USRE40557E1 - Methods for labeling nucleotides, labeled nucleotides and useful intermediates - Google Patents

Methods for labeling nucleotides, labeled nucleotides and useful intermediates Download PDF

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Publication number
USRE40557E1
USRE40557E1 US10/900,902 US90090299A USRE40557E US RE40557 E1 USRE40557 E1 US RE40557E1 US 90090299 A US90090299 A US 90090299A US RE40557 E USRE40557 E US RE40557E
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spacer
label
nucleotide
dna
moiety
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Jan Hendrick Houthoff
Jan Reedijk
Tinka Jelsma
Robert Jochem Heetebrij
Herman Hendricus Volkers
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Kreatech Biotechnology BV
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H23/00—Compounds containing boron, silicon, or a metal, e.g. chelates, vitamin B12
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10S436/00—Chemistry: analytical and immunological testing
    • Y10S436/80—Fluorescent dyes, e.g. rhodamine
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00—Chemistry: analytical and immunological testing
    • Y10T436/14—Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
    • Y10T436/142222—Hetero-O [e.g., ascorbic acid, etc.]
    • Y10T436/143333—Saccharide [e.g., DNA, etc.]

Definitions

  • the invention relates to methods for labeling nucleotides using linkers (linking moieties between labels and bio-organic molecules, which linkers are based on platinum compounds).
  • Platinum (coordination) compounds have been considered interesting molecules for a very long time. For a review of these compounds and their uses we refer to Reedijk et al. (Structure and Bonding 67, p.53-89, 1987). Especially Cis-platinum has received a lot of attention as a possible anti-tumour drug.
  • This anti-tumour reactivity of platinum compounds originates from their having at least two reactive groups (preferably cis-oriented towards each other), which make it possible to cross-link DNA molecules, thereby inhibiting the replication of these DNA molecules.
  • the British patent application 2 148 891 discloses cis-platinum complexes, which are six-coordinated.
  • the platinum is attached to two halogens or hydroxy groups, two additional halogens and to an ethylenediamine derived group, such as 1,2-diamino-2-methylpropane or 1,2-diamino-2-methylbutane.
  • the complexes are said to have an excellent anti-tumor effect.
  • the complexes comprise a diamine bidentate ligand and two 2-arylalkanoic acid or 3-aryl-2-oxoalkanoic acid ligands. These complexes are stated to have a strong growth inhibiting action on certain leukemia cells and are used for their oncostatic activity.
  • U.S. Pat. No. 4,207,416 discloses ethylenediamine-platinum(II) 2,4-dioxopyrimidine complexes as having a high anti-tumor activity and low mammalian toxicity.
  • a major drawback of these known methods is that they are not suitable for labeling all different nucleotides. For instance, Dale et al. reported that their covalent mercuration method leads to negative results for adenine, thymine and guanine bases. In some cases, for example when only a few residues of a certain nucleotide are present in a certain nucleic acid or when the terminating nucleotide residue of a nucleic acid has to be labeled, it is desired to have at one's disposal a method for labeling any nucleotide residue.
  • the present invention provides such a method.
  • the method for labeling nucleotides of the invention comprises the steps of:
  • the linker may first be attached to the nucleotide and then to the spacer, or vice versa and the spacer may first be coupled to the label and then to the linker or vice versa.
  • the reactive moiety of the spacer may be any reactive moiety that will enable the reaction between the spacer and the label in such a manner that a labeling moiety comprising a label and a spacer is formed, which labeling moiety is sufficiently stable.
  • nucleotides can be incorporated in nucleic acid molecules.
  • Modified nucleotides especially those wherein a (bulky) label is attached to the nucleotide, are often built-in into nucleic acids with a much lower efficiency.
  • the methods according to the invention result in labeled nucleotides which are built-in into nucleic acids with a higher efficiency than the labeled nucleotides available to date. This is probably due to the selection of the spacers according to the invention in combination with the platinum-based linkers according to the invention.
  • the label to be used according to the invention is not critical. In principle all labels which can be attached to a nucleotide and are employed to date can be used. These labels may be radioactive labels, enzymes (which need reaction with a substrate to be detected), specific binding pairs components such as avidin, streptavidin or biotin, biocytin, iminobiotin, colloidal dye substances, fluorochromes (rhodamin, etc.), reducing substances, (eosin, erythrosin, etc.), (coloured) latex sols, digoxigenin, metals (ruthenium), metal sols or other particulate sols (selenium, carbon and the like), dansyl lysin, Infra Red Dyes, coumarines (amino methyl coumarine), antibodies, protein A, protein G, etc.
  • the invention has most benefits with bulkier labels such as biotin, avidin, streptavidin, digoxygenin or a functional equivalent thereof.
  • the invention is not limited to nucleotides or nucleosides as such: derivatives and functional equivalents are also included.
  • the usual nucleotides adenine, thymidine, cytosine, guanine and uridine are preferred.
  • Especially the purines are preferred which have a very good incorporation rate.
  • the electron donating moiety is an amine or a thiolate anion, which have both proven to be very successful. It was found that aromatic amines, such as imidazoles or purines, are capable of forming very strong bonds to platinum and thus are very suitable for use as the electron donating moiety.
  • the spacer is an important aspect of the present invention; it provides the easiest coupling between label and linker.
  • the nucleotide For avoiding steric hindrance in incorporation of the nucleotide into the nucleic acid it should at least be four atoms long, preferably it is at least four carbon atoms long and has at least one heteroatom in that carbon chain.
  • a heteroatom confers a certain amount of rigidity on the spacer. This rigidity provides an additional assurance that steric factors will not obstruct a convenient linking of a nucleotide and a label. It is preferred that at least one heteroatom is an oxygen atom, which positively effects the hydrophilicity of the spacer.
  • the spacer comprises no more than 20 carbon atoms in the chain, which is preferably an essentially non-branched chain, thus causing no steric hindrance. The reason for this will be clear.
  • a highly preferred spacer is 1,8-diamino-3,6-dioxaoctane, herein referred to as Dadoo.
  • Dadoo is a very flexible compound with a distal primary amine group and a size that makes it very suitable for use as spacer according to the invention.
  • Another highly preferred spacer of the invention is an oligolysine or a polylysine. Due to their structure and conformation, these molecules create the most convenient environment for an optimal interaction among the actual label, the nucleotide and the platinum.
  • An additional advantage of the use of lysine chains as the spacer is, that by altering the number of lysine units in the chain, the optimal conditions for specific labels and nucleotides or nucleic acids can be attained. Given a certain application, the skilled person will easily determine how many lysine units are required for optimum results.
  • An especially interesting labeling moiety comprising a label and a spacer, has the formula or the formula wherein X represents any stabilizing bridge, Z and Z′ represent a non-leaving ligand and n is an integer of from 2 to 10.
  • linker-spacer-label-system, or labeling substance, with the labeling moiety of formula (II) or formula (III) has the formula or the formula wherein A, X, Z, Z′ and n have the above meanings.
  • the non-leaving ligands Z and/or Z′ are preferably an NH 3 , NH 2 R, NHR 2 or NR 3 group, wherein R represents an alkyl group having from 1 to 6 carbon atoms, because these ligands have an even smaller leaving-group character than other non-leaving ligands.
  • the linkers according to the invention preferably are platinum compounds wherein X represents an aliphatic diamine.
  • X represents an aliphatic diamine.
  • one or both of the nitrogen atoms of the aliphatic diamine are shielded.
  • a suitable manner of shielding these nitrogen atoms consists of substitution with one or two alkyl groups of from 1 to 6 carbon atoms, preferably methyl groups. This is advantageous in that hydrogen bonding between the triphosphate group of a nucleotide and the stabilizing bridge is prevented.
  • a diamine having 2-6 carbon atoms is used, most preferably an ethylene diamine group, which is well-known for its stabilizing effect on this class of platinum compounds.
  • the linker has the formula wherein G represents hydrogen or an alkyl group of from 1 to 6 carbon atoms and A and B represent the same or different reactive moieties.
  • the coupling or reactive moieties A and B are preferably the same and selected from the group consisting of NO 3 ⁇ , SO 3 ⁇ , Cl 31 , I ⁇ , or other halogens.
  • the invention of course also encompasses a labeled nucleotide obtainable by a method as disclosed above.
  • the invention encompasses a labeling substance for labeling nucleotides by a method as disclosed above.
  • the labeling substance of the invention has the formula wherein X and A have the above meanings and the labeling moiety comprises a label and a spacer as described above.
  • the labeling substances of the invention can also be used for labeling purposes other than labeling nucleotides. It was found that numerous (bio-) organic compounds, i.e. nearly every bio-organic molecule which contains an accessible sulphur or nitrogen atom, for example proteins, can be labeled with the platinum compounds of the invention.
  • a great advantage of the invention arises from the use of the platinum compounds having formula (I) as linkers in the methods of preparing labeled nucleotides according to the invention. These linkers can be prepared by very convenient and reliable methods.
  • the starting compounds disclosed for preparing labeled platinum compounds are platinum(II) (ethylenediamine)dichloride and platinum(II) (ethylenediamine)(Me 2 SO)Cl.
  • the first one can be obtained commercially, the second one (the preferred one) must be synthesized.
  • the Cl-ions are less readily substituted by a label or a nucleotide, respectively. In the latter case, the total nucleotide labeling time will be appreciably longer, up to several hours, instead of several minutes.
  • the methods for preparing the linkers that are used in the method of labeling nucleotides according to the invention are based on the selection of suitable starting compounds of the formula PtE 4 wherein E is an electronegative group, preferably a halogen or NO 3 ⁇ or SO 3 ⁇ .
  • E is an electronegative group, preferably a halogen or NO 3 ⁇ or SO 3 ⁇ .
  • the reaction, which is described in the examples, of these starting compounds with e.g. ethylenediamine is very simple and efficient. Moreover, this reaction leads to very suitable symmetric intermediate compounds for producing labeled nucleotides.
  • a major advantage of using these compounds is that when a stabilizing bridge for the resulting platinum compound has to be attached that no blocking reagents have to be employed. Another advantage is that the resulting intermediate compounds can again be labeled without the use of blocking agents.
  • a very suitable intermediate compound according to the invention is platinum(II)(ethylenediamine)(NO 3 ) 2 .
  • This substance can very easily be provided with a suitable spacer and a labeling group, resulting in labeling substances which can, through substitution of the remaining NO 3 -group be linked to a nucleotide quite easily.
  • the methods for producing these compounds and the resulting compounds do not involve highly toxic substances such as DMSO.
  • the intermediate compounds can be labeled with any suitable label (also known as marker) through a spacer as disclosed hereinabove.
  • platinum compounds are of course also obtained with the present methods and compounds.
  • Another advantage of the platinum compounds is that they can be detected more or less directly by using the platinum as a nucleus for depositing silver or other metal crystals.
  • DNA or RNA molecules By binding the labeling substance to a nucleotide residue, DNA or RNA molecules, be it single stranded or otherwise, can be easily detected, but it also allows for the production of probes for hybridization techniques wherein unlabeled DNA/RNA molecules hybridize to the labeled probe.
  • the platinum linker labeled nucleotides hardly interfere with the hybridization, if at all. Also, this technique obviates the use of modified nucleotides in preparing probes.
  • Nucleotides modified in accordance with the practices of this invention and oligo- and polynucleotides into which the modified nucleotides have been incorporated or oligo- and polynucleotides that have been directly modified using these novel platinum compounds may be used as probes in biomedical research, clinical diagnostics and recombinant DNA technology.
  • the filtrate should be clear.
  • Example 1A Repeat the entire procedure of Example 1A, but use N,N,N′, N′-tetramethylethylenediamine instead of ethylenediamine.
  • Dissolve Pt(en)(NO 3 ) 2 (18.2 mg, 0.048 mmol) in 10 ml of Millipore water and heat until dissolving.
  • Dissolve BioDadoo (20 mg, 0.053 mmol, purchased from Boehringer Mannheim) in 5 ml of Millipore water. Add the two solutions together and adjust the pH to 8 by 0.1 N NaOH, react for at least 3 hours at 50° C. Isolate the end product by freeze drying.
  • Dissolve Pt(tmen)(NO 3 ) 2 35 mg, 0.08 mmol
  • Dissolve BioDadoo 32 mg, 0.085 mmol
  • Dissolve Pt(en)(NO 3 ) 2 (5 mg, 0.013 mmol) in 5 ml of Millipore water and heat until dissolving.
  • Dissolve DigDadoo (9 mg, 0.016 mmol, purchased from Boehringer Mannheim) in 5 ml of Millipore water. Add the two solutions together and react for at least 4 hours at 50° C. Isolate the end product by freeze drying.
  • the labeling method has been used to label DNA probes with Biotin for In Situ Hybrization (ISH).
  • ISH Biotin for In Situ Hybrization
  • labeling procedures including the protocols and data for quality control procedures are presented.
  • Biotin labeling a plasmid cloned total DNA of Human Papilloma Virus type 6 (HPV-6, 40% GC basepairs) was used.
  • Plasmid DNA was transferred into E. coli (C-600) and plated onto ampicillin containing LB plates Single colonies were grown overnight in large culture. Plasmid DNA was isolated according to the method of Birnboim and Doly 1 , purified by Sepharose C1-2B columnchromatography (Pharmacia) and checked for inserts by restriction-enzyme-analyses. Plasmid DNA concentration was determined by A260/280 absorbtion. After ethanol precipitation the DNA was reconstituted in 10 mM TRIS/HCl pH 7.2, 0.3 mM EDTA to a final concentration of 1 ⁇ g/ ⁇ l (batch# 150894). Subsequently this DNA was sonicated (Soniprep 150., MSE) for 3 times 10 minutes (amplitude 5 microns) on ice.
  • the size of the resulting DNA fragments was determined by 2% agarose gel electrophoresis and found to be in between 200-400 basepairs (batch# 051094).
  • Plasmid HPV-6 DNA was labeled with BioDadoo-ULS by mixing the following reagents:
  • the detection limit of the biotin probe of the invention was determined by direct spot blot and reversed filterhybridization according to the following protocols:
  • HPV-6 probe (batch# 061094) labeled with biotin according to the invention was 10-fold serially diluted into spot buffer comprising 900 mM sodium chloride, 90 mM sodium citrate and 200 ⁇ g/ml single stranded salmon sperm DNA giving a dilution series varying from 1000-0.1 pg biotin probe per ⁇ l. 1 ⁇ l spots were applied onto nitrocellulose membrane and incubated for 2 hours at 80° C. to blind the DNA. The biotin probe was visualized using a streptavidin-alkaline phosphatase conjugate (Sigma) combined with a NBT/BCIP precipitating substrate solution (Sigma) according to the following protocol:
  • the detection limit of the biotin DNA probe according to the invention was found to be less than 1 pg.
  • HPV-6 DNA (batch# 051094) was1 in 10 diluted in 0.1N NaOH, incubated at 100° C. for 5 minutes and directly placed on ice for 5 minutes to make DNA single stranded.
  • HPV-6 DNA probe that was labeled with biotin according to the invention was diluted in 5 ⁇ SSPE 0.5% SDS solution to yield a concentration of 200 ng/ml.
  • This solution was incubated for 5 minutes at 100° C. and placed directly on ice for 5 minutes.
  • Nylon membranes containing target DNA were soaked in 2 ⁇ SSC for 5 minutes and subsequently incubated with the single stranded probe solution for 2 hours at 37° C.
  • biotin probe of the invention was visualized by performing the same protocol as described in the direct spot blot method.
  • the detection limit of the biotin probe according to the invention was found to be less than 10 pg.
  • test material consisted of 6 ⁇ m paraffin sections of a HPV-6 posotive cervical condyloma mounted on organosilane coated glass slides.
  • Probe solution consisted of biotin HPV-6 probe DNA labeled according to the invention (batch# 061094) in a concentration of 2 ng/ ⁇ l dissolved in hybridization mixture comprising 0.6M NaCl, 0.06M sodium citrate, 35% formamid, 10% dextransulphate, 2,5 ⁇ Denhardts and 10 ⁇ g/ml single stranded salmon sperm DNA.
  • the present method is very well suited for research, routine and for industrial production of labeled nucleic acids, as the method is fast and easy to perform, very sensitive, and does not include any enzymatic step, which makes it highly reproducible and fitted for an overall low cost production.
  • the method of the invention offers a useful alternative equaling conventional non-isotopic labeling methods.
  • the LIDIA technique enables the quantitative analysis of small amounts of DNA (or RNA) e.g. after a PCR amplification of the starting material.
  • the technique is sensitive and specific, due to the use of specific DNA(RNA) probes in accordance with the invention and easy to perform, because of the quick DNA(RNA) Pt-labeling steps of the invention.
  • the technique uses fast Pt labeling compounds of the invention to label DNA(RNA) probes
  • An immobilized DNA probe can be used to catch specific target molecules in a sample by using a hybridization technique. Detection of formed hybrids can be done by using different techniques, e.g. a second labeled DNA probe can be used to hybridize with a different site on the target DNA molecule to form a sandwich hybrid. The label can then be detected by using state of the art immunological detection and colouring techniques.
  • a volume containing (amplified) detectable DNA(RNA) is directly labeled according to the protocol in accordance with the invention.
  • a second step is performed in a microtiter plate precoated with a target specific probe. Incubation is allowed to the formation of stable “Labelled target” and probe hybrids.
  • the direct labeling of target molecules enables the omission of laborious double hybridization techniques where one probe is used to catch the target and another labeled probe is used to detect the immobilized target.
  • the probes are covalently linked to the microtiter plate to the surface of the wells.
  • the second incubation step has the character of a liquid hybridisation and therefore can be performed very rapidly. This is one of the main innovative features of this approach to quantitive DNA hybridisation techniques.
  • Both for the immobilization of DNA probes or DNA targets and for the labeling of DNA probes and targets the newly developed Pt system can be used.
  • These two DNA linking techniques can be combined into one assay where both the “catcher” and the “detector” are linked to a second substance (either a detectable group like biotin, digoxigenin or a carrier surface like a plastic stick, microtiter plate or a membrane).
  • the DNA dipstick technique enables the qualitative and semi-quantitative analysis of small amounts of DNA(or RNA) e.g. after a PCR amplification or freely present in samples of body fluids (blood, urine, sweat etc.)
  • the technique is sensitive and specific, due to the use of specific DNA(RNA) probes and easy to perform because of the quick DNA(RNA) Pt-labeling steps according to the invention.
  • the universal labeling characteristics of the newly developed Pt label can be used in 3 ways to achieve a bound DNA(RNA) molecule.
  • a DNA probe can be labeled with the newly developed Pt labeling compound.
  • This labeled probe can then be used to detect preformed hybrids on a membrane formed between the target DNA sequence and a primary probe. It is essential in this method that the primary probe recognizes a different sequence on the target than the secondary Pt labeled probe. In practice, this can be achieved for instance with RNA hybridization where a POLY T probe is used as a primary probe to immobilize all RNA (recognizable by its POLY A tails) to a membrane.
  • the second approach differs slightly in that in this case the target can be labeled in the test sample fluid, because of the fast and very specific Pt labeling characteristics.
  • a procedure like this would comprise a catch of the labeled target with an immobilized specific unlabeled DNA probe on a suitable membrane. Hence a dipstick version for DNA/RNA applications.
  • a non-labeled Pt compound that is a Pt compound with 2 free binding sites
  • carriers plastic, membrane, microtiter plates etc.
  • the use of the Pt compound of the invention in latex or hydrosol assays is particularly interesting.
  • the compound enables the coupling of DNA molecules to small particles.
  • the DNA molecules can be hybridized to target material.
  • a positive reaction is visualized by an agglutination of the particles, due to crosslinking of the DNA hybrid particle compounds.
  • a test like this can be made quantative, the rate of agglutination can be tuned and measured at a specific wavelength.
  • gold particles have the intrinsic characteristic that a shift in optimal wavelength occurs after agglutination.
  • Platinated DNA/RNA probe can be employed in hydridisation methods to detect DNA/RNA sequences in sample material.
  • the introduction of a platinum compound at the site of the target enables the deposition of Ag molecules in a chemical reaction especially designed to reduce ionic silver to metallic silver.
  • a decomposition of metallic silver(black) occurs due to the catalytic effect of the Pt nucleus.
  • Ionic silver is reduced by a reducing agent (e.g. Na-borohydrid, Hydrochinon) in solution.
  • a reducing agent e.g. Na-borohydrid, Hydrochinon
  • the amount of silver deposited on the Pt is proportional to the length of the enhancement incubation.
  • Visualisation of a non-visible Pt nucleus can be accomplished by the empirical observation of the appearace of a black spot in the test sample.
  • the black spots indicate the site of specific probes binding and thus the site of specific target location.
  • the technique enables a quick and easy diagnostic procedure for the detection of various microorganisms and gene translocations/abnormalities.

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US10/900,902 1996-10-08 1997-10-08 Methods for labeling nucleotides, labeled nucleotides and useful intermediates Expired - Lifetime USRE40557E1 (en)

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PCT/NL1997/000559 WO1998015564A1 (en) 1996-10-08 1997-10-08 Methods for labeling nucleotides, labeled nucleotides and useful intermediates

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EP0937090A1 (en) 1999-08-25
US6797818B2 (en) 2004-09-28
DE69714600D1 (de) 2002-09-12
JP2010166914A (ja) 2010-08-05
NZ334803A (en) 2000-05-26
ES2182121T3 (es) 2003-03-01
JP2001503742A (ja) 2001-03-21
EP0937090B1 (en) 2002-08-07
US7217813B2 (en) 2007-05-15
PT937090E (pt) 2002-12-31
AU4474697A (en) 1998-05-05
CA2267133C (en) 2006-07-18
US20050118621A1 (en) 2005-06-02
ATE221894T1 (de) 2002-08-15
DK0937090T3 (da) 2002-12-02
US6338943B1 (en) 2002-01-15
CA2267133A1 (en) 1998-04-16
DE69714600T2 (de) 2003-03-27
AU726692B2 (en) 2000-11-16
WO1998015564A1 (en) 1998-04-16
JP4981197B2 (ja) 2012-07-18
US20020160396A1 (en) 2002-10-31

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