next indexer. A library of presynthesized indexers consisting of 256 oligonucleotides was used for bidirectional analysis of DNA molecules and provided universal primers for sequencing. RESULTS The proposed protocol was successfully applied to sequencing of cryptic plasmids isolated from pathogenic strains of Escherichia coli. The overall error rate for base-calling was 0.5%, with a mean read length of 550 nucleotides. Approximately 1000 nucleotides of high-quality sequence could be obtained per day from a single clone. CONCLUSIONS Indexer walking can be used as a low-cost procedure for nucleotide sequence determination of DNA molecules, such as natural plasmids, cDNA clones, and longer DNA fragments. It can also serve as an alternative method for gap filling at the final stage of genome sequencing projects.
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Affiliation(s)
- Katarzyna Gromek
- Department of Microbiology, University of Gdańsk, Gdańsk, Poland
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Kraltcheva AI, Hardin SH. Octamer-primed sequencing technology: effects of dNTP supplementation. Nucleic Acids Res 2001; 29:E48. [PMID: 11353093 PMCID: PMC55469 DOI: 10.1093/nar/29.10.e48] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Octamer-primed sequencing is a directed DNA sequencing strategy that employs the use of a presynthesized octamer primer library. Together with electronic octamer sequencing technology (eOST) it provides a faster, less expensive way to obtain DNA sequence information and can be used as a valuable tool for gap closure in large-scale genomic sequencing. In this paper we discuss the effect of dGTP/TTP supplementation on octamer sequencing. We show that addition of 75 microM dGTP and 5 microM TTP can improve the sequencing success rate by increasing the length and accuracy of generated sequence information. We also discuss the effect of template base composition immediately downstream of the octamer primer on the outcome of octamer sequencing.
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Affiliation(s)
- A I Kraltcheva
- Department of Biology and Biochemistry and Institute of Molecular Biology, University of Houston, Houston, TX 77204-5513, USA
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Lyons LC, Darlington TK, Hao H, Houl J, Kay SA, Hardin PE. Specific sequences outside the E-box are required for proper per expression and behavioral rescue. J Biol Rhythms 2000; 15:472-82. [PMID: 11106064 DOI: 10.1177/074873040001500604] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A 69 bp circadian regulatory sequence (CRS) upstream of the per gene is sufficient to drive circadian transcription, mediate proper spatial expression, and rescue behavioral rhythmicity in per01 flies. Within the CRS, an E-box is required for transcriptional activation by two basic-helix-loop-helix (bHLH) PERARNT-SIM (PAS) transcription factors, dCLOCK (dCLK) and CYCLE (CYC). To define sequences within the CRS that are required for spatial expression, circadian expression, and behavioral rhythmicity, a series of mutants that alter blocks of 3 to 12 nucleotides across the entire CRS were used to drive lacZ or per expression in vivo. As expected, the E-box within the CRS is necessary for high-level expression and behavioral rhythmicity, but sequences outside the E-box are also required for transcriptional activation, proper spatial expression, and behavioral rhythmicity. These results indicate that the dCLK-CYC target site extends beyond the E-box and that factors other than dCLK and CYC modulate per transcription.
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Affiliation(s)
- L C Lyons
- Department of Biology and Biochemistry, University of Houston, TX, USA
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Mei G, Hardin SH. Octamer-primed sequencing technology: development of primer identification software. Nucleic Acids Res 2000; 28:E22. [PMID: 10710439 PMCID: PMC102805 DOI: 10.1093/nar/28.7.e22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Octamer sequencing technology (OST) is a primer-directed sequencing strategy in which an individual octamer primer is selected from a pre-synthesized octamer primer library and used to sequence a DNA fragment. However, selecting candidate primers from such a library is time consuming and can be a bottleneck in the sequencing process. To accelerate the sequencing process and to obtain high quality sequencing data, a computer program, electronic OST or eOST, was developed to automatically identify candidate primers from an octamer primer library. eOST integrates the base calling software PHRED to provide a quality assessment for target sequences and identifies potential primer binding sites located within a high quality target region. To increase the sequencing success rate, eOST includes a simple dynamic folding algorithm to automatically calculate the free energy and predict the secondary structure within the template in the vicinity of the octamer-binding site. Several parameters were found to be important, including base quality threshold, the window size of the template sequence segment, and the threshold [Delta] G value. OST, coupled with the eOST software, can be used to sequence short DNA fragments or in the finishing assembly stage of large-scale sequencing of genomic DNA.
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Affiliation(s)
- G Mei
- Department of Biology and Biochemistry, Institute of Molecular Biology, University of Houston, Houston, TX 77204-5513, USA
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7
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The 69 bp circadian regulatory sequence (CRS) mediates per-like developmental, spatial, and circadian expression and behavioral rescue in Drosophila. J Neurosci 1999. [PMID: 9920662 DOI: 10.1523/jneurosci.19-03-00987.1999] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The period (per) gene is an essential component of the circadian timekeeping mechanism in Drosophila. This gene is expressed in a circadian manner, giving rise to a protein that feeds-back to regulate its own transcription. A 69 bp clock regulatory sequence (CRS) has been identified previously upstream of the period gene. The CRS confers wild-type mRNA cycling when used to drive a lacZ reporter gene in transgenic flies. To determine whether the CRS also mediates proper developmental and spatial expression and behavioral rescue, we used the CRS to drive either lacZ or per in transgenic flies. The results show that the CRS is able to activate expression in pacemaker neuron precursors in larvae and essentially all tissues that normally express per in pupae and adults. The CRS is sufficient to rescue circadian feedback loop function and behavioral rhythms in per01 flies. However, the period of locomotor activity rhythms shortens if a stronger basal promoter is used. This study shows that regulatory elements sufficient for clock-dependent and tissue-specific per expression in larvae, pupae, and adults are present in the CRS and that the period of adult locomotor activity rhythms is dependent, in part, on the overall level of per transcripts.
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Allen BL, Uhlmann F, Gaur LK, Mulder BA, Posey KL, Jones LB, Hardin SH. DNA recognition properties of the N-terminal DNA binding domain within the large subunit of replication factor C. Nucleic Acids Res 1998; 26:3877-82. [PMID: 9705493 PMCID: PMC147807 DOI: 10.1093/nar/26.17.3877] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Replication Factor C (RFC) is a five-subunit protein complex required for eukaryotic DNA replication and repair. The large subunit within this complex contains a C-terminal DNA binding domain which provides specificity for PCNA loading at a primer-template and a second, N-terminal DNA binding domain of unknown function. We isolated the N-terminal DNA binding domain from Drosophila melanogaster and defined the region within this polypeptide required for DNA binding. The DNA determinants most efficiently recognized by both the Drosophila minimal DNA binding domain and the N-terminal half of the human large subunit consist of a double-stranded DNA containing a recessed 5' phosphate. DNA containing a recessed 5' phosphate was preferred 5-fold over hairpined DNA containing a recessed 3' hydroxyl. Combined with existing data, these DNA binding properties suggest a role for the N-terminal DNA binding domain in the recognition of phosphorylated DNA ends.
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Affiliation(s)
- B L Allen
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
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Abstract
Octamer Sequencing Technology, OST, is a method of DNA sequencing using single octamer oligonucleotides to prime cycle sequencing reactions. This sequencing strategy is faster than a traditional primer-walking strategy, since access to this optimized octamer library eliminates delays associated with designing and synthesizing gene specific primers. In this report, OST has been optimized for fluorescent, dye-terminator cycle sequencing reactions to facilitate parallel processing of samples. The successful adaptation of OST to an automated sequencing platform and the design of and access to an octamer library are critical steps towards developing an efficient 'closed-loop' DNA sequencing system.
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Affiliation(s)
- L B Jones
- Department of Biology and Biochemistry, and Institute of Molecular Biology, University of Houston, Houston, TX 77204-5513, USA
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Hao H, Allen DL, Hardin PE. A circadian enhancer mediates PER-dependent mRNA cycling in Drosophila melanogaster. Mol Cell Biol 1997; 17:3687-93. [PMID: 9199302 PMCID: PMC232220 DOI: 10.1128/mcb.17.7.3687] [Citation(s) in RCA: 184] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Genes expressed under circadian-clock control are found in organisms ranging from prokaryotes to humans. In Drosophila melanogaster, the period (per) gene, which is required for clock function, is transcribed in a circadian manner. We have identified a circadian transcriptional enhancer within a 69-bp DNA fragment upstream of the per gene. This enhancer drives high-amplitude mRNA cycling under light-dark-cycling or constant-dark conditions, and this activity is per protein (PER) dependent. An E-box sequence within this 69-bp fragment is necessary for high-level expression, but not for rhythmic expression, indicating that PER mediates circadian transcription through other sequences in this fragment.
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Affiliation(s)
- H Hao
- Department of Biology, Texas A & M University, College Station 77843-3258, USA
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Raja MC, Zevin-Sonkin D, Shwartzburd J, Rozovskaya TA, Sobolev IA, Chertkov O, Ramanathan V, Lvovsky L, Ulanovsky LE. DNA sequencing using differential extension with nucleotide subsets (DENS). Nucleic Acids Res 1997; 25:800-5. [PMID: 9016632 PMCID: PMC146503 DOI: 10.1093/nar/25.4.800] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Here we describe template directed enzymatic synthesis of unique primers, avoiding the chemical synthesis step in primer walking. We have termed this conceptually new technique DENS (differential extension with nucleotide subsets). DENS works by selectively extending a short primer, making it a long one at the intended site only. The procedure starts with a limited initial extension of the primer (at 20-30 degrees C) in the presence of only two out of the four possible dNTPs. The primer is extended by 6-9 bases or longer at the intended priming site, which is deliberately selected, (as is the two-dNTP set), to maximize the extension length. The subsequent termination reaction at 60-65 degrees C then accepts the extended primer at the intended site, but not at alternative sites, where the initial extension (if any) is generally much shorter. DENS allows the use of primers as long as 8mers (degenerate in two positions) which prime much more strongly than modular primers involving 5-7mers and which (unlike the latter) can be used with thermostable polymerases, thus allowing cycle-sequencing with dye-terminators compatible with Taq DNA polymerase, as well as making double-stranded DNA sequencing more robust.
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Affiliation(s)
- M C Raja
- Center for Mechanistic Biology and Biotechnology, Argonne National Laboratory IL 60439-4833, USA
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