Enzymatic Breakage and Joining of Deoxyribonucleic Acid

Fareed, George C.; Wilt, Elaine M.; Richardson, Charles C.

doi:10.1016/s0021-9258(18)62412-3

Cited by 73 publications

(4 citation statements)

References 35 publications

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“…Similar extents of RNA-to-RNA ligation by the T4 enzyme were observed when assays were performed using homopolymeric substrates (Fareed et al, 1971). The rate of RNA-to-RNA ligation on a DNA template by T4 DNA ligase was 1% of that of DNA-to-DNA strand joining (Fareed et al, 1971). Vaccinia DNA ligase appears to be even less active than the T4 protein in sealing two RNA strands on a DNA scaffold, as far as the yield of the RNApRNA ligation product is concerned.…”

Section: Discussionsupporting

confidence: 61%

“…substrate was not accurately bridged to form a nicked duplex (Moore & Sharp, 1992). Similar extents of RNA-to-RNA ligation by the T4 enzyme were observed when assays were performed using homopolymeric substrates (Fareed et al, 1971). The rate of RNA-to-RNA ligation on a DNA template by T4 DNA ligase was 1% of that of DNA-to-DNA strand joining (Fareed et al, 1971).…”

Section: Discussionmentioning

confidence: 67%

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Ligation of RNA-Containing Duplexes by Vaccinia DNA Ligase

Sekiguchi

Shuman

1997

Biochemistry

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Vaccinia virus DNA ligase repairs nicked duplex DNA substrates consisting of a 5'-phosphate-terminated strand and a 3'-hydroxyl-terminated strand annealed to a bridging template strand. This study addresses the ability of vaccinia DNA ligase to seal nicked substrates containing one or more RNA strands. We found that the viral enzyme rapidly and efficiently joined a 3'-OH RNA to 5'-phosphate DNA when the reacting polynucleotides were annealed to a bridging DNA strand. In contrast, ligation of 3'-OH DNA to 5'-phosphate RNA was slow (0.2% of the rate of RNA-to-DNA ligation) and entailed the accumulation of high levels of RNA-adenylate intermediate. A native gel mobility shift assay showed that vaccinia DNA ligase discriminates at the substrate binding step between ligands containing 5'-phosphate DNA versus 5'-phosphate RNA at the nick. The enzyme displayed weak activity in RNA-to-RNA ligation on a bridging DNA template (0.01% of RNA-to-DNA activity). Vaccinia DNA ligase was incapable of joining two DNAs annealed on an RNA template. These results can be explained by a requirement for B-form helical conformation on the 5'-phosphate side of the nick. The robust RNA-to-DNA strand joining activity underscores the potential for vaccinia DNA ligase to catalyze RNA-based integration of host cell genetic information into the genome of cytoplasmic poxviruses.

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Section: Discussionsupporting

confidence: 61%

Section: Discussionmentioning

confidence: 67%

Ligation of RNA-Containing Duplexes by Vaccinia DNA Ligase

Sekiguchi

Shuman

1997

Biochemistry

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“…Some prokaryotic DNA ligases also catalyze the joining of RNA and DNA in duplex conformations. T4 DNA ligase seals limited amounts of RNA to RNA in the presence of a complementary DNA strand, and of DNA to DNA in the presence of complementary RNA (Kleppe et al, 1970;Fareed et al, 1971). T4 and E. coli DNA ligases join S'-phosphoryl DNA to 3'-hydroxyl RNA on a complementary DNA strand (Nath and Hurwitz, 1974).…”

mentioning

confidence: 99%

L cell DNA ligase joins RNA to DNA on a DNA template

Bedows¹,

Wachsman²,

Gumport³

1977

Biochemistry

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L cell DNA ligase catalyzes a covalent linkage between 5'-hosphoryl oligodeoxyribonucleotides and 3'-hydroxyl oligoribonucleotides on a complementary polydeoxyribonucleotide template. This reaction occurs to a substantially lesser extent than does the sealing of DNA to DNA. The joining of [5'32P]d(pA)12-18 to (Ap)11A on poly[d(T)] or of [5'-32P]d(pG)12-18 to 5'-hydroxyl, 3'-hydroxyl oligo(I) ON POLY[D(C)] was demonstrated by the formation of alkaline phosphatase resistant radioactivity. The 32P of the hybrid reaction products became sensitive to the action of alkaline phosphatase after treatment with alkali. Furthermore, hydrolysis of the products of the linkage of [5'-32P]d(pG)12-18 to 5'-hydroxyl, 3'-hydroxyl oligo(I) on poly[d(C)] with micrococcal nuclease and spleen phosphodiesterase resulted in the formation of [3'-32P]IMP. Attempts to seal [5'-32p[-(pA)12 to d(Ap)11-17A on poly[d(T) or [5'-32P]oligo(pI) to d(Gp)11-17G on poly[d(C)] were unsuccessful.

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“…However, compared to DNA, RNA sequences are less efficient templates for circularization of padlock probes mediated by most DNA ligases. [117][118][119][120][121] Hence, although detection of RNA targets by RCA of circularized padlock probes has been reported 44,50,56,122,123 these assays often suffer from a rather low efficiency. Exceptions are the recently reported detections of specific miRNA or mRNA targets at fM concentrations using a dumbbell shaped padlock-like probe, 124 hyperbranched RCA (hRCA), 125,126 or a preformed circle DNA sensor of which RCA is primed from the RNA target.…”

Section: Insight Innovation Integrationmentioning

confidence: 99%

Strategies for highly sensitive biomarker detection by Rolling Circle Amplification of signals from nucleic acid composed sensors

et al. 2011

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The use of nucleic acids as components in highly sensitive biosensors has attracted increasing interest during recent years, not least due to the ease by which nucleic acids can be synthesized, manipulated and signal-amplified. To date, several enzymatic reactions, including Polymerase Chain Reaction, Rolling Circle- and Strand Displacement Amplification for signal enhancement of nucleic acid biosensors, have been presented. Of these, the isothermal Rolling Circle Amplification, in which a small single-stranded DNA circle is replicated to generate long tandem repeat products, presents the advantage of allowing single molecule detection and easy quantification as well as of posing little requirement to equipment and personnel training. Rolling Circle Amplification has been used to enhance signals of nucleic acid based sensors specific for a large variety of important biomarkers, including nucleotide sequences, small molecules, proteins and enzyme activities, allowing detection of biomarkers even at the aM concentration level. Moreover, Rolling Circle Products have been adapted to a broad variety of low technological and cost efficient readout formats making the technique appealing for future basic discovery research as well as for at-point-of-care diagnostic or prognostic tests.

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Enzymatic Breakage and Joining of Deoxyribonucleic Acid

Cited by 73 publications

References 35 publications

Ligation of RNA-Containing Duplexes by Vaccinia DNA Ligase

Ligation of RNA-Containing Duplexes by Vaccinia DNA Ligase

L cell DNA ligase joins RNA to DNA on a DNA template

Strategies for highly sensitive biomarker detection by Rolling Circle Amplification of signals from nucleic acid composed sensors

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