Source 1review2020Frontiers in Chemistry
Toolkit/environment-sensitive fluorescent labels
environment-sensitive fluorescent labels
Also known as: advanced fluorescent dyes, environment-sensitive fluorescent probes
Taxonomy: Mechanism Branch / Component. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment.
Usefulness & Problems
Why this is useful
These labels are fluorescent dyes introduced through nucleobase replacement or modification so that their fluorescence parameters report the local nucleic acid environment. The review frames them as probes of structure, dynamics, and interactions.; probing nucleic acid structure; measuring conformational dynamics of DNA and RNA; probing nucleic acid-protein interactions; single-nucleobase or base-pair level fluorescence readout
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These labels are fluorescent dyes introduced through nucleobase replacement or modification so that their fluorescence parameters report the local nucleic acid environment. The review frames them as probes of structure, dynamics, and interactions.
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probing nucleic acid structure
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measuring conformational dynamics of DNA and RNA
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probing nucleic acid-protein interactions
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single-nucleobase or base-pair level fluorescence readout
Problem solved
They help reveal structural and conformational dynamics of DNA and RNA at single-nucleobase or base-pair resolution. They are also presented as tools to probe interactions between nucleic acids and proteins.; providing local-environment-responsive fluorescence signals within nucleic acids; enabling structural and dynamic readout beyond bulk nucleic acid quantification
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They help reveal structural and conformational dynamics of DNA and RNA at single-nucleobase or base-pair resolution. They are also presented as tools to probe interactions between nucleic acids and proteins.
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providing local-environment-responsive fluorescence signals within nucleic acids
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enabling structural and dynamic readout beyond bulk nucleic acid quantification
Problem links
enabling structural and dynamic readout beyond bulk nucleic acid quantification
LiteratureThey help reveal structural and conformational dynamics of DNA and RNA at single-nucleobase or base-pair resolution. They are also presented as tools to probe interactions between nucleic acids and proteins.
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They help reveal structural and conformational dynamics of DNA and RNA at single-nucleobase or base-pair resolution. They are also presented as tools to probe interactions between nucleic acids and proteins.
providing local-environment-responsive fluorescence signals within nucleic acids
LiteratureThey help reveal structural and conformational dynamics of DNA and RNA at single-nucleobase or base-pair resolution. They are also presented as tools to probe interactions between nucleic acids and proteins.
Source:
They help reveal structural and conformational dynamics of DNA and RNA at single-nucleobase or base-pair resolution. They are also presented as tools to probe interactions between nucleic acids and proteins.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Component: A low-level RNA part used inside a larger architecture that realizes a mechanism.
Mechanisms
conformational uncagingConformational Uncagingenvironment-sensitive fluorescence reportingTechniques
Structural CharacterizationTarget processes
No target processes tagged yet.
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationoperating role: sensorswitch architecture: uncaging
Use requires chemically modified or base-replaced nucleic acids carrying the fluorescent label and fluorescence measurement capability. The signal depends on local environmental features such as polarity, hydration, base flipping, and hydrogen bonding.; require nucleobase replacement or modification; depend on fluorescence changes linked to local polarity, hydration, flipping dynamics, or hydrogen-bond changes
The abstract does not show that existing labels fully solve all nucleic acid probing needs, and explicitly says new probes and approaches are urgently needed.; the abstract states that new probes and approaches are still urgently needed
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Environment-sensitive fluorescent labels can report local nucleic acid environment through fluorescence changes associated with altered polarity, hydration, flipping dynamics, and formation or breaking of hydrogen bonds.
advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds)
New fluorescent probes and approaches are urgently needed to accurately determine DNA and RNA structural and conformational dynamics at the level of single nucleobases or base pairs and to probe nucleic acid-protein interactions.
However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins.
Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification.
Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification.
Approval Evidence
1 source3 linked approval claimsfirst-pass slug environment-sensitive-fluorescent-labels
This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment.
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mechanism of actionsupports
Environment-sensitive fluorescent labels can report local nucleic acid environment through fluorescence changes associated with altered polarity, hydration, flipping dynamics, and formation or breaking of hydrogen bonds.
advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds)
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need statementsupports
New fluorescent probes and approaches are urgently needed to accurately determine DNA and RNA structural and conformational dynamics at the level of single nucleobases or base pairs and to probe nucleic acid-protein interactions.
However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins.
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review summarysupports
Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification.
Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification.
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Comparisons
Source-stated alternatives
The abstract contrasts these labels with general fluorescence labeling and probing approaches used for nucleic acid analysis and quantification, but does not name specific alternative probe chemistries.
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The abstract contrasts these labels with general fluorescence labeling and probing approaches used for nucleic acid analysis and quantification, but does not name specific alternative probe chemistries.
Source-backed strengths
respond to local environment changes; support probing at the level of single nucleobases or base pairs
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respond to local environment changes
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support probing at the level of single nucleobases or base pairs
Compared with phosphorothioate-caged antisense oligonucleotides
environment-sensitive fluorescent labels and phosphorothioate-caged antisense oligonucleotides address a similar problem space.
Shared frame: same top-level item type; shared mechanisms: conformational_uncaging
Strengths here: looks easier to implement in practice.
Compared with RNA nanostar-derived scaffold
environment-sensitive fluorescent labels and RNA nanostar-derived scaffold address a similar problem space.
Shared frame: same top-level item type; shared mechanisms: conformational_uncaging
Compared with sequence-activated fluorescent RNA
environment-sensitive fluorescent labels and sequence-activated fluorescent RNA address a similar problem space.
Shared frame: same top-level item type; shared mechanisms: conformational_uncaging
Ranked Citations
- 1.