Gamma-substituted peptide nucleic acids constructed from L-lysine are a versatile scaffold for multifunctional display.
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DNA↗
Biomedical subjects
Daniel H Appella
Publications and source records attributed to Daniel H Appella.
PNA-DNA duplexes, triplexes, and quadruplexes are stabilized with trans-cyclopentane units.
Peptide nucleic acids (PNAs) are non-natural nucleic acid mimics that bind to complementary DNA and RNA with high affinity and selectivity. PNA can bind to nucleic acids in a number of different ways. Currently, the formation of PNA-oligonucleotide duplex, triplex, and quadruplex structures have been reported. PNAs have been used in numerous biomedicial applications, but there are few strategies to predictably improve the binding properties of PNAs by backbone modification. We have been studying the benefits of incorporating (S,S)-trans-cyclopentane diamine units (tcyp) into the PNA backbone. In this Communication, we report the improvement in stability associated with tcyp incorporation into PNA-DNA duplexes, triplexes, and quadruplexes. The broad utility of this modification across multiple types of PNA structures is unique and should prove useful in the development of applications that rely on PNA.
Cyclopentanes↗
Practical synthesis of trans-tert-butyl-2-aminocyclopentylcarbamate and resolution of enantiomers.
Optically active trans-tert-butyl-2-aminocyclopentylcarbamate (1) has potential utility as a scaffold for chiral ligands and as a modified backbone unit for peptide nucleic acids (PNAs). We have developed a short and practical synthesis of 1 via aziridine opening of tosyl-activated cyclopentene aziridine 2 and optical resolution of racemic 1 with 10-camphorsulfonic acid (CSA). The route provides ready access to multigram quantities of both enantiomers without the need for chromatography.
Azides↗
Probing the structural requirements of peptoids that inhibit HDM2-p53 interactions.
Many cellular processes are controlled by protein-protein interactions, and selective inhibition of these interactions could lead to the development of new therapies for several diseases. In the area of cancer, overexpression of the protein, human double minute 2 (HDM2), which binds to and inactivates the protein p53, has been linked to tumor aggressiveness and drug resistance. In general, inhibition of protein-protein interactions with synthetic molecules is challenging and currently remains a largely uncharted area for drug development. One strategy to create inhibitors of protein-protein interactions is to recreate the three-dimensional arrangement of side chains that are involved in the binding of one protein to another, using a nonnatural scaffold as the attachment point for the side chains. In this study, we used oligomeric peptoids as the scaffold to begin to develop a general strategy in which we could rationally design synthetic molecules that can be optimized for inhibition of protein-protein interactions. Structural information on the HDM2-p53 complex was used to design our first class of peptoid inhibitors, and we provide here, in detail, the strategy to modify peptoids with the appropriate side chains that are effective inhibitors of HDM2-p53 binding. While we initially tried to develop rigid, helical peptoids as HDM2 binders, the best inhibitors were surprisingly peptoids that lacked any helix-promoting groups. These results indicate that starting with rigid peptoid scaffolds may not always be optimal to develop new inhibitors.
Calorimetry↗
Peptide nucleic acid microarrays made with (S,S)-trans-cyclopentane-constrained peptide nucleic acids.
Procedures to attach trans-cyclopentane-modified peptide nucleic acid oligomers to a glass slide are described. Peptide nucleic acids can offer distinct advantages to DNA detection compared to typically used DNA microarrays, especially with regard to chemical stability and quality of data. The trans-cyclopentane modification incorporated into the peptide nucleic acid is, in some cases, essential for successful DNA detection. It is hoped that these peptide nucleic acid-bearing glass slides will find application in several areas of DNA microarray technology.
Cyclopentanes↗
Synthesis of gamma-substituted peptide nucleic acids: a new place to attach fluorophores without affecting DNA binding.
Molecular beacon strategies using PNA are currently restricted to fluorophore attachment to the ends of the PNA. We report the synthesis of PNA oligomers wherein fluorophores can be attached to the PNA backbone from novel gamma-lysine PNA monomers. Oligomers incorporating the modified PNA showed comparable thermal stability to the corresponding aegPNA oligomer with DNA. When the modified PNA oligomer was annealed with complementary DNA, the fluorescence intensity increased 4-fold over the unbound PNA. [structure: see text]
Base Sequence↗
A new family of small molecules to probe the reactivation of mutant p53.
Cells that express mutant p53 derived from cancers are selectively killed by a new class of small organic molecules. The protein p53 is recognized as one of the most important guardians in the body that prevents tumor development. Mutant forms of p53 are present in approximately 50% of all human cancers. Molecules that selectively kill cells expressing mutant p53 could become important chemotherapeutic agents. Our research focuses on developing a synthetically accessible class of molecules that can be easily modified to examine structural activity relationships and mechanism of biological activity or to optimize for anticancer activity. In this communication, a new class of molecules that selectively arrests growth of cells expressing two forms of mutant p53 is described. Synthetic routes to these compounds are also presented.
Acetophenones↗
Cyclopentane-modified PNA improves the sensitivity of nanoparticle-based scanometric DNA detection.
trans-Cyclopentane-modified PNA has been successfully utilized as a target capture strand to improve the detection limit of a known DNA detection assay, and provide high levels of mismatch discrimination.
Antigens, Bacterial↗
Peptide nucleic acids with a flexible secondary amine in the backbone maintain oligonucleotide binding affinity.
[structure: see text] Replacing a secondary amide in a peptide nucleic acid backbone with a more flexible secondary amine affords an oligomer that surprisingly maintains the same binding affinity to complementary oligonucleotides as the unmodified polyamide oligomer.
Amines↗
(S,S)-trans-cyclopentane-constrained peptide nucleic acids. a general backbone modification that improves binding affinity and sequence specificity.
Replacing the ethylenediamine portion of aminoethylglycine peptide nucleic acids (aegPNAs) with one or more (S,S)-trans-cyclopentane diamine units significantly increases binding affinity and sequence specificity to complementary DNA, making these modified PNAs ideal for use as nucleic acid probes in genomic analysis. The synthesis and study of this new class of PNAs (tcypPNAs) is described in which trans-cyclopentane diamine has been incorporated into several positions, and in varying number, within PNA backbones of mixed-base sequences.
Base Pair Mismatch↗
Nonionic side chains modulate the affinity and specificity of binding between functionalized polyamines and structured RNA.
This Communication introduces side-chain-bearing polyamines as molecules for selective recognition of folded RNA structures. The complex folded structures associated with RNA create binding pockets for proteins, and also binding sites for small molecules. Developing organic molecules that can bind RNA with high affinity and specificity is a challenge that must be overcome for RNA to be considered a viable drug target. In this work, six polyamines with different side chains were synthesized to test for effects on binding affinity and specificity to TAR RNA and RRE RNA of HIV. Binding interactions between polyamines and RNAs were examined using two footprinting assays, based on terbium-induced cleavage and magnesium-catalyzed cleavage at higher pH. The binding constants and the binding specificity were highly dependent on the side chains of the polyamines, demonstrating that this class of molecules is a very promising starting point for development of highly selective RNA-binding ligands.
Base Sequence↗
An efficient synthesis of a probe for protein function: 2,3-diaminopropionic acid with orthogonal protecting groups.
[reaction: see text] An efficient and cost-effective synthesis of N(alpha)-Boc2-N(beta)-Cbz-2,3-diaminopropionic acid is reported. The synthesis starts from commercially available N(alpha)-Boc-Asp(OBn)-OH and employs a Curtius rearrangement to establish the beta-nitrogen. Proper protection of the alpha-nitrogen is essential for the success of the Curtius rearrangement.
Molecular Structure↗
A cyclopentane conformational restraint for a peptide nucleic acid: design, asymmetric synthesis, and improved binding affinity to DNA and RNA.
[structure: see text] A strategy to restrict the highly flexible backbone conformation of a peptide nucleic acid (PNA) by incorporation of a cyclopentane ring is proposed. An asymmetric synthesis of cyclopentane-modified PNA is reported, and its binding properties were determined. The cyclopentane ring leads to a significant improvement in the binding properties of the resulting PNA to DNA and RNA.
Alkylation↗
Enhanced oligonucleotide binding to self-assembled nanofibers.
A peptide nucleic acid/peptide amphiphile conjugate (PNA-PA) that self-assembles into fiber-shaped nanostructures was designed to bind oligonucleotides with high affinity and specificity. Oligonucleotide binding to PNA-PA nanofibers was studied using fluorescence polarization, and thermal stability was examined by UV-vis measurement of duplex melting temperatures. The self-assembled PNA-PA DNA system was observed to bind more strongly than the corresponding DNA-DNA duplex. We also observed single base specificity with a 16 degrees C in thermal stability. As expected from the previous PNA studies, PNA-PA RNA binding is also stronger than the corresponding RNA-RNA duplex.
Microscopy, Electron, Transmission↗