Delineating Binding Modes of Gal/GalNAc and Structural Elements of the Molecular Recognition of Tumor‐Associated Mucin Glycopeptides by the Human Macrophage Galactose‐Type Lectin

The human macrophage galactose‐type lectin (MGL) is a key physiological receptor for the carcinoma‐associated Tn antigen (GalNAc‐α‐1‐O‐Ser/Thr) in mucins. NMR and modeling‐based data on the molecular recognition features of synthetic Tn‐bearing glycopeptides by MGL are presented. Cognate epitopes on the sugar and matching key amino acids involved in the interaction were identified by saturation transfer difference (STD) NMR spectroscopy. Only the amino acids close to the glycosylation site in the peptides are involved in lectin contact. Moreover, control experiments with non‐glycosylated MUC1 peptides unequivocally showed that the sugar residue is essential for MGL binding, as is Ca²⁺. NMR data were complemented with molecular dynamics simulations and Corcema‐ST to establish a 3D view on the molecular recognition process between Gal, GalNAc, and the Tn‐presenting glycopeptides and MGL. Gal and GalNAc have a dual binding mode with opposite trend of the main interaction pattern and the differences in affinity can be explained by additional hydrogen bonds and CH–π contacts involving exclusively the NHAc moiety.     

Deciphering the Non‐Equivalence of Serine and Threonine O‐Glycosylation Points: Implications for Molecular Recognition of the Tn Antigen by an anti‐MUC1 Antibody

The structural features of MUC1‐like glycopeptides bearing the Tn antigen (α‐O‐GalNAc‐Ser/Thr) in complex with an anti MUC‐1 antibody are reported at atomic resolution. For the α‐O‐GalNAc‐Ser derivative, the glycosidic linkage adopts a high‐energy conformation, barely populated in the free state. This unusual structure (also observed in an α‐S‐GalNAc‐Cys mimic) is stabilized by hydrogen bonds between the peptidic fragment and the sugar. The selection of a particular peptide structure by the antibody is thus propagated to the carbohydrate through carbohydrate/peptide contacts, which force a change in the orientation of the sugar moiety. This seems to be unfeasible in the α‐O‐GalNAc‐Thr glycopeptide owing to the more limited flexibility of the side chain imposed by the methyl group. Our data demonstrate the non‐equivalence of Ser and Thr O‐glycosylation points in molecular recognition processes. These features provide insight into the occurrence in nature of the APDTRP epitope for anti‐MUC1 antibodies.     

The Tn antigen-structural simplicity and biological complexity

Glycoproteins in animal cells contain a variety of glycan structures that are added co‐ and/or posttranslationally to proteins. Of over 20 different types of sugar–amino acid linkages known, the two major types are N‐glycans (Asn‐linked) and O‐glycans (Ser/Thr‐linked). An abnormal mucin‐type O‐glycan whose expression is associated with cancer and several human disorders is the Tn antigen. It has a relatively simple structure composed of N‐acetyl‐D ‐galactosamine with a glycosidic α linkage to serine/threonine residues in glycoproteins (GalNAcα1‐O‐Ser/Thr), and was one of the first glycoconjugates to be chemically synthesized. The Tn antigen is normally modified by a specific galactosyltransferase (T‐synthase) in the Golgi apparatus of cells. Expression of active T‐synthase is uniquely dependent on the molecular chaperone Cosmc, which is encoded by a gene on the X chromosome. Expression of the Tn antigen can arise as a consequence of mutations in the genes for T‐synthase or Cosmc, or genes affecting other steps of O‐glycosylation pathways. Because of the association of the Tn antigen with disease, there is much interest in the development of Tn‐based vaccines and other therapeutic approaches based on Tn expression.     

Specific Identification of Glycoproteins Bearing the Tn Antigen in Human Cells

Glycoproteins contain a wealth of valuable information regarding the development and disease status of cells. In cancer cells, some glycans (such as the Tn antigen) are highly up‐regulated, but this remains largely unknown for glycoproteins with a particular glycan. Herein, an innovative method combining enzymatic and chemical reactions was first designed to enrich glycoproteins with the Tn antigen. Using synthetic glycopeptides with O‐GalNAc (the Tn antigen) or O‐GlcNAc, we demonstrated that the method is selective for glycopeptides with O‐GalNAc and can distinguish between these two modifications. The diagnostic ions from the tagged O‐GalNAc further confirmed the effectiveness of the method and confidence in the identification of glycopeptides with the Tn antigen by mass spectrometry. Using this method, we identified 96 glycoproteins with the Tn antigen in Jurkat cells. The method can be extensively applied in biological and biomedical research.     

Synthesis and Immunostimulating Activity of A Thioglycolipopeptide Glycomimetic As A Potential Anticancer Vaccine Derived From Tn Antigen

ABSTRACT

The Tn epitope is one of the tumor associated O-linked cell surface glycopeptides. It is expressed in over 70% of human epithelial cancers such as lung, colon, stomach and breast carcinomas. The glycosidic linkage of the Tn antigen, between N-acetylgalactosamine and serine or threonine, can be cleaved either chemically or enzymatically in the presence of glycosidases. The latter case is particularly a problem in vivo. Therefore, it would be of great interest to obtain a metabolically stable analogue of the Tn antigen that maintains or improves the immunogenic activity of the latter. The purpose of this work was to synthesize a totally synthetic vaccine using a chemically and metabolically stable glycomimetic of the Tn antigen in which the interglycosidic oxygen was replaced by a sulphur atom (S-Tn). The S-Tn thioglycopeptide was linked to the P₃CS immunoadjuvant to obtain the potential S-Tn vaccine. Moreover, we synthesized the natural Tn antigen and derivatized it similarly to obtain the Tn vaccine. Last, we evaluated the immunostimulating activity of the two synthetic potential vaccines in vitro using cultured mouse splenocytes. The S-Tn construct showed immunostimulating activity comparable, in terms of maximal response, to the Tn analogue. Moreover, due to its higher stability the S-Tn construct reached its maximal effect at lower doses compared to the Tn analogue.     

Fast Epitope Mapping for the Anti‐MUC1 Monoclonal Antibody by Combining a One‐Bead‐One‐Glycopeptide Library and a Microarray Platform

Anti‐MUC1 monoclonal antibodies (mAbs) are powerful tools that can be used to recognize cancer‐related MUC1 molecules, the O‐glycosylation status of which is believed to affect binding affinity. We demonstrate the feasibility of using a rapid screening methodology to elucidate those effects. The approach involves i) “one‐bead‐one‐compound”‐based preparation of bilayer resins carrying glycopeptides on the shell and mass‐tag tripeptides coding O‐glycan patterns in the core, ii) on‐resin screening with an anti‐MUC1 mAb, iii) separating positive resins by utilizing secondary antibody conjugation with magnetic beads, and (iv) decoding the mass‐tag that is detached from the positive resins pool by using mass spectrometric analysis. We tested a small library consisting of 27 MUC1 glycopeptides with different O‐glycosylations against anti‐MUC1 mAb clone VU‐3C6. Qualitative mass‐tag analysis showed that increasing the number of glycans leads to an increase in the binding affinity. Six glycopeptides selected from the library were validated by using a microarray‐based assay. Our screening provides valuable information on O‐glycosylations of epitopes leading to high affinity with mAb.     

Monitoring Glycan–Protein Interactions by NMR Spectroscopic Analysis: A Simple Chemical Tag That Mimics Natural CH–π Interactions

Detection of molecular recognition processes requires robust, specific, and easily implementable sensing methods, especially for screening applications. Here, we propose the difluoroacetamide moiety (an acetamide bioisoster) as a novel tag for detecting by NMR analysis those glycan–protein interactions that involve N‐acetylated sugars. Although difluoroacetamide has been used previously as a substituent in medicinal chemistry, here we employ it as a specific sensor to monitor interactions between GlcNAc‐containing glycans and a model lectin (wheat germ agglutinin). In contrast to the widely employed trifluoroacetamide group, the difluoroacetamide tag contains geminal ¹H and ¹⁹F atoms that allow both ¹H and ¹⁹F NMR methods for easy and robust detection of molecular recognition processes involving GlcNAc‐ (or GalNAc‐) moieties over a range of binding affinities. The CHF₂CONH‐ moiety behaves in a manner that is very similar to that of the natural acetamide fragment in the involved aromatic‐sugar interactions, providing analogous binding energy and conformations, whereas the perfluorinated CF₃CONH‐ analogue differs more significantly.     

Oligonucleotides Containing Novel 4′‐C‐ or 3′‐C‐(Aminoalkyl)‐Branched Thymidines

The synthesis of four novel 3′‐C‐branched and 4′‐C‐branched nucleosides and their transformation into the corresponding 3′‐O‐phosphoramidite building blocks for automated oligonucleotide synthesis is reported. The 4′‐C‐branched key intermediate 11 was synthesized by a convergent strategy and converted to its 2′‐O‐methyl and 2′‐deoxy‐2′‐fluoro derivatives, leading to the preparation of novel oligonucleotide analogues containing 4′‐C‐(aminomethyl)‐2′‐O‐methyl monomer X and 4′‐C‐(aminomethyl)‐2′‐deoxy‐2′‐fluoro monomer Y (Schemes 2 and 3). In general, increased binding affinity towards complementary single‐stranded DNA and RNA was obtained with these analogues compared to the unmodified references (Table 1). The presence of monomer X or monomer Y in a 2′‐O‐methyl‐RNA oligonucleotide had a negative effect on the binding affinity of the 2′‐O‐methyl‐RNA oligonucleotide towards DNA and RNA. Starting from the 3′‐C‐allyl derivative 28 , 3′‐C‐(3‐aminopropyl)‐protected nucleosides and 3′‐O‐phosphoramidite derivatives were synthesized, leading to novel oligonucleotide analogues containing 3′‐C‐(3‐aminopropyl)thymidine monomer Z or the corresponding 3′‐C‐(3‐aminopropyl)‐2′‐O,5‐dimethyluridine monomer W (Schemes 4 and 5). Incorporation of the 2′‐deoxy monomer Z induced no significant changes in the binding affinity towards DNA but decreased binding affinity towards RNA, while the 2′‐O‐methyl monomer Z induced decreased binding affinity towards DNA as well as RNA complements (Table 2).     

Conformational Selection in Glycomimetics: Human Galectin‐1 Only Recognizes syn‐Ψ‐Type Conformations of β‐1,3‐Linked Lactose and Its C‐Glycosyl Derivative

The human lectin galectin‐1 (hGal‐1) translates sugar signals, that is, β‐galactosides, into effects on the level of cells, for example, growth regulation, and has become a model for studying binding of biopharmaceutically relevant derivatives. Bound‐state conformations of Galβ‐C‐(1→3)‐Glcβ‐OMe ( 1 ) and its βGal‐(1→3)‐βGlc‐OMe disaccharide parent compound were studied by using NMR spectroscopy (transferred (TR)‐NOESY data), assisted by docking experiments and molecular dynamics (MD) simulations. The molecular recognition process involves a conformational selection event. Although free C‐glycoside access four distinct conformers in solution, hGal‐1 recognizes shape of a local minimum of compound 1 , the syn‐Φ/syn‐Ψ conformer, not the structure at global minimum. MD simulations were run to explain, in structural terms, the observed geometry of the complex.     

Fullerene‐sp2‐Iminosugar Balls as Multimodal Ligands for Lectins and Glycosidases: A Mechanistic Hypothesis for the Inhibitory Multivalent Effect

Concerted functioning of lectins and carbohydrate‐processing enzymes, mainly glycosidases, is essential in maintaining life. It was commonly assumed that the mechanisms by which each class of protein recognizes their cognate sugar partners are intrinsically different: multivalency is a characteristic feature of carbohydrate–lectin interactions, whereas glycosidases bind to their substrates or substrate‐analogue inhibitors in monovalent form. Recent observations on the glycosidase inhibitory potential of multivalent glycomimetics have questioned this paradigm and led to postulate an inhibitory multivalent effect. Here the mechanisms at the origin of this phenomenon have been investigated. A D ‐gluco‐configured sp²‐iminosugar glycomimetic motif, namely 1‐amino‐5N,6O‐oxomethylydenenojirimycin (1N‐ONJ), behaving, simultaneously, as a ligand of peanut agglutinin (PNA) lectin and as an inhibitor of several glycosidases, has been identified. Both the 1N‐ONJ–lectin‐ and 1N‐ONJ–glycosidase‐recognition processes have been found to be sensitive to multivalency, which has been exploited in the design of a lectin–glycosidase competitive assay to explore the implication of catalytic and non‐glycone sites in enzyme binding. A set of isotropic dodecavalent C₆₀‐fullerene–sp²‐iminosugar balls incorporating matching or mismatching motifs towards several glycosidases (inhitopes) was synthesized for that purpose, thereby preventing differences in binding modes arising from orientational preferences. The data supports that: 1) multivalency allows modulating the affinity and selectivity of a given inhitope towards glycosidases; 2) multivalent presentation can switch on the inhibitory capacity for some inhitope–glycosidase pairs, and 3) interactions of the multivalent inhibitors with non‐glycone sites is critical for glycosidase recognition. The ensemble of results point to a shift in the binding mode on going from monovalent to multivalent systems: in the first case a typical ′′key–lock′′ model involving, essentially, the high‐affinity active site can be assumed, whereas in the second, a lectin‐like behavior implying low‐affinity non‐glycone sites probably operates. The differences in responsiveness to multivalency for different glycosidases can then be rationalized in terms of the structure and accessibility of the corresponding carbohydrate‐binding regions.     

A Synthetic Lectin for O‐Linked β‐N‐Acetylglucosamine

Changing employment : Receptor 1 binds β‐N‐acetylglucosaminyl (β‐GlcNAc) up to 100 times more strongly than it does glucose. This synthetic lectin shows affinities similar to wheat germ agglutinin (WGA), a natural lectin used to bind GlcNAc. Remarkably, 1 is more selective than WGA. It favors especially the glycoside unit in glycopeptide 2 , a model of the serine‐O‐GlcNAc posttranslational protein modification.

     

Breaking the Limits in Analyzing Carbohydrate Recognition by NMR Spectroscopy: Resolving Branch‐Selective Interaction of a Tetra‐Antennary N‐Glycan with Lectins

The biological recognition of complex‐type N ‐glycans is part of many key physiological and pathological events. Despite their importance, the structural characterization of these events remains unsolved. The inherent flexibility of N ‐glycans hampers crystallization and the chemical equivalence of individual branches precludes their NMR characterization. By using a chemoenzymatically synthesized tetra‐antennary N ‐glycan conjugated to a lanthanide binding tag, the NMR signals under paramagnetic conditions discriminated all four N ‐acetyl lactosamine antennae with unprecedented resolution. The NMR data revealed the conformation of the N ‐glycan and permitted for the first time the direct identification of individual branches involved in the recognition by two N ‐acetyllactosamine‐binding lectins, Datura stramonium seed lectin (DSL) and Ricinus Communis agglutinin (RCA120).     

sp2‐Iminosugar O‐, S‐, and N‐Glycosides as Conformational Mimics of α‐Linked Disaccharides; Implications for Glycosidase Inhibition

The synthesis of mimics of the α(1→6)‐ and α(1→4)‐linked disaccharides isomaltose and maltose featuring a bicyclic sp²‐iminosugar nonreducing moiety O‐, S‐, or N‐linked to a glucopyranoside residue is reported. The strong generalized anomeric effect operating in sp²‐iminosugars determines the α‐stereochemical outcome of the glycosylation reactions, independent of the presence or not of participating protecting groups and of the nature of the heteroatom. It also imparts chemical stability to the resulting aminoacetal, aminothioacetal, or gem‐diamine functionalities. All the three isomaltose mimics behave as potent and very selective inhibitors of isomaltase and maltase, two α‐glucosidases that bind the parent disaccharides either as substrate or inhibitor. In contrast, large differences in the inhibitory properties were observed among the maltose mimics, with the O‐linked derivative being a more potent inhibitor than the N‐linked analogue; the S‐linked pseudodisaccharide did not inhibit either of the two target enzymes. A comparative conformational analysis based on NMR and molecular modelling revealed remarkable differences in the flexibility about the glycosidic linkage as a function of the nature of the linking atom in this series. Thus, the N‐pseudodisaccharide is more rigid than the O‐linked derivative, which exhibits conformational properties very similar to those of the natural maltose. The analogous pseudothiomaltoside is much more flexible than the N‐ or O‐linked derivatives, and can access a broader area of the conformational space, which probably implies a strong entropic penalty upon binding to the enzymes. Together, the present results illustrate the importance of taking conformational aspects into consideration in the design of functional oligosaccharide mimetics.     

Substrate‐Guided Front‐Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N‐Acetylgalactosaminyltransferase 2

The retaining glycosyltransferase GalNAc‐T2 is a member of a large family of human polypeptide GalNAc‐transferases that is responsible for the post‐translational modification of many cell‐surface proteins. By the use of combined structural and computational approaches, we provide the first set of structural snapshots of the enzyme during the catalytic cycle and combine these with quantum‐mechanics/molecular‐mechanics (QM/MM) metadynamics to unravel the catalytic mechanism of this retaining enzyme at the atomic‐electronic level of detail. Our study provides a detailed structural rationale for an ordered bi–bi kinetic mechanism and reveals critical aspects of substrate recognition, which dictate the specificity for acceptor Thr versus Ser residues and enforce a front‐face S_Ni‐type reaction in which the substrate N‐acetyl sugar substituent coordinates efficient glycosyl transfer.     

2,2′‐[(Disulfanediyl)bis{5‐[(1E)‐(2‐hydroxybenzylidene)amino]‐1,3‐thiazole‐4,2‐diyl}]diphenol: synthesis,crystal structure and calculation of molecular hyperpolarizability

The title Schiff base compound {systematic name: 2‐[5‐[(E )‐(2‐hydroxybenzylidene)amino]‐4‐(2‐{5‐[(E )‐(2‐hydroxybenzylidene)amino]‐2‐(2‐hydroxyphenyl)‐1,3‐thiazol‐4‐yl}disulfanyl)‐1,3‐thiazol‐2‐yl]phenol}, C₃₂H₂₂N₄O₄S₄, incorporating a disulfanediyl (dithio) linkage, was obtained from the condensation reaction between two equivalents of salicylaldehyde and one equivalent of dithiooxamide in dimethylformamide, and was characterized by elemental analysis, IR spectroscopic analysis and single‐crystal X‐ray diffraction. A one‐dimensional chain is formed along the b axis via double intermolecular C—H…S hydrogen bonds. The HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) energies and some related molecular parameters were calculated at the B3LYP/6‐311G(d,p) level of theory. The molecular hyperpolarizability was also calculated.     

Synthesis and Conformational Analysis of Hybrid α/β‐Dipeptides Incorporating S‐Glycosyl‐β2,2‐Amino Acids

We synthesized and carried out the conformational analysis of several hybrid dipeptides consisting of an α‐amino acid attached to a quaternary glyco‐β‐amino acid. In particular, we combined a S‐glycosylated β^2,2‐amino acid and two different types of α‐amino acid, namely, aliphatic (alanine) and aromatic (phenylalanine and tryptophan) in the sequence of hybrid α/β‐dipeptides. The key step in the synthesis involved the ring‐opening reaction of a chiral cyclic sulfamidate, inserted in the peptidic sequence, with a sulfur‐containing nucleophile by using 1‐thio‐β‐D ‐glucopyranose derivatives. This reaction of glycosylation occurred with inversion of configuration at the quaternary center. The conformational behavior in aqueous solution of the peptide backbone and the glycosidic linkage for all synthesized hybrid glycopeptides was analyzed by using a protocol that combined NMR experiments and molecular dynamics with time‐averaged restraints (MD‐tar). Interestingly, the presence of the sulfur heteroatom at the quaternary center of the β‐amino acid induced θ torsional angles close to 180° (anti). Notably, this value changed to 60° (gauche) when the peptidic sequence displayed aromatic α‐amino acids due to the presence of CH–π interactions between the phenyl or indole ring and the methyl groups of the β‐amino acid unit.     

Different molecular conformations co‐exist in each of three 2‐aryl‐N‐(1,5‐dimethyl‐3‐oxo‐2‐phenyl‐2,3‐dihydro‐1H‐pyrazol‐4‐yl)acetamides: hydrogen bonding in zero,one and two dimensions

4‐Antipyrine [4‐amino‐1,5‐dimethyl‐2‐phenyl‐1H‐pyrazol‐3(2H)‐one] and its derivatives exhibit a range of biological activities, including analgesic, antibacterial and anti‐inflammatory, and new examples are always of potential interest and value. 2‐(4‐Chlorophenyl)‐N‐(1,5‐dimethyl‐3‐oxo‐2‐phenyl‐2,3‐dihydro‐1H‐pyrazol‐4‐yl)acetamide, C₁₉H₁₈ClN₃O₂, (I), crystallizes with Z′ = 2 in the space group P, whereas its positional isomer 2‐(2‐chlorophenyl)‐N‐(1,5‐dimethyl‐3‐oxo‐2‐phenyl‐2,3‐dihydro‐1H‐pyrazol‐4‐yl)acetamide, (II), crystallizes with Z′ = 1 in the space group C2/c; the molecules of (II) are disordered over two sets of atomic sites having occupancies of 0.6020 (18) and 0.3980 (18). The two independent molecules of (I) adopt different molecular conformations, as do the two disorder components in (II), where the 2‐chlorophenyl substituents adopt different orientations. The molecules of (I) are linked by a combination of N—H…O and C—H…O hydrogen bonds to form centrosymmetric four‐molecule aggregates, while those of (II) are linked by the same types of hydrogen bonds forming sheets. The related compound N‐(1,5‐dimethyl‐3‐oxo‐2‐phenyl‐2,3‐dihydro‐1H‐pyrazol‐4‐yl)‐2‐(3‐methoxyphenyl)acetamide, C₂₀H₂₁N₃O₃, (III), is isomorphous with (I) but not strictly isostructural; again the two independent molecules adopt different molecular conformations, and the molecules are linked by N—H…O and C—H…O hydrogen bonds to form ribbons. Comparisons are made with some related structures, indicating that a hydrogen‐bonded R₂²(10) ring is the common structural motif.     

Solution 1H and 13C NMR of new chiral 1,4‐oxazepinium heterocycles and their intermediates from the reaction of 2,4‐pentanedione with α‐L‐amino acids and (R)‐(—)‐2‐phenylglycinol

The reaction of 2,4‐pentanedione ( 1 ) with (R)‐(—)‐2‐phenylglycine methyl ester ( 2 ), (R)‐(—)‐2‐phenylglycinol ( 3 ) and the proteinogenic amino acids (2S,3R)‐(—)‐2‐amino‐3‐hydroxybutyric acid (L ‐threonine) ( 4 ) and (R)‐(—)‐2‐amino‐3‐mercaptopropionic acid (L ‐cysteine) ( 5 ) methyl esters was investigated. The corresponding enamines 6 , 7 and 8 were isolated and characterized spectroscopically whereas 9 , which is unstable, was transformed in situ into 13 . Treatment of 7 , 8 and 9 with boron trifluoride etherate afforded the new [1,4]oxazepines 10 , 11 and [1,4]thiazepine ( 12 ) as their BF₃O^? salts. The structures of the enamines and their corresponding seven‐membered heterocycles were assessed by 1D and 2D NMR spectroscopy. Variable‐temperature experiments revealed different molecular mobility behavior among these heterocycles. Copyright © 2003 John Wiley & Sons, Ltd.     

Relative Lectin Binding Properties of T‐Antigen‐Containing Glycopolymers: Copolymerization of N‐Acryloylated T‐Antigen Monomer vs. Graft Conjugation of Aminated T‐Antigen Ligands onto Poly(N‐acryloxysuccinimide)

Water‐soluble T‐antigen‐ (Galβ(1–3)‐GalNAcα) containing random glycopolymers were synthesized by two strategies: i) radical copolymerization of N‐acryloylated monomers with (NH₄)₂S₂O₈ and ii) graft conjugation of an end‐group‐aminated T‐antigen together with labeling reagent ( 16 ) by amidation onto poly(N‐acryloxysuccinimide) and its derivatives followed by quenching with NH₄OH. All glycoconjugates demonstrated antigenicity by double‐radial immunodiffusion assays with peanut lectin from Arachis hypogaea. The biocytin‐labeled terpolymer ( 23 ) also showed practical heterobifunctional antigenicity toward peanut lectin and streptavidin, giving the corresponding two precipitin bands in the assay.     

(2′‐O‐Methyl‐RNA)‐3′‐PNA Chimeras: A New Class of Mixed Backbone Oligonucleotide Analogues with High Binding Affinity to RNA

The automated on‐line synthesis of DNA‐3′‐PNA chimeras 1 – 4 and (2′‐O‐methyl‐RNA)‐3′‐PNA chimeras 5 – 8 is described, in which the 3′‐terminal part of the oligonucleotide is linked to the N‐terminal part of the PNA via N‐(ω‐hydroxyalkyl)‐N‐[(thymin‐1‐yl)acetyl]glycine units (alkyl=Et, Ph, Bu, and pentyl). By means of UV thermal denaturation, the binding affinities of all chimeras were directly compared by determining their T_m values in the duplex with complementary DNA and RNA. All investigated DNA‐3′‐PNA chimeras and (2′‐O‐methyl‐RNA)‐3′‐PNA chimeras form more‐stable duplexes with complementary DNA and RNA than the corresponding unmodified DNA. Interestingly, a N‐(3‐hydroxypropyl)glycine linker resulted in the highest binding affinity for DNA‐3′‐PNA chimeras, whereas the (2′‐O‐methyl‐RNA)‐3′‐PNA chimeras showed optimal binding with the homologous N‐(4‐hydroxybutyl)glycine linker. The duplexes of (2′‐O‐methyl‐RNA)‐3′‐PNA chimeras and RNA were significantly more stable than those containing the corresponding DNA‐3′‐PNA chimeras. Surprisingly, we found that the charged (2′‐O‐methyl‐RNA)‐3′‐PNA chimera with a N‐(4‐hydroxybutyl)glycine‐based unit at the junction to the PNA part shows the same binding affinity to RNA as uncharged PNA. Potential applications of (2′‐O‐methyl‐RNA)‐3′‐PNA chimeras include their use as antisense agents acting by a RNase‐independent mechanism of action, a prerequisite for antisense‐oligonucleotide‐mediated correction of aberrant splicing of pre‐mRNA.