Solid-phase synthesis of DNA binding polyamides on oxime resin

Control of the energetics and specificity of DNA binding polyamides is necessary for inhibition of protein-DNA complex formation and gene regulation studies. Typically, solid-phase methods using Boc monomers for synthesis have depended on Boc-beta-Ala-PAM resin which affords a beta-alanine-Dp tail at the C-terminus, after cleavage with N,N-dimethylaminopropylamine (Dp). To address the energetic consequences of this tail for DNA minor groove binding, we describe an alternative solid phase method employing the Kaiser oxime resin which allows the synthesis of polyamides with incrementally shortened C-terminal tails. Polyamides without Dp and having methyl amide tails rather than beta-alanine show similar affinity relative to the standard beta-Dp tail. The truncated tail diminishes the A,T base pair energetic preference of the beta-Dp tail which will allow a greater variety of DNA sequences to be targeted by hairpin polyamides.     

Development of programmable small DNA-binding molecules with epigenetic activity for induction of core pluripotency genes

Epigenetic modifications that govern the gene expression are often overlooked with the design of artificial genetic switches. N-Methylpyrrole-N-methylimidazole (PI) hairpin polyamides are programmable small DNA binding molecules that have been studied in the context of gene regulation. Recently, we synthesized a library of compounds by conjugating PI polyamides with SAHA, a chromatin-modifier. Among these novel compounds, PI polyamide-SAHA conjugate 1 was shown to epigenetically activate pluripotency genes in mouse embryonic fibroblasts. Here, we report the synthesis of the derivatives of conjugate 1 and demonstrate that these epigenetically active molecules could be developed to improve the induction of pluripotency factors.     

A practical approach to the synthesis of hairpin polyamide-peptide conjugates through the use of a safety-catch linker

Hairpin polyamides are high-affinity, sequence selective DNA binders. The use of a safety-catch linker for the solid phase synthesis of hairpin polyamides allows for easy preparation of derivatives ready for chemoselective ligation with unprotected peptides. Examples of ligations reported include thioether bond formation and thioester-mediated amide bond formation ('Native Chemical Ligation').     

Efficient DNA alkylation by a pyrrole-imidazole CBI conjugate with an indole linker: sequence-specific alkylation with nine-base-pair recognition

Conjugates 7, 8, and 10 of N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides and 1,2,9,9a-tetrahydrocyclopropa[1,2-c]benz[1,2-e]indol-4-one (CBI) with a 5-amino-1H-indole-2-carbonyl linker were synthesized by Fmoc solid-phase synthesis and a subsequent liquid-phase coupling procedure. The DNA alkylating abilities of conjugates 7, 8, 6b, and 10 were examined using Texas Red-labeled PCR fragments and high-resolution denaturing gel electrophoresis. CBI conjugates 7 and 8 exhibited highly efficient sequence-specific DNA alkylation comparable with previous CBI conjugates with a vinyl linker. In particular, conjugate 10, with a 10-ringed hairpin Py-Im polyamide, alkylated at the adenine of 5'-ACAAATCCA-3'. Introduction of an indole linker greatly facilitated the synthesis of sequence-specific alkylating Py-Im polyamides.     

Polyamide recognition-mass spectrometry for distinguishing hairpin DNA from coil DNA

The discrimination between hairpin DNA and coil DNA has been well achieved through polyamides as probes by electrospray ionization (ESI) mass spectrometry. ESI mass spectra showed that polyamides bind to hairpin DNA with high selectivity, and almost no binding with coil DNA. In addition, the noncovalent interaction between polyamides and hairpin DNA was also studied; the results show that hairpin DNA with longer stem and polyamides with more heterocycles have higher binding affinity and stability in gas phase.     

Synthesis of D-mannitol and L-iditol derivatives as monomers for the preparation of new regioregular AABB-type polyamides

1,6-Diamino-1,6-dideoxy-2,3,4,5-tetra-O-methyl-D-mannitol (and its L-iditol analogue) suitable for their utilization as monomers in the preparation of linear polyamides are described. Regio- and stereoregular polyamides of the AABB-type have been prepared by the active ester polycondensation method from these C(2) symmetric monomers and suberic and dodecanedioic acids. The resulting polyamides were obtained in fair yields (70-60%) and were characterized by elemental analyses and infrared and 1H and 13C NMR spectroscopies. Their M(w) and M(w)/M(n) were determined by GPC relative to polystyrene standards. All of them were gummy non-crystalline solids.     

Novel diamino imidazole and pyrrole-containing polyamides: Synthesis and DNA binding studies of mono- and diamino-phenyl-ImPy*Im polyamides designed to target 5'-ACGCGT-3'

Pyrrole- and imidazole-containing polyamides are widely investigated as DNA sequence selective binding agents that have potential use as gene control agents. The key challenges that must be overcome to realize this goal is the development of polyamides with low molar mass so the molecules can readily diffuse into cells and concentrate in the nucleus. In addition, the molecules must have appreciable water solubility, bind DNA sequence specifically, and with high affinity. It is on this basis that the orthogonally positioned diamino/dicationic polyamide Ph-ImPy*Im 5 was designed to target the sequence 5'-ACGCGT-3'. Py* denotes the pyrrole unit that contains a N-substituted aminopropyl pendant group. The DNA binding properties of diamino polyamide 5 were determined using a number of techniques including CD, ΔT(M), DNase I footprinting, SPR and ITC studies. The effects of the second amino moiety in Py* on DNA binding affinity over its monoamino counterpart Ph-ImPyIm 3 were assessed by conducting DNA binding studies of 3 in parallel with 5. The results confirmed the minor groove binding and selectivity of both polyamides for the cognate sequence 5'-ACGCGT-3'. The diamino/dicationic polyamide 5 showed enhanced binding affinity and higher solubility in aqueous media over its monoamino/monocationic counterpart Ph-ImPyIm 3. The binding constant of 5, determined from SPR studies, was found to be 1.5 × 10(7)M(-1), which is ～3 times higher than that for its monoamino analog 3 (4.8 × 10(6)M(-1)). The affinity of 5 is now approaching that of the parent compound f-ImPyIm 1 and its diamino equivalent 4. The advantages of the design of diamino polyamide 5 over 1 and 4 are its sequence specificity and the ease of synthesis compared to the N-terminus pyrrole analog 2.     

Profiling solid-phase synthesis products by free-solution conjugate capillary electrophoresis

Solid-phase synthesis of oligomers, both natural and nonnatural, has proved to be invaluable for the development of many areas of biotechnology. A critical step in the solid-phase synthesis of any oligomer is determining the number and concentration of different constituents present in the product mixture resulting from the synthesis, both before and after purification. Most typically, this analysis is performed by reversed-phase high performance liquid chromatography (RP-HPLC), with the separated components detected by UV absorbance. Recently, we described a novel technique, free-solution conjugate electrophoresis (FSCE), for the high-resolution separation and sensitive laser-induced fluorescence (LIF) detection of uncharged, synthetic polymers, PEG in particular. In this report, we apply this bioconjugate capillary electrophoresis technique to analyze products of the solid-phase synthesis of oligomeric polyamides, namely poly(N-substituted glycines), or polypeptoids. When compared to more traditional RP-HPLC analysis, FSCE analysis of oligomeric peptoids results in separation resolutions that are approximately five times higher and separation efficiencies that are increased by 150%. Moreover, when FSCE with LIF detection is applied to the analysis of oligomeric polyamides after HPLC purification, impurities that are not detectable in RP-HPLC analysis are readily separated and detected. With the advent of capillary array electrophoresis (CAE), which allows for automated, parallel analysis of many different samples, we believe that FSCE will be especially applicable to the analysis of combinatorial synthesis products, by allowing researchers to evaluate many different samples in a single, highly parallel, fully automated analysis. This is in contrast to RP-HPLC analysis, in which samples must be analyzed in series.     

A versatile access to new macrocyclic oligoheterocycles (MOH)

An efficient and straightforward methodology for the parallel solid-phase synthesis of a variety of new macrocyclic oligoheterocycles is described. Exhaustive reduction of resin-bound cyclic polyamides using borane generates polyamines. Treatment of separated pairs of amines with a variety of bifunctional reagents provides, following cleavage from the solid support, the desired macrocyclic oligoheterocyclic (MOH) compounds in good yields and purities.     

生物法合成戊二胺研究进展

随着经济快速发展,大气污染和全球变暖的趋势日益恶化。世界上每年消耗大量石化资源来源的聚酰胺,戊二胺作为聚酰胺的重要组成单体,生物法合成戊二胺具有经济学和生态学双重意义。目前,生物法合成戊二胺的工程菌主要有谷氨酸棒状杆菌和大肠杆菌,文中从微生物中戊二胺的代谢、戊二胺合成途径的关键酶和转运蛋白、戊二胺生产最佳代谢途径和戊二胺产量的预测、代谢工程研究进展等方面综述了生物法合成戊二胺的最新研究现状和进展,并对其前景进行了展望。     

Recognition of the DNA minor groove by pyrrole-imidazole polyamides: comparison of desmethyl- and N-methylpyrrole

Polyamides consisting of N-methylpyrrole (Py), N-methylimidazole (Im), and N-methyl-3-hydroxypyrrole (Hp) are synthetic ligands that recognize predetermined DNA sequences with affinities and specificities comparable to many DNA-binding proteins. As derivatives of the natural products distamycin and netropsin, Py/Im/Hp polyamides have retained the N-methyl substituent, although structural studies of polyamide:DNA complexes have not revealed an obvious function for the N-methyl. In order to assess the role of the N-methyl moiety in polyamide:DNA recognition, a new monomer, desmethylpyrrole (Ds), where the N-methyl moiety has been replaced with hydrogen, was incorporated into an eight-ring hairpin polyamide by solid-phase synthesis. MPE footprinting, affinity cleavage, and quantitative DNase I footprinting revealed that replacement of each Py residue with Ds resulted in identical binding site size and orientation and similar binding affinity for the six-base-pair (bp) target DNA sequence. Remarkably, the Ds-containing polyamide exhibited an 8-fold loss in specificity for the match site versus a mismatched DNA site, relative to the all-Py parent. Polyamides with Ds exhibit increased water solubility, which may alter the cell membrane permeability properties of the polyamide. The addition of Ds to the repertoire of available monomers may prove useful as polyamides are applied to gene regulation in vivo. However, the benefits of Ds incorporation must be balanced with a potential loss in specificity.     

Detection of triplet repeat sequences in the double-stranded DNA using pyrene-functionalized pyrrole-imidazole polyamides with rigid linkers

Methods for sequence-specific detection in double-stranded DNA (dsDNA) are becoming increasingly useful and important as diagnostic and imaging tools. Recently, we designed and synthesized pyrrole (Py)-imidazole (Im) polyamides possessing two pyrene moieties, 1, which showed an increased excimer emission in the presence of (CAG)(12)-containing oligodeoxynucleotides (ODN) 1 and 2. In this study, we synthesized bis-pyrenyl Py-Im polyamides with rigid linkers 2, 3, and 4 to improve their fluorescence properties. Among the conjugates, 2 showed a marked increase in excimer emission, which was dependent on the concentration of the target ODN and the number of CAG repeats in the dsDNA. Unlike conjugate 1, which has flexible linkers, the excimer emission intensity of 2 was retained at over 85%, even after 4h. Py-Im polyamides have the potential to be important diagnostic molecules for detecting genetic differences between individuals.     

Alpha-diaminobutyric acid-linked hairpin polyamides

A hairpin polyamide-chlorambucil conjugate linked by alpha-diaminobutyric acid (alpha-DABA) has been shown to have interesting biological properties in cellular and small animal models. Remarkably, this new class of hairpin polyamides has not been previously characterized with regard to energetics and sequence specificity. Herein we present a series of pyrrole-imidazole hairpin polyamides linked by alpha-DABA and compare them to polyamides containing the standard gamma-DABA turn unit. The alpha-DABA hairpins have overall decreased binding affinities. However, alpha-DABA polyamide-chlorambucil conjugates are sequence-specific DNA alkylators with increased specificities. Affinity cleavage studies of alpha-DABA polyamide-EDTA conjugates confirmed their preference for binding DNA in a forward hairpin conformation. In contrast, an unsubstituted glycine-linked polyamide prefers to bind in an extended binding mode. Thus, substitution on the turn unit locks the alpha-DABA polyamide into the forward hairpin binding motif.     

Kinetic consequences of covalent linkage of DNA binding polyamides

Polyamides composed of N-methylpyrrole (Py) and N-methylimidazole (Im) subunits can bind in the minor groove of DNA at predetermined sequences with subnanomolar affinity and high specificity. Covalent linkage of polymer subunits using a gamma-aminobutyric acid linker has been shown to increase both the affinity and specificity of polyamides. Using a fluorescence detected stopped-flow assay, we have studied the differences in association and dissociation kinetics of a series of polyamides representing unlinked, hairpin and cyclic analogues of the four ring polyamide ImPyPyPy-beta-Dp. Whereas the large differences seen in the equilibrium association constants between the unlinked and covalently linked polyamides are primarily due to higher association rate constants, discrimination between matched and mismatched sites by each polyamide can be ascribed in large part to differences in their dissociation rate constants. The consequences of this kinetic behavior for future design are discussed.     

Chromatin opening of DNA satellites by targeted sequence-specific drugs

There are few tools available for dissecting and elucidating the functions of DNA satellites and other nongenic DNA. To address this, we have explored the experimental potential of DNA sequence-specific drugs containing pyrrole and imidazole amino acids (polyamides). Compounds were synthesized that target different Drosophila melanogaster satellites. Dimeric oligopyrroles were shown to target the AT-rich satellites I, III, and SARs (scaffold associated regions). One polyamide (P31) specifically binds the GAGAA satellite V. Specificity of targeting was established by footprinting, epifluorescence of nuclei, and polytene chromosomes stained with fluorescent derivatives. These polyamides were shown to mediate satellite-specific chromatin opening of the chromatin fiber. Remarkably, certain polyamides induced defined gain or loss-of-function phenotypes when fed to Drosophila melanogaster.     

Binding of hairpin pyrrole and imidazole polyamides to DNA: relationship between torsion angle and association rate constants

N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides are small organic molecules that bind to DNA with sequence specificity and can be used as synthetic DNA-binding ligands. In this study, five hairpin eight-ring Py–Im polyamides 1–5 with different number of Im rings were synthesized, and their binding behaviour was investigated with surface plasmon resonance assay. It was found that association rate (k_a) of the Py–Im polyamides with their target DNA decreased with the number of Im in the Py–Im polyamides. The structures of four-ring Py–Im polyamides derived from density functional theory revealed that the dihedral angle of the Py amide carbonyl is 14∼18°, whereas that of the Im is significantly smaller. As the minor groove of DNA has a helical structure, planar Py–Im polyamides need to change their conformation to fit it upon binding to the minor groove. The data explain that an increase in planarity of Py–Im polyamide induced by the incorporation of Im reduces the association rate of Py–Im polyamides. This fundamental knowledge of the binding of Py–Im polyamides to DNA will facilitate the design of hairpin Py–Im polyamides as synthetic DNA-binding modules.     

Synthesis of pyrrole-imidazole-duocarmycin polyamide and its sequence selective DNA alkylation.

The new solid phase synthesis of sequence-specific DNA alkylating polyamides containing segment A of Du86 (Duo), N-methylimidazole (Im) and N-methylpyrrole (Py) amino acids is described. New monomer building block N-carboxylmethyl Py (Pyc) was synthesized from 2-methylpyrrolecarboxylate by eight steps. After normal coupling of FMOC-protected-Im and -Py monomer, the deprotection of silyl group generates free carboxylic acid. Introduction of various types of functional groups on solid support will be presented.