Molecular marking

from Wikipedia, the free encyclopedia

The molecular marking ( English labeling , labeling , tagging ) is a method of chemistry and biochemistry for the selective binding of an atom or molecule to a molecule. The marking is used for further tracking of the marked molecule or to elucidate a reaction mechanism ( English crossover experiment ).

properties

GFP from Aequorea victoria , a typical fluorescent label

Depending on their characteristic functional groups, molecules can be provided with a selectively binding label that carries a traceable signal molecule ( reporter molecule ). The label consists of a binding group (coupling group), occasionally a connector (linker) and a detectable molecule (reporter). The marking is mostly covalently linked via the coupling group. In the case of nuclides , however, it can also be bound ionically and, in the case of indirect detection, via a mixture of ionic bonds, van der Waals bonds , hydrophobic effects , hydrogen bonds and sometimes also disulphide bonds . In contrast to staining with most selectively binding protein dyes or nucleic acid dyes, biomolecules are covalently labeled either on individual atoms or in a sequence-specific manner.

Reporter types

The reporter molecules are generally about selectively reactive coupling groups covalently linked to a flexible spacer ( English left , connector ') coupled to certain functional groups of the molecule to be labeled. Nuclides are a special case, because of their comparatively small molecule size, they can also be coupled directly to another molecule (without a reactive coupling group or a linker). While isotope labeling is mostly used to label small molecules , many different types of reporter have been developed for labeling various biopolymers such as proteins and DNA.

As reporter molecules in marks are nuclides ( radioactive and non-radioactive), biotin , reporter enzymes , oligonucleotides , fluorophores (as part of a fluorescent label ) or proteins and protein tags used.

Coupling types

The markings with nuclides have the smallest changes in molar mass among the markings and therefore lead to a comparatively smaller change in the protein structure and biological activity , but the radioactive nuclides are accompanied by increased safety measures and requirements for the safety laboratory. Nuclides ( isotopes and isobars ) can be directly covalently coupled to the molecule to be labeled ( chemical coupling ), besides being covalently attached via a coupling group, ionically coupled (e.g. via chelators such as DTPA , TTHA or chelating peptides such as protein -Tag His-Tag ) by a chemical total synthesis (e.g. by peptide synthesis, by phosphoramidite synthesis) or in a biosynthesis by the conversion of nuclide-labeled precursor substances ( metabolic labeling ). In the course of chemical isotope labeling or metabolic isotope labeling, molecules with radioactive isotopes (e.g. 3 H, 11 C, 13 C, 14 C, 13 N, 15 O, 18 F, 26 Al, 32 P, 33 P, 35 S, 36 Cl, 41 Ca, 125 I, 131 I). The isotopes of elements that do not naturally occur in biomolecules such as iodine , 99 technetium or 113 indium must first be chemically coupled to the precursor molecules in the case of metabolic labeling.

The other types of reporter molecules can be covalently attached via a coupling group, generated by a chemical total synthesis or in a biosynthesis. The biosynthesis takes place in the metabolism through the conversion of reporter-marked precursor substances ( metabolic marking ). With high selectivity and low toxicity , labeling can also take place partly metabolically and partly synthetically, as in the case of bioorthogonal labeling . Metabolically incorporated precursor substances are then used after protein purification or DNA purification for the subsequent chemical coupling of a reporter molecule using the selectively reactive group, e.g. B. via click chemistry (1,3-dipolar cycloaddition with azides and cyclooctynes , a copper-free click chemistry), via cycloaddition between nitrones and cyclooctynes, via oxime / hydrazone formation from aldehydes or ketones , via tetrazine ligation, by isonitrile-based click reaction, by quadricyclane ligation and by Staudinger reaction between azides and triarylphosphines.

For tracking the time course of a labeled molecule in the context of metabolism is a variant of metabolic labeling, the pulse-labeling ( English pulse labeling ) was used. In the case of pulse marking, the marking period is limited in time, so that the marking of the molecule and its metabolites can be more precisely delimited and the change in marking to individual subsequent substances in a metabolic pathway can be observed. The tracking multiple metabolites is also known as metabolic flux analysis (at the same English metabolic flux analysis indicated). Through the molecular marking , the cell membranes of whole cells can also be marked by marking surface proteins and / or the glycocalyx , e.g. B. for flow cytometry , fluorescence microscopy or fluorescence tomography .

In a protection assay , markers are used, among other things, to mark uncovered areas on the surface of a molecule, whereby the surface or the binding site of a binding molecule can be determined. The areas of a protein accessible for marking are an indication that the marked amino acids are freely accessible on the protein surface. Folded areas of proteins and areas that have bound another molecule are less amenable to labeling.

Direct and indirect evidence

In the case of a molecular marking, the molecule to be detected can either be provided directly with a reporter molecule or indirectly detected by selectively binding reporter-carrying molecules. Molecular labeling methods are:

Protein labeling

Reactive groups in proteins

In contrast to carbohydrates and nucleic acids, some of the structural motifs of the biomolecules only occur in proteins due to the different amino acids they contain , e.g. B. sulfhydryl -containing cysteines or phenol residues in tyrosines . These structural motifs can be selectively marked with appropriate coupling reagents. Strategies are being investigated to mark only one of several amino acids of the same type.

  • Thiol or sulfhydryl group on cysteine

  • Amino group on lysine and on the N terminus

  • Carboxy group on aspartic acid, glutamic acid and at the C terminus

coupling

Coupling of amines with succinimidyl esters
Fluorescein isothiocyanate (FITC) reacts with amino groups

Cysteines can with maleimides , disulfides , iodoacetamide (eg. IAEDANS ), Haloacetylen , aziridines , Acryloylen , arylating agents , vinyl sulphones , pyridyl - and other disulfides react selectively. Amino acids with primary amines on the side chain such as lysine can be labeled by succinimide esters ( N -hydroxysuccinimide , sulfosuccinimide or other succinimidyl esters) or certain isothiocyanates such as PITC or FITC . Carboxy groups can be coupled to amine groups by activation with carbodiimides . After oxidation of proteins or by reductive alkylation , various reporter molecules can be coupled. Nucleophilic groups in proteins can be coupled via tosylation . With enzymes, proteins can often be labeled with an increased selectivity on protein tags, e.g. B. by Sortase , by Transglutaminase , by Haloalkandehalogenase or by Phosphopantetheinyltransferase. The crosslinking and fixation of various amino acid side chains in proteins is based on the same principle as labeling by coupling .

Diazirine.

Photoreactive molecules (e.g. aryl azides , diazirines ) can also be used as a reactive group of a label on proteins in order to be able to better control the time of coupling, since the reaction is only triggered with UV radiation, e.g. B. in the course of photoaffinity labeling . Because of the lower selectivity of these free-radical coupling groups, the functionality of the protein is often reduced by reaction of the free-radical coupling group with important functions (e.g. an active center of an enzyme or a binding site ). An advantage of radical couplings, on the other hand, is the independence from the occurrence of certain amino acids in the protein to be coupled. Therefore, photoreactive markings are mostly used when no or only one amine or sulfhydryl group is available for selective coupling or when subsequent functionality is insignificant. There are also photoreactive diazirine or azide-containing analogs of the amino acids leucine ( photo-leucine ), methionine and p-benzoyl- phenylalanine , which can be incorporated into the protein during translation. By peptide synthesis or in vitro translation can peptides with labeled amino acid derivatives are prepared.

Some protease inhibitors lead to selective labeling of proteins. In a label transfer experiment, a cleavable cross-link with a reporter between two neighboring molecules is used in order to transfer the reporter molecule between these molecules by cleaving the cross-link and thereby to prove their proximity. The cleavable crosslinker used here contains the reporter group between the cleavage point of the crosslinker and the coupling group for the mostly unknown binding target molecule. In the DIGE , differently labeled samples are separated together using SDS-PAGE or 2D gel electrophoresis . In a proximity ligation assay , the neighborhood of oligonucleotide-labeled proteins is detected by PCR. Proteins can be labeled with oligonucleotides for detection by hybridization. Proteins can also be biotinylated in vitro with biotin succinimidyl esters or provided with a protein tag with biotinylation (e.g. Avi-Tag, BCCP-Tag, Strep-Tag) in vivo and then indirectly labeled with avidin or streptavidin conjugates become.

Nuclide markings

Nuclide labeling mostly uses radioactive nuclides due to the comparatively high sensitivity (low detection limit ) and the simplicity of detection by autoradiography , by scintillation counter or by positron emission tomography . In nuclear magnetic resonance spectroscopy and mass spectrometry , non-radioactive nuclides can also be used.

The nuclide labeling is done either chemically or biosynthetically. The biosynthetic labeling takes place z. B. as metabolic labeling by feeding cell cultures or test animals with labeled precursor molecules. By radioiodination, tyrosines can be labeled in vitro with radioactive iodine . Phosphorylations of serine , threonine and tyrosine are usually carried out enzymatically with suitable protein kinases and radioactive phosphorus-containing adenosine triphosphate . A radioactively labeled prenylation can be carried out with 3 H- mevalonic acid . In addition, the C-terminus is methylated in the course of a prenylation , which can be reversibly radiolabeled by 3 H-labeled S-adenosyl-methionine . N-terminal labeling can be carried out by myristylation . A geranylgeranylation can be performed with Azidogeranylen. Sulphation can be detected with 35 S-labeled sulphate. Hydrogen atoms can by a deuterium with deuterium to be replaced. Marking with radioactive isotopes allows tracking by autoradiography . In mass spectrometry, isobaric labeling is used to differentiate between different samples. In addition to the normally used nuclides 1 hydrogen or 15 nitrogen , markings with 13 carbon or 19 fluorine are used in NMR spectroscopy .

Bioorthogonal markings

Amino acids for bio-orthogonal labeling.
Coupling of membrane proteins with azides.

Proteins can be labeled bioorthogonally . Various selective coupling reactions are used here, e.g. B. via Sonogashira coupling , via copper-catalyzed alkyne-azide cycloaddition , via Heck reaction , via oxime ligation, via cyclopropene-azide coupling, via myristylation, via cyanobenzothiazole condensation or via tetrazole-alkene cycloaddition. After biosynthesis, membrane proteins can be enzymatically coupled with azides , which in turn are coupled with reporter molecules via the Staudinger reaction.

Recombinant Tags

Proteins can be produced as recombinant proteins with a protein tag or with a reporter protein as fusion protein, which are attached N-terminally or C-terminally to the protein during translation . A protein can be purified or detected via the protein tag inserted into the recombinant protein , e.g. B. with GFP or with reporter enzymes . Some protein tags are subsequently coupled bioorthogonally with a reporter molecule after the biosynthesis, e.g. B. the Snap-Tag , the Polyhistidine-Tag , the Flash-Tag , the ReAsH-Tag , the Flag-Tag , the Clip-Tag , the HyRe -Tag , the Beta-Lactamase-Tag , the LAP-Tag and the Sortase day. Proteins can be marked post-translationally by inteins .

Indirect markings

In the case of an immunolabeling with immunoconjugates , the selectivity of the marking is based on the binding of antibodies . In addition, the antibody is usually marked with a reporter molecule itself or via a secondary antibody, which is used indirectly for detection, e.g. B. in fluorescence microscopy, Western blot and ELISA . The epitope bound by the antibody is either in the protein or on a protein tag. Proteins can also be detected indirectly using reporter genes.

Nucleic acid labeling

Reactive groups in nucleic acids

Adenosine monophosphate

Compared to proteins, DNA has a lower number of available functional groups due to the nucleotides used , including an amino group in the nucleobase adenine that can be used for coupling .

Coupling types

Commonly used markers in DNA sequencing.

The phosphate group can be marked by radioactive phosphate with a 32 phosphorus atom in vitro in the course of random priming , nick translation , generation by phosphoramidite synthesis or in vivo by biosynthesis with radioactive phosphate. DNA can also be labeled bioorthogonally, e.g. B. with 5-ethynyl-2'dUTP. The amino group of adenine can react in vitro with succinimidyl esters or isothiocyanates.

A polymerase chain reaction can label DNA in vitro with unnatural nucleotide analogs , e.g. B. BrdU , digoxigenin -dUTP, hydroxymethyl-dCTP and fluorescent nucleotides in DNA sequencing according to Sanger, QPCR or in-situ hybridization with hybridization probes .

RNA

RNA can be labeled biosynthetically with RNA tags, chemically or with hybridization probes, among other things. In the case of RNA tags, DNA sequences of aptamers are usually cloned into the open reading frame of a gene . After the RNA has been generated with the RNA tag by transcription , secondary structures are formed . B. bind selectively to dextran , streptavidin or dyes .

Carbohydrate marking

Bioorthogonal labeling with modified glucosamine .

Marked carbohydrates are generated by metabolic or bioorthogonal marking, chemically marked or the carbohydrates are detected indirectly via lectins .

literature

Individual evidence

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