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DNA Dendrimers
Thor W. Nilsen, Poly Probe, Inc., 15 Bala Avenue, P.O. Box 2675, Bala Cynwyd, PA 19004, U.S.A. E-mail: 75240.34@compuserve.com. WWW site: http://www.polyprobe.com.
The work reported in this Abstract was awarded the 1996 LVMH Vinci of Excellence Prize.
Dendritic molecules are highly branched arborescent structures that have found applications in such products as chemical reagents, lubricants and contrast media for magnetic resonance. A new class of these molecules is comprised of dendrimers constructed entirely from unique nucleic acid monomers designed such that sequential hybridization adds successive layers of monomer, resulting in a geometric expansion of both the molecule's mass and free single-stranded ends (Fig. 4).
My contribution to DNA dendrimers began in Spring 1986. The publication of the Polymerase Chain Reaction (PCR) in December 1985 [1] had dramatically changed my thoughts regarding the detection of nucleic acids. Until that time, nucleic acid blot assay was the standard method for detecting nucleic acids. PCR assay opened my mind to the possibilities of alternative detection methods. I immediately recognized the power of the PCR lay in the geometric expansion of target molecules---however, this is also the source of one of its greatest drawbacks: the difficulty of quantifying the initial number of target molecules in a sample.
I began working on alternatives to PCR. A key component of any alternative would have to be superior quantitation ability---the new method should be capable of single-target molecule detection. I had known for some time of signal amplification methods for blot assay based on building an aggregate of signal molecules. The spark for the idea of DNA dendrimers was an image in my mind of removing the aggregate from a membrane and assembling it in free space. Once the concept of macromolecular assembly independent of a surface came to me, I rapidly proceeded to the concept of the DNA dendrimer. Interestingly, both the PCR assay and the DNA dendrimers are based on geometric expansion: PCR amplifies the target; dendrimers amplify the signal.
It was one thing to conceptualize DNA dendrimers and quite another to actually build them. I began by designing the sequences. I wanted the sequences to have an absolute minimum of non-specific homology---in essence, a Euler sequence. In this case, the Euler sequence was to utilize each possible 5-mer (AAAAA, AAAAC, AAAAG, AAAAT, etc.) only once in a double-stranded molecule. I converted each of the bases to the numbers 1, 2, 3, 4, assembled a grid of all the 5-mers (a base 4 count from 11111 to 44444). I then added two other elements to the plane of the spreadsheet: (1) a matrix for calculating the available choices extending three bases into the future and (2) an "enzyme" consisting of a set of instructions for adding the next base to the growing solution and then moving one column over to reiterate the process. The program did not create the ultimate sequence---that is, one with 512 bases---but it did produce a sequence that was 506 bases long. That 506-base sequence served as the starting material for the design of the single strands for dendrimer assembly.
The next step was the incorporation of the Euler sequence into seven monomer strands. I devised a cloning strategy based on the hybridization of complementary oligonucleotides. The process then moved from the theoretical to the laboratory. I synthesized and assembled 52 oligonucleotides into seven double-stranded inserts, which I cloned, sequenced and ultimately multimerized (tandemly repeated within plasmid). The inserts (designed sequences) were cloned such that restriction (cutting) with two enzymes yields a (+) strand eight bases shorter than the (-) strand. Large-scale plasmid preparations were completed, the plasmid restricted and the strands separated via preparative gel electrophoresis.
At this point I had the seven strands required for dendrimer assembly. One remaining hiccup was the discovery of strand exchange. Hybridization of the strands produced the desired dendrimer monomers---yet when hybridized, the structure fell apart into small groups of DNA molecules. After some experimentation, I determined that by hybridizing and subsequently cross-linking the DNA molecules, strand exchange was effectively eliminated and with that, stable and useful DNA dendrimers could be built.
DNA dendrimers have been shown to provide signal amplification of at least 60 fold in many blot formats, including Northern blots, Southern blots and dot blots [2]. Current research is underway to amplify protein detection in Western blots. Since individual fluorescently labeled four-layer DNA dendrimers are easily counted, research is being directed toward furthering the applications of dendritic nucleic acid molecules in a flowing stream---a "flow fluorescence" assay---that my colleagues and I expect to be applicable to the measurement of viral burden in people suffering from hepatitis, HIV infection and other diseases [3].
References and Notes
1.
R.K. Saiki, S. Scharf, F. Faloona, K.B. Mullis, G.T. Horn, H.A. Erlich and N. Arnheim, "Enzymatic Amplification of Beta-Globin Genomic Sequences and Restriction Site Analysis for Diagnosis of Sickle Cell Anemia," Science 230, No. 4732 (December 1985) pp. 1350--1354.
2.
Nucleic acid blots began with Dr. Southern (hence the name). DNA is electrophoresed, transferred (blotted) onto a membrane and "probed." DNA blots are Southern blots; RNA blots are Northern blots. A dot blot refers to a direct application of sample to membrane.
3.
For more information, see http://www.polyprobe.com.
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Figure Captions
Fig. 1.
Ryozo Fujii. Diagram showing the system for control of motile activities of common chromatophores in teleosts. (ACh = acetylcholine; ACh-r = ACh receptor; AS-r = adenosine receptor; ATP = adenosine triphosphate; Ca²+; = calcium ions; cAMP = cyclic adenosine monophosphate; cGMP = cyclic guanosine monophosphate; Epi = epinephrine; ET = endothelin; ET-r = endothelin receptor; Glu = glutamate; Glu-r = glutamate receptor; IP3D>, = inositol triphosphate; MCH = melanin-concentrating hormone; MCH-r = MCH receptor; MIH = MSH-release inhibiting hormone; MSH = melanophore-stimulating hormone; MSH-r = MSH receptor; MT = melatonin; MT-r = melatonin receptor; NANC fiber = non-adrenergic, non-cholinergic nerve fiber; NE = norepinephrine; NO = nitric oxide; -r = -adrenergic receptor; -r = -adrenergic receptor.)
Fig. 2.
Arpád Furka. Schematic representation of the portioning-mixing synthesis. P denotes the solid polymer; the white, gray and black discs represent three different amino acids. The divergent, parallel and convergent arrows show portioning, coupling and mixing, respectively. As can be seen in this illustration, the nine resultant dimers comprise all possible combinations of the white, gray and black discs.
Fig. 3.
Elliot Meyerowitz. (left) A typical flower of Arabidopsis thaliana, greatly enlarged (in life it is only 2--3 mm across). The flower has four whorls of organs: at the periphery (barely visible) are four sepals, inside of which are four petals, six stamens and a central ovary consisting of two fused carpels. (right) An Arabidopsis thaliana flower from a transgenic plant in which the B organ identity function has been activated everywhere in the flower. The result is four petals in the positions normally occupied by sepals, and stamens in the positions where carpels are normally found, but no change in the second-whorl petals or third-whorl stamens. The flower thus has eight petals (in two whorls of four) and extra stamens, but no ovary.
Fig. 4.
Thor W. Nilsen. Dendritic molecules: (top left) Initiator. (top, right) One-layer dendrimer. (bottom) Two-layer dendrimer). A new class of dendritic molecules has been created from unique nucleic acid monomers. Each monomer is a heterodimer of two single-stranded nucleic acid oligomers possessing a central double-stranded waist and four single-stranded arms. Several different monomers have been constructed such that, when assembled in the appropriate order, they will form mostly hollow spheres having multiple single-stranded DNA arms available for binding at the molecular surface. The molecular structure grows exponentially as each sequential layer is added. Molecules with two layers have 36 free ends, molecules with three layers have 108 free ends, molecules with four layers have 324 free ends, etc.