Effects of Different DNA Polymerases in Ligation-mediated PCR: Enhanced Genomic Sequencing and in Vivo Footprinting

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1992 Feb 1

PMID 1736283

Citations 77

Authors

P A Garrity

B J Wold

Affiliations

Soon will be listed here.

Abstract

We have developed a simplified procedure for the ligation-mediated polymerase chain reaction (LMPCR) using Thermococcus litoralis DNA polymerase (Vent DNA polymerase). We show that Vent DNA polymerase produces correct, blunt-ended primer extension products with substantially higher efficiency than Thermus aquaticus (Taq) DNA polymerase or modified T7 DNA polymerase (Sequenase). This difference leads to significantly improved genomic sequencing, methylation analysis, and in vivo footprinting with LMPCR. These improvements include representation of all bands with more uniform intensity, clear visualization of previously difficult regions of sequence, and reduction in the occurrence of spurious bands. It also simplifies the use of DNase I cut DNA for LMPCR footprinting.

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References

Kara C, Glimcher L . In vivo footprinting of MHC class II genes: bare promoters in the bare lymphocyte syndrome. Science. 1991; 252(5006):709-12. DOI: 10.1126/science.1902592. View

Pfeifer G, Riggs A . Chromatin differences between active and inactive X chromosomes revealed by genomic footprinting of permeabilized cells using DNase I and ligation-mediated PCR. Genes Dev. 1991; 5(6):1102-13. DOI: 10.1101/gad.5.6.1102. View

Lyon M . The quest for the X-inactivation centre. Trends Genet. 1991; 7(3):69-70. DOI: 10.1016/0168-9525(91)90271-Q. View

Mirkovitch J, Darnell Jr J . Rapid in vivo footprinting technique identifies proteins bound to the TTR gene in the mouse liver. Genes Dev. 1991; 5(1):83-93. DOI: 10.1101/gad.5.1.83. View

Tanguay R, Pfeifer G, Riggs A . PCR-aided DNaseI footprinting of single copy gene sequences in permeabilized cells. Nucleic Acids Res. 1990; 18(19):5902. PMC: 332351. DOI: 10.1093/nar/18.19.5902. View

Sternberg E, Spizz G, Perry W, Vizard D, Weil T, Olson E . Identification of upstream and intragenic regulatory elements that confer cell-type-restricted and differentiation-specific expression on the muscle creatine kinase gene. Mol Cell Biol. 1988; 8(7):2896-909. PMC: 363509. DOI: 10.1128/mcb.8.7.2896-2909.1988. View

Clark J . Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases. Nucleic Acids Res. 1988; 16(20):9677-86. PMC: 338772. DOI: 10.1093/nar/16.20.9677. View

Solter D . Differential imprinting and expression of maternal and paternal genomes. Annu Rev Genet. 1988; 22:127-46. DOI: 10.1146/annurev.ge.22.120188.001015. View

Zhang L, Gralla J . In situ nucleoprotein structure at the SV40 major late promoter: melted and wrapped DNA flank the start site. Genes Dev. 1989; 3(11):1814-22. DOI: 10.1101/gad.3.11.1814. View

10.

Pfeifer G, Steigerwald S, Mueller P, Wold B, Riggs A . Genomic sequencing and methylation analysis by ligation mediated PCR. Science. 1989; 246(4931):810-3. DOI: 10.1126/science.2814502. View

11.

Mueller P, Wold B . In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. Science. 1989; 246(4931):780-6. DOI: 10.1126/science.2814500. View

12.

Mueller P, Salser S, Wold B . Constitutive and metal-inducible protein:DNA interactions at the mouse metallothionein I promoter examined by in vivo and in vitro footprinting. Genes Dev. 1988; 2(4):412-27. DOI: 10.1101/gad.2.4.412. View

13.

Jaynes J, Johnson J, Buskin J, Gartside C, Hauschka S . The muscle creatine kinase gene is regulated by multiple upstream elements, including a muscle-specific enhancer. Mol Cell Biol. 1988; 8(1):62-70. PMC: 363080. DOI: 10.1128/mcb.8.1.62-70.1988. View

14.

Ephrussi A, Church G, Tonegawa S, Gilbert W . B lineage--specific interactions of an immunoglobulin enhancer with cellular factors in vivo. Science. 1985; 227(4683):134-40. DOI: 10.1126/science.3917574. View

15.

Rideout 3rd W, Coetzee G, Olumi A, Jones P . 5-Methylcytosine as an endogenous mutagen in the human LDL receptor and p53 genes. Science. 1990; 249(4974):1288-90. DOI: 10.1126/science.1697983. View

16.

Church G, Gilbert W . Genomic sequencing. Proc Natl Acad Sci U S A. 1984; 81(7):1991-5. PMC: 345422. DOI: 10.1073/pnas.81.7.1991. View

17.

Maxam A, Gilbert W . Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980; 65(1):499-560. DOI: 10.1016/s0076-6879(80)65059-9. View