Limits...
Use of molecular beacons to verify that the serine hydroxymethyltransferase pseudogene SHMT-ps1 is unique to the order Primates.

Devor EJ - Genome Biol. (2001)

Bottom Line: In a search for SHMT-ps1-specific sequences using molecular beacons across a range of mammalian species, SHMT-ps1 was only found in primates.The molecular beacon assays also showed that SHMT-ps1 is present in both Old World and New World species but not among prosimians.These results suggest that SHMT-ps1 originated close to the origin of the Anthropoidea, some 40 to 50 million years ago.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Genetics and Bioinformatics, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA. rdevor@idtdna.com

ABSTRACT

Background: The serine hydroxymethyltransferase processed pseudogene SHMT-ps1 has been suggested to be unique to the order Primates because of the failure to amplify this sequence by PCR from genomic DNAs of any non-primate mammal species. Here, 'molecular beacon' probes specific to SHMT-ps1 were used in an attempt to verify this suggestion.

Results: In a search for SHMT-ps1-specific sequences using molecular beacons across a range of mammalian species, SHMT-ps1 was only found in primates. The molecular beacon assays also showed that SHMT-ps1 is present in both Old World and New World species but not among prosimians.

Conclusions: These results suggest that SHMT-ps1 originated close to the origin of the Anthropoidea, some 40 to 50 million years ago.

Show MeSH
Representation of the SHMT-ps1 region amplified by the C1/B6 primers. The positions of the two molecular beacon sequences E8/E9 and E9/E10 are shown in relation to the exon-exon boundaries in SHMT-ps1.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC25776&req=5

Figure 2: Representation of the SHMT-ps1 region amplified by the C1/B6 primers. The positions of the two molecular beacon sequences E8/E9 and E9/E10 are shown in relation to the exon-exon boundaries in SHMT-ps1.

Mentions: Thermodynamic studies of molecular beacons suggest that conformationally constrained probes display enhanced hybridization specificity as a general feature [8]. The states in which a molecular beacon can exist are a random coil, the closed hairpin/loop structure, and a linearized structure bound to the target PCR product. When two or more competing molecular beacons are present, the enhanced hybridization specificity results in the ability to discriminate between target sequences that differ by as little as a single nucleotide [8,9,10,11]. In the present study, in which molecular beacon probes were used singly as end-point reporters, they were able to tolerate multiple mismatches in the target sequences. Comparative sequences homologous to the E8/E9 and E9/E10 probes (Figure 2) from several species are shown in Table 1. As can be seen, the species-specific target sequences differed from the probe sequences by as many as nine bases, with the average difference being 2.5 bases. Confidence in the ability of these highly sensitive probes to reliably detect the presence of target sequences that differ from the probe sequence by numerous bases is supported by the observation that the most divergent targets, those belonging to the Old World monkey species for the E8/E9 probe, still gave positive, albeit weakened, results. On the other hand, potential targets that were perfect matches or that differed by only one or two bases did not give any positive indications in the lemur and non-primate mammal samples (Figure 1).


Use of molecular beacons to verify that the serine hydroxymethyltransferase pseudogene SHMT-ps1 is unique to the order Primates.

Devor EJ - Genome Biol. (2001)

Representation of the SHMT-ps1 region amplified by the C1/B6 primers. The positions of the two molecular beacon sequences E8/E9 and E9/E10 are shown in relation to the exon-exon boundaries in SHMT-ps1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC25776&req=5

Figure 2: Representation of the SHMT-ps1 region amplified by the C1/B6 primers. The positions of the two molecular beacon sequences E8/E9 and E9/E10 are shown in relation to the exon-exon boundaries in SHMT-ps1.
Mentions: Thermodynamic studies of molecular beacons suggest that conformationally constrained probes display enhanced hybridization specificity as a general feature [8]. The states in which a molecular beacon can exist are a random coil, the closed hairpin/loop structure, and a linearized structure bound to the target PCR product. When two or more competing molecular beacons are present, the enhanced hybridization specificity results in the ability to discriminate between target sequences that differ by as little as a single nucleotide [8,9,10,11]. In the present study, in which molecular beacon probes were used singly as end-point reporters, they were able to tolerate multiple mismatches in the target sequences. Comparative sequences homologous to the E8/E9 and E9/E10 probes (Figure 2) from several species are shown in Table 1. As can be seen, the species-specific target sequences differed from the probe sequences by as many as nine bases, with the average difference being 2.5 bases. Confidence in the ability of these highly sensitive probes to reliably detect the presence of target sequences that differ from the probe sequence by numerous bases is supported by the observation that the most divergent targets, those belonging to the Old World monkey species for the E8/E9 probe, still gave positive, albeit weakened, results. On the other hand, potential targets that were perfect matches or that differed by only one or two bases did not give any positive indications in the lemur and non-primate mammal samples (Figure 1).

Bottom Line: In a search for SHMT-ps1-specific sequences using molecular beacons across a range of mammalian species, SHMT-ps1 was only found in primates.The molecular beacon assays also showed that SHMT-ps1 is present in both Old World and New World species but not among prosimians.These results suggest that SHMT-ps1 originated close to the origin of the Anthropoidea, some 40 to 50 million years ago.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Genetics and Bioinformatics, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA. rdevor@idtdna.com

ABSTRACT

Background: The serine hydroxymethyltransferase processed pseudogene SHMT-ps1 has been suggested to be unique to the order Primates because of the failure to amplify this sequence by PCR from genomic DNAs of any non-primate mammal species. Here, 'molecular beacon' probes specific to SHMT-ps1 were used in an attempt to verify this suggestion.

Results: In a search for SHMT-ps1-specific sequences using molecular beacons across a range of mammalian species, SHMT-ps1 was only found in primates. The molecular beacon assays also showed that SHMT-ps1 is present in both Old World and New World species but not among prosimians.

Conclusions: These results suggest that SHMT-ps1 originated close to the origin of the Anthropoidea, some 40 to 50 million years ago.

Show MeSH