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The most probable origin of the primer(s) is viral RNase H-generated fragments of the viral RNA template.
Our results highlight the linker as directly involved in lifting the first boundary to processive RNA synthesis, the formation of the first dinucleotide primer.
Weiss and Nakamoto have presented preliminary evidence indicating that the relative position of ribonucleotides in enzymatically prepared RNA is determined by the primer used for the reaction.8 This information, along with the similar base composition found, suggests, but does not prove, that synthesis occurs with replication of the nucleotide sequences of the primer.
While chemical synthesis and gel or chromatographic purification of RNA is costly and difficult for sequences longer than tens of nucleotides, a pipeline of primer assembly of DNA templates, in vitro transcription by T7 RNA polymerase and kit-based purification provides a cost-effective and fast alternative for preparing RNA molecules.
This result suggests that the substantial mass of RNA can be accommodated between the binding site for the primer (and nascent RNA) and the catalytic center of RNA polymerization.
We report here a server named Primerize that makes available an efficient algorithm for primer design developed and experimentally tested in our laboratory for RNA domains with lengths up to 300 nucleotides.
Covalent linkage between the RNA and the newly synthesized complementary DNA chain indicates that the RNA transcript serves as a primer.
Efforts to provide experimental support for the RNA world hypothesis have focused on producing such a polymerase, and in vitro evolution methods have led to the isolation of a polymerase ribozyme that catalyzes primer extension which is accurate and general, but slow.
Open accessJournal ArticleDOI
J M Taylor, R Illmensee 
152 Citations
The present study confirms that finding and demonstrates that, at least for the majority of 35S RNA molecules, the primer is bound at a site close to the 5'-terminus.
Open accessJournal ArticleDOI
01 Nov 1995-Genome Research
15 Citations
We show that RNA can serve as a primer in PCR.

Related Questions

Why RNA polymerase doesn't need primer?5 answersRNA polymerases, like the optimized ribozyme polymerase and the polymerase from a dsRNA virus, do not require primers due to their ability to engage substrates entirely through tertiary interactions. For instance, the ribozyme polymerase recognizes the RNA template, primer, and incoming nucleoside 5'-triphosphate through tertiary contacts, enabling unconstrained genetic information transmission. Similarly, the dsRNA virus polymerase catalyzes RNA synthesis without the need for a primer, showcasing high processivity and a primer-independent initiation capability. These polymerases exhibit unique structural features and interactions that allow them to efficiently initiate and carry out RNA synthesis without the reliance on primers, highlighting their adaptability and efficiency in genetic material replication.
Whats the difference between designing a primer for DNA and RNA in bacteria?5 answersDesigning a primer for DNA and RNA in bacteria differs in terms of the type of polymerase used and the requirements for primer synthesis. DNA primers are typically designed for PCR-based cloning, where a DNA part is copied and restrictive sites are added for easy cloning into a plasmid. On the other hand, RNA primers are synthesized by specialized enzymes called primases for DNA replication. The main requirement for an RNA primer is an exposed RNA 3' end annealed to the DNA template. However, some replication systems in bacteria have evolved to use cellular DNA-dependent RNA polymerase for primer synthesis. These RNA primers are formed in a previously unrecognized kind of transcription complex, where the RNA-DNA hybrid is overextended and bound in the RNA polymerase trough. This allows the 3' end of the RNA to interact with DNA polymerase for replication.
How is RNA sequencing used to study gene expression?5 answersRNA sequencing is a widely used method for studying gene expression. It allows researchers to quantify and compare gene expression changes in different experimental conditions. By sequencing RNA transcripts, researchers can identify different cell subpopulations and their respective marker genes. This technique also enables the investigation of transcriptional responses to mechanical stimulation. Additionally, RNA sequencing can be used to estimate the gene expression profile of individual cells, allowing for the analysis of biological phenomena that cannot be observed in bulk RNA sequencing. It has been shown that RNA sequencing can accurately detect differentially expressed genes and has the added benefits of alternative splicing detection and gene-body variant detection. However, it is important to note that the inclusion of realistic amounts of transcriptional noise can lead to systematic errors in measuring gene expression levels.
Are RNA primers reused?9 answers
Do you need RNA polymerase for DNA sequencing?10 answers
How is Covid RNA made?9 answers

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