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Related Concept Videos

RNA Splicing01:32

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
pre-mRNA Processing02:01

pre-mRNA Processing

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl guanosine). This 5’ cap helps the...

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Related Experiment Video

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Aptamer-Based Target Detection Facilitated by a 3-Stage G-Quadruplex Isothermal Exponential Amplification Reaction
03:38

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ValFold: Program for the aptamer truncation process.

Joe Akitomi1, Shintaro Kato, Yoshihito Yoshida

  • 1VALWAY Technology Center, NEC Soft, Ltd., 1-18-7, Shinkiba Koto-ku, Tokyo 136-8627, Japan.

Bioinformation
|September 10, 2011
PubMed
Summary

A new software, ValFold, enhances aptamer design by accurately predicting DNA/RNA secondary structures, including G-quadruplexes. This tool aids in developing next-generation antibody-like molecules for medical and diagnostic applications.

Keywords:
SELEXaptameraptamer truncationsecondary structure prediction

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Area of Science:

  • Biotechnology and Bioinformatics
  • Molecular Biology
  • Computational Chemistry

Background:

  • Aptamers are emerging as advanced antibody-like molecules for medical diagnostics and therapeutics.
  • Accurate secondary structure prediction is crucial for optimizing aptamer sequences and chemical modifications during SELEX (Systematic Evolution of Ligands by EXponential enrichment).
  • Existing prediction tools may not fully capture the unique structural characteristics of aptamers, such as G-quadruplex formation.

Purpose of the Study:

  • To introduce ValFold, a novel software package designed for enhanced secondary structure prediction of nucleic acid aptamers.
  • To improve the accuracy of secondary structure prediction by accounting for unique aptamer features, including G-quadruplexes.
  • To facilitate the rational design and optimization of aptamers for improved binding affinity and functionality.

Main Methods:

  • Development of a novel software package named ValFold.
  • Implementation of a stem candidate selection algorithm within ValFold.
  • ValFold's capability to predict both canonical Watson-Crick base pairs and non-canonical G-G pairs characteristic of G-quadruplex structures.

Main Results:

  • ValFold demonstrates improved accuracy in predicting aptamer secondary structures compared to conventional tools.
  • The software successfully predicts G-quadruplex forming G-G pairs, a critical feature for many aptamers.
  • ValFold provides a valuable tool for researchers involved in aptamer design and SELEX.

Conclusions:

  • ValFold offers a significant advancement in computational tools for aptamer research.
  • The accurate prediction of complex secondary structures, including G-quadruplexes, by ValFold aids in the development of superior aptamer-based applications.
  • The software is freely available, promoting wider adoption and further research in aptamer technology.