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Related Concept Videos

RNA Stability01:53

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
RNA Stability01:53

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
Phosphodiester Linkages01:01

Phosphodiester Linkages

Overview
Phosphodiester bond forms when a phosphoric acid molecule (H3PO4) links with two hydroxyl groups (–OH) of two other molecules, forming two ester bonds. Two water molecules are released in this process. The phosphodiester bond is commonly found in nucleic acids (DNA and RNA) and plays a critical role in their structure and function.
Phosphodiester Bonds Link Nucleotides Together
DNA and RNA are polynucleotides or long chains of nucleotides that are linked together. A nucleotide is...
Restriction Enzymes01:11

Restriction Enzymes

Restriction enzymes are bacterial enzymes used to cut DNA in a sequence-specific manner. To cleave DNA, they bind to specific palindromic sequences called restriction sites. Such palindromic DNA sequences or inverted repeats are commonly found in regions of functional significance, such as the origin of replication, gene operator sites, and regions containing transcription termination signals.
The host bacteria protect their own genomic DNA from these enzymes by methylating these sites. Some...
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...

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Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
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Published on: September 21, 2017

Molecular duplexes with encoded sequences and stabilities.

Bing Gong1

  • 1Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, USA. bgong@buffalo.edu

Accounts of Chemical Research
|May 15, 2012
PubMed
Summary
This summary is machine-generated.

Researchers developed programmable molecular duplexes using oligoamide strands. These biomimetic molecules mimic DNA

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Area of Science:

  • Supramolecular Chemistry
  • Polymer Chemistry
  • Chemical Biology

Background:

  • Biomacromolecules like DNA encode structural and functional information through specific molecular shapes and polymeric sequences.
  • Developing synthetic molecules that mimic this information-encoding capability is a key challenge in materials science and nanotechnology.
  • Understanding and controlling intermolecular associations is crucial for creating complex molecular architectures.

Purpose of the Study:

  • To design and develop a novel class of molecular duplexes with programmable hydrogen-bonding sequences and adjustable stabilities.
  • To explore the potential of these duplexes in forming supramolecular structures and templating chemical reactions.
  • To investigate the incorporation of dynamic covalent interactions for stimuli-responsive molecular assemblies.

Main Methods:

  • Synthesis of oligoamide strands using readily available monomeric modules via standard amide (peptide) chemistry.
  • Creation of diverse hydrogen-bonding sequences by varying the order of covalently linked building blocks.
  • Formation of double-stranded pairs (duplexes) through sequence-specific hydrogen bonding between oligoamide strands.

Main Results:

  • Demonstrated strict sequence specificity and tunable stability in the oligoamide duplex system.
  • Showcased features analogous to DNA, including programmable specificity, shape complementarity, and cooperative interactions.
  • Successfully formed supramolecular structures like beta-sheets and non-covalent block copolymers.
  • Incorporated dynamic covalent interactions, leading to sequence-specific association and ligation in various solvents.
  • Developed stimuli-responsive duplexes whose formation/dissociation is controlled by external factors like pH.
  • Observed gelation of organic solvents tunable by adjusting side chains on the duplexes.

Conclusions:

  • The developed oligoamide duplexes offer a systematic approach for precise control over molecular association.
  • This system provides a versatile platform for constructing dynamic covalent and supramolecular structures with tailored properties.
  • The programmable nature and ease of modification position these duplexes as promising candidates for information-storing molecules and self-replication systems.