Methods of copying the methylation pattern of DNA during isothermal amplification and microarrays
First Claim
1. A method for copying the methylation patterns of molecules of genomic DNA (MGD) during isothermal amplification of the MGD, which method comprises:
- (i) obtaining MGD,(ii) copying the methylation patterns of the MGD using a DNA methylation-maintenance enzyme, while isothermally amplifying the MGD using a DNA polymerase with strand displacement activity, under conditions that simultaneously promote activity of the DNA methylation-maintenance enzyme and the DNA polymerase with strand displacement activity, wherein the DNA methylation-maintenance enzyme is DNA methyltransferase 1 (DNMT-1) and wherein the DNMT- 1 is optionally modified to reduce or eliminate de novo methylation activity, and(iii) optionally purifying the MGD, whereupon the MGD are amplified and their methylation patterns are copied.
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Abstract
A method for copying the methylation patterns of molecules of genomic DNA (MGD) during isothermal amplification of the MGD comprising obtaining MGD, copying the methylation patterns of the MGD using a DNA methylation-maintenance enzyme, while isothermally amplifying the MGD using a DNA polymerase with strand displacement activity, under conditions that simultaneously promote activity of the DNA methylation-maintenance enzyme and the DNA polymerase; a method for copying the methylation patterns in double-stranded DNA molecules during isothermal amplification of the DNA molecules comprising obtaining DNA molecules, contacting the DNA molecules with transposable elements and an enzyme, which can randomly insert the transposable elements into the DNA molecules, copying the methylation patterns of the DNA molecules using a DNA methylation-maintenance enzyme, while isothermally amplifying the DNA molecules using a DNA polymerase with strand displacement activity, under conditions that simultaneously promote activity of the DNA methylation-maintenance enzyme and the DNA polymerase; a buffer comprising a divalent ion, deoxynucleotide triphosphates (dNTPs), primers, and S-adenosyl-methionine (SAM); and a composition comprising a DNA methylation-maintenance enzyme, a DNA polymerase with strand displacement activity, and the buffer.
43 Citations
13 Claims
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1. A method for copying the methylation patterns of molecules of genomic DNA (MGD) during isothermal amplification of the MGD, which method comprises:
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(i) obtaining MGD, (ii) copying the methylation patterns of the MGD using a DNA methylation-maintenance enzyme, while isothermally amplifying the MGD using a DNA polymerase with strand displacement activity, under conditions that simultaneously promote activity of the DNA methylation-maintenance enzyme and the DNA polymerase with strand displacement activity, wherein the DNA methylation-maintenance enzyme is DNA methyltransferase 1 (DNMT-1) and wherein the DNMT- 1 is optionally modified to reduce or eliminate de novo methylation activity, and (iii) optionally purifying the MGD, whereupon the MGD are amplified and their methylation patterns are copied. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)
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13. A composition for methylation-coupled amplification of DNA comprising a DNMT-1, a DNA polymerase with strand displacement activity, and a buffer comprising a divalent ion, dNTPs, primers, and SAM, wherein the buffer is suitable for simultaneously promoting the activity of a DNA methylation-maintenance enzyme and a DNA polymerase with strand displacement activity and wherein the composition lacks a divalent cation chelator.
Specification