Mapping Polyamide–DNA Interactions in Human Cells Reveals a New Design Strategy for Effective Targeting of Genomic Sites

Targeting the genome with sequence‐specific synthetic molecules is a major goal at the interface of chemistry, biology, and personalized medicine. Pyrrole/imidazole‐based polyamides can be rationally designed to target specific DNA sequences with exquisite precision in vitro; yet, the biological outcomes are often difficult to interpret using current models of binding energetics. To directly identify the binding sites of polyamides across the genome, we designed, synthesized, and tested polyamide derivatives that enabled covalent crosslinking and localization of polyamide–DNA interaction sites in live human cells. Bioinformatic analysis of the data reveals that clustered binding sites, spanning a broad range of affinities, best predict occupancy in cells. In contrast to the prevailing paradigm of targeting single high‐affinity sites, our results point to a new design principle to deploy polyamides and perhaps other synthetic molecules to effectively target desired genomic sites in vivo.     

Influence of a terminal formamido group on the sequence recognition of DNA by polyamides

Pyrrole (Py)-imidazole (Im)-containing polyamides bind in the minor groove of DNA and can recognize specific sequences through a stacked antiparallel dimer. It has been proposed that there are two different low energy ways to form the stacked dimer and that these are sensitive to the presence of a terminal formamido group: (i) a fully overlapped stacking mode in which the N-terminal heterocycles of the dimer stack on the amide groups between the two heterocycles at the C-terminal and (ii) a staggered stacking mode in which the N-terminal heterocycles are shifted by approximately one unit in the C-terminal direction (Structure 1997, 5, 1033-1046). Two different DNA sequences will be recognized by the same polyamide stacked in these two different modes. Despite the importance of polyamides as sequence specific DNA recognition agents, these stacking possibilities have not been systematically explored. As part of a program to develop agents that can recognize mismatched base pairs in DNA, a set of four polyamide trimers with and without terminal formamido groups was synthesized, and their interactions with predicted DNA recognition sequences in the two different stacking modes were evaluated. Experimental difficulties in monitoring DNA complex formation with polyamides were overcome by using surface plasmon resonance (SPR) detection of the binding to immobilized DNA hairpin duplexes. Both equilibrium and kinetic results from SPR show that a terminal formamido group has a pronounced effect on the affinity, sequence specificity, and rates of DNA-dimer complex formation. The formamido polyamides bind preferentially in the staggered stacking mode, while the unsubstituted analogues bind in the overlapped mode. Affinities for cognate DNA sequences increase by a factor of around 100 when a terminal formamido is added to a polyamide, and the preferred sequences recognized are also different. Both the association and the dissociation rates are slower for the formamido derivatives, but the effect is larger for the dissociation kinetics. The formamido group thus strongly affects the interaction of polyamides with DNA and changes the preferred DNA sequences that are recognized by a specific polyamide stacked dimer.     

Synthesis and cellular effect of a novel conjugate of polyamide and phospholipid

In order to improve the cell penetration of polyamide and its movement toward nucleic DNA we synthesized a conjugate of polyamide and phospholipid, which showed a significantly reducecd cytotoxicity and effective apoptosis when comparing with the native polyamide.     

N ‐Formamido‐Containing Mono‐ and Diheterocyclic Pyrrole‐and Imidazole‐2‐carboxylic Acids as Building Blocks for Polyamide Synthesis

Four N‐formamido‐containing mono‐and diheterocyclic pyrrole‐ and imidazole‐2‐containing acids 1–4 were synthesized as intermediates for the preparation of polyamide molecules. The N‐formamido‐moiety forces the compounds to bind strongly as a stacked dimer, and in a staggered fashion, at specific sequences in the minor‐groove of DNA. The acid moiety at the C‐terminus of compounds enables these molecules to be coupled to amine‐containing intermediates to form the amide linkages of the target polyamide. This convergent approach increases the synthetic diversity in polyamide chemistry by enabling one acid to be used with a variety of different C‐terminus‐functionalized intermediates.     

肽核酸的合成、修饰和应用

肽核酸是寡核苷酸模拟物, 它的糖-磷酸骨架被N-(2-氨基乙基)甘氨酸骨架所代替. 为了优化肽核酸的性质, 各种结构的肽核酸(PNA)单体被合成出来. 综述了肽核酸的合成、结构修饰及应用.     

Synthesis, DNA-binding and antiproliferative properties of acridine and 5-methylacridine derivatives

Several acridine derivatives were synthesized and their anti-proliferative activity was determined. The most active molecules were derivatives of 5-methylacridine-4-carboxylic acid. The DNA binding properties of the synthesized acridines were analyzed by competitive dialysis and compared with the anti-proliferative activities. While inactive acridine derivatives showed high selectivity for G-quadruplex structures, the most active 5-methylacridine-4-carboxamide derivatives had high affinity for DNA but showed poor specificity. An NMR titration study was performed with the most active 5-methylacridine-4-carboxamide, confirming the high affinity of this compound for both duplex and quadruplex DNAs.     

Sequence‐Specific DNA Alkylation by Tandem Py–Im Polyamide Conjugates

Tandem N‐methylpyrrole? N‐methylimidazole (Py? Im) polyamides with good sequence‐specific DNA‐alkylating activities have been designed and synthesized. Three alkylating tandem Py? Im polyamides with different linkers, which each contained the same moiety for the recognition of a 10 bp DNA sequence, were evaluated for their reactivity and selectivity by DNA alkylation, using high‐resolution denaturing gel electrophoresis. All three conjugates displayed high reactivities for the target sequence. In particular, polyamide 1 , which contained a β‐alanine linker, displayed the most‐selective sequence‐specific alkylation towards the target 10 bp DNA sequence. The tandem Py? Im polyamide conjugates displayed greater sequence‐specific DNA alkylation than conventional hairpin Py? Im polyamide conjugates ( 4 and 5 ). For further research, the design of tandem Py? Im polyamide conjugates could play an important role in targeting specific gene sequences.     

Synthesis of aromatic polyamides having pyridine moiety and their lyotropic properties in solution

Fully aromatic polyamide containing pyridine moieties (PPy) were successfully synthesized either by interfacial or solution polycondensation to prepare polyamide with inherent viscosity as high as 4. Solution properties of PPy in sulfuric acid were investigated in terms of solution viscosity and lyotropic behavior. The polyamide had a better solubility in sulfuric acid than in poly(p-phenylene terephthalamide) (PT) and the PPy solution in sulfuric acid exhibited an optically anisotropic property in a wider range of concentrations at relatively low temperatures in comparison with the PT solution. Viscosities of the PPy solution and the film cast from the PPy solution indicated a phenomenon characteristic of a highly oriented rigid polymer molecule caused by a lyotropic behavior.     

Design and synthesis of novel thiazole-containing cross-linked polyamides related to the antiviral antibiotic distamycin

A family of naturally occurring oligopeptides includes netropsin, distamycin, anthelvencin, kikumycin B, amidinomycin, and norformycin. Netropsin (I) and distamycin (II) express their biological activities by targeting specific sequences of chemical functionalities in the minor groove of DNA. Both netropsin and distamycin can be regarded as polyamide chains in which each alpha-carbon has been replaced by a five-membered pyrrole ring. The repeat distance in such an augmented polyamide chain is almost the same as the distance from one base pair to the next along the floor of a minor groove within beta-DNA. In this paper we report the synthesis of 16-21 cross-linked polyamides containing a thiazole heterocyclic ring bearing the active functionalites NH(2), NHCHO, or H. 16 and 17 were synthesized by DCC and HOBt catalyzed reaction of 5 with 14 and 15, while the formylation products 18 and 19 were obtained by coupling the formylated 4-methyl-thiazolated acid 6 with 14 and 15. The deaminated compounds 20 and 21 were obtained by the coupling of 5-trichloroacetyl-4-methylthiazole 7 synthesized from 4-methylthiazole. All the six cross-linked polyamides 16-21 were tested for their DNA gyrase inhibition. The studies have shown these polyamides have better sequence recognition and a greater percentage of inhibition than the corresponding monomers. The compound 17 shows complete inhibition of gyrase at 0.5 microM concentration as compared to the naturally occurring distamycin at 1.0 microM.     

Sequence‐Specific DNA Recognition by Cyclic Pyrrole–Imidazole Cysteine‐Derived Polyamide Dimers

Pyrrole–imidazole (PI) polyamides bind to the minor groove of the DNA duplex in a sequence‐specific manner and thus have the potential to regulate gene expression. To date, various types of PI polyamides have been designed as sequence‐specific DNA binding ligands. One of these, cysteine cyclic PI polyamides containing two β‐alanine molecules, were designed to recognize a 7 bp DNA sequence with high binding affinity. In this study, an efficient cyclization reaction between a cysteine and a chloroacetyl residue was used for dimerization in the synthesis of a unit that recognizes symmetrical DNA sequences. To evaluate specific DNA binding properties, dimeric PI polyamide binding was measured by using a surface plasmon resonance (SPR) method. Extending this molecular design, we synthesized a large dimeric PI polyamide that can recognize a 14 bp region in duplex DNA.     

MODIFICATION OF POLYAMIDE 6 WITH POLYAMINOAMIDE-g-POLY(ETHYLENE GLYCOL) VIA HYDROLYTIC POLYMERIZATION

To enhance the impact strength of polyamide 6,hydrolytic polymerization modification by the polyaminoamide-gpoly (ethylene glycol)(PAAEG)derivatives with poly(ethylene glycol)(PEG)molecular weight of 400-10000 was studied. Amide groups of polyaminoamide segments were postulated to form hydrogen bonding with polyamide 6,and hydroxy groups of PAAEG units were expected to react with carboxylic acid groups of polyamide 6 forming copolymers during the polymerization.The improved compatibility in amorphous reg...     

Synthesis and DNA cleavage evaluation of epoxypiperidine derivatives bearing a dehydroamino acid unit

Epoxypiperidine derivatives bearing a dehydroamino acid unit were designed and synthesized as novel DNA alkylating agents based on the structure of azinomycins. A relaxation assay of plasmid DNA revealed that the epoxypiperidine derivative 3 has a DNA cleavage activity. Based on the studies, it would appear that the electron density of the amino group of epoxypiperidines plays a critically important role in the DNA cleavage.     

Synthesis of a Novel Conjugate of Bromoarene and Polyamide Containing N-Methylimidazoles

DNA-photocleavage agents have generated considerable attention in chemistry,biology and medicine1,2,because their DNA-cleavage activities can be easily controlled by photoirradiation.In the past decade,several DNA-cleavage agents have been successfully attached to polyamide3,4,to obtain new conjugates with higher and specific DNA-cleavage activities.Most of them contain only one photocleavage group to induce single-strand breaks,and the conjugates inducing double-strand breaks have been ra…     

Synthesis of functional polyamides by the ritter reaction

Polyamides having pendant functional groups such as hydroxyl, mercapto, or imine groups were synthesized by the Ritter reaction of dinitriles and trioxane in concentrated sulfuric acid. The polymerization of β-hydroxyl glutaronitrile yielded a water-soluble polyamide having a low molecular weight which might be ascribed to the participation of the hydroxyl group with the polymerization, while the polymerization of β-mercaptoglutaronitrile resulted in the formation of a crosslinked polyamide which was insoluble in common solvents. Polymerization of dinitriles having imine groups yielded water-soluble polyamides which were effective as a coagulation agent for colloidal solutions.     

Alkylidene derivatives of datiscin

With lower ketones (acetone, methyl ethyl ketone) in weakly acidic solution, flavonoid rhamnosides and rutinosides form alkylidene derivatives at the cisdiol grouping of the rhamnose residue. It has been found that the formation of alkylidene derivatives of flavonoid glycosides is a side reaction that takes place during the chromatographic process on an “acid” polyamide sorbent.     

Polyamide Layer Chromatography. Identification of Amino Acids in Angelica acutiloba Kitagawa via DNP Derivative

Eighteen amino acids; proline, alanine, valine, leucine, isoleucine, hydroxyproline, phenylalanine, ornithine, glycine, serine, aspartic acid, glutamic acid, threonine, asparagine, lysine, tyrosine, tryptophan, and arginine were identified by polyamide layer chromatography via DNP (dinitrophenly) derivatives in Angelica acutiloba Kitagawa (Tang-Kwei)     

Microwave assisted synthesis of Py-Im polyamides

Microwave synthesis was utilized to rapidly build Py-Im polyamides in high yields and purity using Boc-protection chemistry on Kaiser oxime resin. A representative polyamide targeting the 5'-WGWWCW-3' (W = A or T) subset of the consensus Androgen and Glucocorticoid Response Elements was synthesized in 56% yield after 20 linear steps and HPLC purification. It was confirmed by Mosher amide derivatization of the polyamide that a chiral α-amino acid does not racemize after several additional coupling steps.     

Sequence-specific trapping of topoisomerase I by DNA binding polyamide-camptothecin conjugates

Hairpin pyrrole-imidazole polyamides are synthetic ligands that bind in the minor groove of DNA with affinities and specificities comparable to those of DNA binding proteins. Three polyamide-camptothecin conjugates 1-3 with linkers varying in length between 7, 13, and 18 atoms were synthesized to trap the enzyme Topoisomerase I and induce cleavage at predetermined DNA sites. One of these, polyamide-camptothecin conjugate 3 at nanomolar concentration (50 nM) in the presence of Topo I (37 degrees C), induces DNA cleavage between three and four base pairs from the polyamide binding site in high yield (77%).