Pyrrolidinyl peptide nucleic acid with α/β-peptide backbone: A conformationally constrained PNA with unusual hybridization properties

Artificial DNA: PNA and XNA

Volumn 2, Issue 2, 2011, Pages 50-59

  Vilaivan, Chotima ^a   Srisuwannaket, Choladda ^b   Ananthanawat, Cheeraporn ^a   Suparpprom, Chaturong ^c   Kawakami, Junji ^d,e   Yamaguchi, Yoshie ^d,e   Tanaka, Yuko ^d,e   Vilaivan, Tirayut ^a  

^a CHULALONGKORN UNIVERSITY   (Thailand)

^b KING MONGKUT'S UNIVERSITY OF TECHNOLOGY THONBURI   (Thailand)

^c NARESUAN UNIVERSITY   (Thailand)

^d Department of Nanobiochemistry   (Thailand)

^e Konan University   (Thailand)

Author keywords

peptide; DNA recognition; Foldamer; Nucleic acid; Peptide nucleic acid; Pre organization; RNA recognition

Indexed keywords

2 AMINOCYCLOPENTANECARBOXYLIC ACID; 2',4' NUCLEOBASE SUBSTITUTED PROLINE; AMINO ACID; PEPTIDE NUCLEIC ACID; PYRROLIDINYL PEPTIDE NUCLEIC ACID; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CIRCULAR DICHROISM; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DNA BINDING; DNA DENATURATION; DNA HYBRIDIZATION; NUCLEIC ACID HYBRIDIZATION; NUCLEIC ACID STRUCTURE; PEPTIDE ANALYSIS; PROTEIN SYNTHESIS; SEQUENCE ANALYSIS; STEREOCHEMISTRY; STEREOISOMERISM; THERMODYNAMICS;

EID: 80054781870     PISSN: 1949095X     EISSN: 19490968     Source Type: Journal    
DOI: 10.4161/adna.2.2.16340     Document Type: Article

References (53)

1. Nielsen PE. Peptide nucleic acid. A molecule with two identities. Acc Chem Res 1999; 32:624-630.
2. Uhlman E, Peyman A, Breipohl G, Will DW. PNA: Synthetic polyamide nucleic acids with unusual binding properties. Angew Chem Int Ed 1998; 37:2796-2823.
3. Nielsen PE, Haaima G. Peptide nucleic acid (PNA). A DNA mimic with a pseudopeptide backbone. Chem Soc Rev 1997; 26:73-78.
4. Egholm M, Buchardt O, Christensen L, Behrens C, Freier SM, Driver DA, et al. PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules. Nature 1993; 365:566-568.
5. Leumann CJ. DNA analogues: From supramolecular principles to biological properties. Bioorg Med Chem 2002; 10:841-854.
6. Tomac S, Sarkar M, Ratilainen T, Wittung P, Nielsen PE, Nordén B, Gräslund A. Ionic effects on the stability and conformation of peptide nucleic acid complexes. J Am Chem Soc 1996; 118:5544-5552.
7. Bentin T, Hansen GI, Nielsen PE. Structural diversity of target-specific homopyrimidine peptide nucleic aciddsDNA complexes. Nucl Acids Res 2006; 34:5790-5799.
8. Nielsen PE, Egholm M, Berg RH, Buchardt O. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 1991; 254:1497-1500.
9. Li M, Zengeya T, Rozners E. Short peptide nucleic acids bind strongly to homopurine tract of double helical RNA at pH 5.5. J Am Chem Soc 2010; 132:8676-8681.
10. Demidov VV, Potaman VN, Frank-Kamenetskii MD, Egholm M, Buchardt O, Sönnichsen SH, Nielsen PE. Stability of peptide nucleic acids in human serum and cellular extracts. Biochemical Pharmacology 1994; 48:1310-1313.
11. Brandt O, Hoheisel JD. Peptide nucleic acids on microarrays and other biosensors. Trends Biotechnol 2004; 22:617-622.
12. Pellestor F, Paulasova P, Hamamah S. Peptide nucleic acids (PNAs) as diagnostic devices for genetic and cytogenetic analysis. Curr Pharm Des 2008; 14:2439-2344.
13. Braasch DA, Corey DR. Novel antisense and peptide nucleic acid strategies for controlling gene expression. Biochemistry 2002; 41:4503-4510.
14. Ray A, Nordén B. Peptide nucleic acid (PNA): its medical and biotechnical applications and promise for the future. FASEB J 2000; 14:1041-1060.
15. Pokorski JK, Witschi MA, Purnell BL, Appella DH. (S,S)-trans-Cyclopentane-constrained peptide nucleic acids. A general backbone modification that improves binding affinity and sequence specificity. J Am Chem Soc 2004; 126:15067-15073.
16. Govindaraju T, Kumar VA, Ganesh KN. (SR/RS)-Cyclohexanyl PNAs: Conformationally preorganized PNA analogues with unprecedented preference for duplex formation with RNA. J Am Chem Soc 2005; 127:4144-4145.
17. Govindaraju T, Madhuri V, Kumar VA, Ganesh KN. Cyclohexanyl peptide nucleic acids (chPNAs) for preferential RNA binding: Effective tuning of dihedral angle β in PNAs for DNA/RNA discrimination. J Org Chem 2006; 71:14-21.
18. Kumar VA, Ganesh KN. Conformationally constrained PNA analogues: Structural evolution toward DNA/RNA binding selectivity. Acc Chem Res 2005; 38:404-412.
19. Dragulescu-Andrasi A, Rapireddy S, Frezza BM, Gayathri C, Gil RR, Ly DH. A simple γ-backbone modification preorganizes peptide nucleic acid into a helical structure. J Am Chem Soc 2006; 128:10258-10267.
20. Yeh JI, Shivachev B, Rapireddy S, Crawford MJ, Gil RR, Du SC, et al. Crystal structure of chiral γPNA with complementary DNA strand: Insights into the stability and specificity of recognition and conformational preorganization. J Am Chem Soc 2010; 132:10717-1027.
21. Englund EA, Appella DH. γ-Substituted peptide nucleic acids constructed from L-Lysine are a versatile scaffold for multifunctional display. Angew Chem Int Ed 2007; 46:1414-1418.
22. Ngamwiriyawong P, Vilaivan T. Synthesis and nucleic acids binding properties of diastereomeric aminoethylprolyl peptide nucleic acids (aepPNA). Nucleosides Nucleotides and Nucleic Acids 2011; 30:97-112.
23. Tan THS, Hickman DT, Morral J, Beadham IG, Micklefield J. Nucleic acid binding properties of thyminyl and adeninyl pyrrolidine-amide oligonucleotide mimics (POM). Chem Comm 2004; 516-517.
24. Tan THS, Worthington RJ, Pritchard RG, Morral J, Micklefield J. Homopolymeric pyrrolidine-amide oligonucleotide mimics: Fmoc-synthesis and DNA/RNA binding properties. Org Biomol Chem 2007; 5:239-248.
25. Worthington RJ, O'Rourke AP, Morral J, Tan THS, Micklefield J. Mixed sequence pyrrolidine-amide oligonucleotide mimics: Boc(Z) synthesis and DNA/RNA binding properties. Org Biomol Chem 2007; 5:249-259.
26. Lonkar PS, Ganesh KN, Kumar VA. Chimeric (aegpyrrolidine) PNAs: synthesis and stereodiscriminative duplex binding with DNA/RNA. Org Biomol Chem 2004; 2:2604-2611.
27. Choi SH, Guzei IA, Spencer LC, Gellman SH. Crystallographic characterization of helical secondary structures in α/β-peptides with 1:1 residue alternation. J Am Chem Soc 2008; 130:6544-6550.
28. Hayen A, Schmitt MA, Ngassa FN, Thomasson KA, Gellman SH. Two helical conformations from a single foldamer backbone: "Split personality" in short α/β- peptides. Angew Chem Int Ed 2004; 43:505-510.
29. Gogoi K, Kumar VA. Chimeric (α-amino acid +nucleoside-β-amino acid)n peptide oligomers show sequence specific DNA/RNA recognition. Chem Commun 2008; 706-708.
30. Vilaivan T, Suparpprom C, Harnyuttanakorn P, Lowe G. Synthesis and properties of novel pyrrolidinyl PNA carrying β-amino acid spacers. Tetrahedron Lett 2001; 42:5533-5536.
31. Vilaivan T, Lowe G. A novel pyrrolidinyl PNA showing high sequence specificity and preferential binding to DNA over RNA. J Am Chem Soc 2002; 124:9326-9327.
32. Suparpprom C, Srisuwannaket C, Sangvanich P, Vilaivan T. Synthesis and oligodeoxynucleotide binding properties of pyrrolidinyl peptide nucleic acids bearing prolyl-2-aminocyclopentanecarboxylic acid (ACPC) backbones. Tetrahedron Lett 2005; 46:2833-2837.
33. Vilaivan T, Srisuwannaket C. Hybridization of pyrrolidinyl peptide nucleic acids and DNA: Selectivity, base-pairing specificity and direction of binding. Org Lett 2006; 8:1897-1900.
34. Ananthanawat C, Vilaivan T, Hoven VP, Su X. Comparison of DNA, aminoethylglycyl PNA and pyrrolidinyl PNA as probes for detection of DNA hybridization using surface plasmon resonance technique. Biosens Bioelectron 2010; 25:1064-1069.
35. Boontha B, Nakkuntod J, Hirankarn N, Chaumpluk P, Vilaivan T. Multiplex mass spectrometric genotyping of single nucleotide polymorphisms employing pyrrolidinyl peptide nucleic acid in combination with ion-exchange capture. Anal Chem 2008; 80:8178-8186.
36. Taechalertpaisarn J, Sriwarom P, Boonlua C, Yotapan N, Vilaivan C, Vilaivan T. DNA-, RNAand self-pairing properties of a pyrrolidinyl peptide nucleic acid with a (2'R,4'S)-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid backbone. Tetrahedron Lett 2010; 51:5822-5826.
37. Egholm M, Buchardt O, Nielsen PE, Berg RH. Peptide nucleic acids (PNA). Oligonucleotide analogues with an achiral peptide backbone. J Am Chem Soc 1992; 114:1895-1897.
38. Kim SK, Nielsen PE, Egholm M, Buchardt O, Berg RH, Nordén B. Right-handed triplex formed between peptide nucleic acid PNA-T8 and poly(dA) shown by linear and circular dichroism spectroscopy. J Am Chem Soc 1993; 115:6477-6481.
39. Sforza S, Corradini R, Ghirardi S, Dossena A, Marchelli R. DNA binding of a D-lysine-based chiral PNA: Direction control and mismatch recognition. Eur J Org Chem 2000; 2905-2913.
40. Igloi GL. Variability in the stability of DNA-peptide nucleic acid (PNA) single-base mismatched duplexes: Real-time hybridization during affinity electrophoresis in PNA-containing gels. Proc Natl Acad Sci USA 1998; 95:8562-8567.
41. Sen A, Nielsen PE. Unique properties of purine/pyrimidine asymmetric PNA·DNA duplexes: Differential stabilization of PNA·DNA duplexes by purines in the PNA strand. Biophys J 2006; 90:1329-1337.
42. In an extreme case, the Tm difference between two complementary acpcPNA·DNA hybrids with purine rich (AGG TAA CGA G) and pyrimidine rich (CTC GTT ACC T) sequences is only 8.4°C compared to a difference of 26.0°C for the corresponding aegPNA·DNA hybrids under identical conditions (data extracted from reference 41).
43. Siriwong K, Chuichay P, Saen-oon S, Suparpprom C, Vilaivan T, Hannongbua S. Insight into why pyrrolidinyl peptide nucleic acid binding to DNA is more stable than the DNA·DNA duplex. Biochem Biophys Res Commun 2008; 372:765-771.
44. Kawakami J, Tanaka Y, Kishimoto K. Accurate curve fitting procedure for UV melting analysis of highly thermostable RNA hairpins. Nucleic Acids Symp Series 2009; 53:227-228.
45. Marky LA, Breslauer KJ. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers 1987; 26:1601-1620.
46. Guckian KM, Schweitzer BA, Ren RXF, Sheils CJ, Tahmassebi DC, Kool ET. Factors contributing to aromatic stacking in water: Evaluation in the context of DNA. J Am Chem Soc 2000; 122:2213-2222.
47. Bommarito S, Peyret N, SantaLucia J Jr. Thermodynamic parameters for DNA sequences with dangling ends. Nucl Acids Res 2000; 28:1929-1934.
48. Sugimoto N, Kierzek R, Turner DH. Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid. Biochemistry 1987; 26:4554-4558.
49. Demidov VV, Protozanova E, Izvolsky KI, Price C, Nielsen PE, Frank-Kamenetskii MD. Kinetics and mechanism of the DNA double helix invasion by pseudocomplementary peptide nucleic acids. Proc Natl Acad Sci USA 2002; 99:5953-5958.
50. Ishizuka T, Yoshida J, Yamamoto Y, Sumaoka J, Tedeschi T, Corradini R, et al. Chiral introduction of positive charges to PNA for double-duplex invasion to versatile sequences. Nucleic Acids Res 2008; 36:1464-1471.
51. Tyagi S, Kramer FR. Molecular beacons: Probes that fluoresce upon hybridization. Nat Biotechnol 1996; 14:303-308.
52. Ahlborn C, Siegmund K, Richert C. Isostable DNA. J Am Chem Soc 2007; 129:15218-15232.
53. Egholm M, Nielsen PE, Buchardt O, Berg RH. Recognition of guanine and adenine in DNA by cytosine and thymine containing peptide nucleic acids (PNA). J Am Chem Soc 1992; 114:9677-9678.