Abstract
Nucleic acid biosensors have a growing number of applications in genetics and biomedicine. This contribution is a critical review of the current state of the art concerning the use of nucleic acid analogues, in particular peptide nucleic acids (PNA) and locked nucleic acids (LNA), for the development of high-performance affinity biosensors. Both PNA and LNA have outstanding affinity for natural nucleic acids, and the destabilizing effect of base mismatches in PNA- or LNA-containing heterodimers is much higher than in double-stranded DNA or RNA. Therefore, PNA- and LNA-based biosensors have unprecedented sensitivity and specificity, with special applicability in DNA genotyping. Herein, the most relevant PNA- and LNA-based biosensors are presented, and their advantages and their current limitations are discussed. Some of the reviewed technology, while promising, still needs to bridge the gap between experimental status and the harder reality of biotechnological or biomedical applications.
Similar content being viewed by others
References
Thevenot DR, Toth K, Durst RA, Wilson GS (1999) Electrochemical biosensors: recommended definitions and classification - (Technical report). Pure Appl Chem 71(12):2333–2348. doi:10.1351/pac199971122333
Newman JD, Tigwell LJ, Turner APF, Warner PJ (2004) Biosensors: a clearer view. Cranfield University
Zourob M (2010) Recognition receptors in biosensors Springer. N Y. doi:10.1007/978-1-4419-0919-0
Labuda J, Oliveira Brett AM, Evtugyn G, Fojta M, Mascini M, Ozsoz M, Palchetti I, Palecek E, Wang J (2010) Electrochemical nucleic acid-based biosensors: concepts, terms, and methodology (IUPAC Technical report). Pure Appl Chem 82(5):1161–1187. doi:10.1351/pac-rep-09-08-16
Juskowiak B (2011) Nucleic acid-based fluorescent probes and their analytical potential. Anal Bioanal Chem 399(9):3157–3176. doi:10.1007/s00216-010-4304-5
Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346(6287):818–822. doi:10.1038/346818a0
Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249(4968):505–510
Rasooly A, Herold K (2009) Biosensors and biodetection: methods and protocols volume1: optical-based detectors, vol 503. Humana Press. doi:10.1007/978-1-60327-567-5
Rasooly A, Herold K (2009) Biosensors and biodetection: methods and protocols volume 2: electrochemical and mechanical detectors, lateral flow and ligands for biosensors vol 504. Humana Press. doi:10.1007/978-1-60327-569-9
Poulsen L, Soe MJ, Moller LB, Dufva M (2011) Investigation of parameters that affect the success rate of microarray-based allele-specific hybridization assays. PLoS One 6(3):e14777. doi:10.1371/journal.pone.0014777
Benner SA, Battersby TR, Eschgfaller B, Hutter D, Kodra JT, Lutz S, Arslan T, Baschlin DK, Blattler M, Egli M, Hammer C, Held HA, Horlacher J, Huang Z, Hyrup B, Jenny TF, Jurczyk SC, Konig M, von Krosigk U, Lutz MJ, MacPherson LJ, Moroney SE, Muller E, Nambiar KP, Piccirilli JA, Switzer CY, Vogel JJ, Richert C, Roughton AL, Schmidt J, Schneider KC, Stackhouse J (1998) Redesigning nucleic acids. Pure Appl Chem 70(2):263–266. doi:10.1351/pac199870020263
Geyer CR, Battersby TR, Benner SA (2003) Nucleobase pairing in Watson-Crick-like genetic expanded information systems. Structure 11(12):1485–1498. doi:10.1016/j.str.2003.11.008
Schneider KC, Benner SA (1990) Oligonucleotides containing flexible nucleoside analogs. J Am Chem Soc 112(1):453–455. doi:10.1021/ja00157a073
Zhang S, Chaput JC (2010) Synthesis of Glycerol Nucleic Acid (GNA) phosphoramidite monomers and oligonucleotide polymers. In: Current protocols in nucleic acid chemistry. John Wiley & Sons, Inc. doi:10.1002/0471142700.nc0440s42
Pitsch S, Wendeborn S, Jaun B, Eschenmoser A (1993) Why pentose- and not hexose-nucleic acids?? Part VII. Pyranosyl-RNA (‘p-RNA’). Preliminary communication. Helvetica Chimica Acta 76(6):2161–2183. doi:10.1002/hlca.19930760602
Ilin S, Schlonvogt I, Ebert MO, Jaun B, Schwalbe H (2002) Comparison of the NMR spectroscopy solution structures of pyranosyl-RNA and its nucleo-delta-peptide analogue. ChemBioChem 3(1):93–99. doi:10.1002/1439-7633(20020104)3:1<93::aid-cbic93>3.0.co;2-0
Micura R, Kudick R, Pitsch S, Eschenmoser A (1999) Chemistry of Pyranosyl-RNA, part 8. Chemistry of alpha-aminonitriles, part 24. Opposite orientation of backbone inclination in pyranosyl-RNA and homo-DNA correlates with opposite directionality of duplex properties. Angew Chem Int Ed 38(5):680–683. doi:10.1002/(sici)1521-3773(19990301)38:5<680::aid-anie680>3.0.co;2-c
Schoning KU, Scholz P, Guntha S, Wu X, Krishnamurthy R, Eschenmoser A (2000) Chemical etiology of nucleic acid structure: the alpha-threofuranosyl-(3′ → 2′) oligonucleotide system. Science 290(5495):1347–1351. doi:10.1126/science.290.5495.1347
Ahn DR, Egger A, Lehmann C, Pitsch S, Leumann CJ (2002) Bicyclo 3.2.1 amide-DNA: A chiral, nonchiroselective base-pairing system. Chem- Eur J 8(23):5312–5322. doi:10.1002/1521-3765(20021202)8:23<5312::aid-chem5312>3.0.co;2-m
Tarkoy M, Bolli M, Schweizer B, Leumann C (1993) Nucleic-acid analogs with constraint conformational flexibility in the sugar-phosphate backbone (bicyclo-DNA).1. Preparation of (3′s,5′r)-2′-deoxy-3′,5′-ethano-alpha-beta-d-ribonucleosides (bicyclonucleosides). Helvetica Chimica Acta 76(1):481–510. doi:10.1002/hlca.19930760132
Koshkin AA, Singh SK, Nielsen P, Rajwanshi VK, Kumar R, Meldgaard M, Olsen CE, Wengel J (1998) LNA (Locked Nucleic Acids): Synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron 54(14):3607–3630
Obika S, Nanbu D, Hari Y, Andoh J, Morio K, Doi T, Imanishi T (1998) Stability and structural features of the duplexes containing nucleoside analogues with a fixed N-type conformation, 2 ′-O,4 ′-C-methyleneribonucleosides. Tetrahedron Lett 39(30):5401–5404. doi:10.1016/s0040-4039(98)01084-3
Braasch DA, Corey DR (2001) Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA. Chem Biol 8(1):1–7
Doessing H, Vester B (2011) Locked and unlocked nucleosides in functional nucleic acids. Molecules 16(6):4511–4526
Petersen M, Wengel J (2003) LNA: a versatile tool for therapeutics and genomics. Trends Biotechnol 21(2):74–81
Schneider KC, Benner SA (1990) Building-blocks for oligonucleotide analogs with dimethylene-sulfide, dimethylene-sulfoxide, and dimethylene-sulfone groups replacing phosphodiester linkages. Tetrahedron Lett 31(3):335–338. doi:10.1016/s0040-4039(00)94548-9
Benner SA (2004) Understanding nucleic acids using synthetic chemistry. Acc Chem Res 37(10):784–797. doi:10.1021/ar040004z
Huang Z, Schneider KC, Benner SA (1993) Oligonucleotide analogs with dimethylenesulfide, -sulfoxide, and -sulfone groups replacing phosphodiester linkages protocols for oligonucleotides and analogs. In: Agrawal S (ed), vol 20. Methods in molecular biology. Humana Press, pp 315-353. doi:10.1385/0-89603-281-7:315
Nielsen PE, Egholm M, Berg RH, Buchardt O (1991) Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 254(5037):1497–1500. doi:10.1126/science.1962210
Egholm M, Buchardt O, Christensen L, Behrens C, Freier SM, Driver DA, Berg RH, Kim SK, Norden B, Nielsen PE (1993) PNA hybridizes to complementary oligonucleotides obeying the watson-crick hydrogen-bonding rules. Nature 365(6446):566–568. doi:10.1038/365566a0
Menchise V, De Simone G, Tedeschi T, Corradini R, Sforza S, Marchelli R, Capasso D, Saviano M, Pedone C (2003) Insights into peptide nucleic acid (PNA) structural features: the crystal structure of a D-lysine-based chiral PNA-DNA duplex. Proc Natl Acad Sci U S A 100(21):12021–12026. doi:10.1073/pnas.2034746100
Wittung P, Nielsen PE, Buchardt O, Egholm M, Norden B (1994) DNA-like double helix formed by peptide nucleic-acid. Nature 368(6471):561–563. doi:10.1038/368561a0
Ura Y, Beierle JM, Leman LJ, Orgel LE, Ghadiri MR (2009) Self-assembling sequence-adaptive peptide nucleic acids. Science 325(5936):73–77. doi:10.1126/science.1174577
Ratilainen T, Holmen A, Tuite E, Nielsen PE, Norden B (2000) Thermodynamics of sequence-specific binding of PNA to DNA. Biochemistry 39(26):7781–7791. doi:10.1021/bi000039g
Eriksson M, Nielsen PE (1996) Solution structure of a peptide nucleic acid DNA duplex. Nat Struct Biol 3(5):410–413. doi:10.1038/nsb0596-410
Brown SC, Thomson SA, Veal JM, Davis DG (1994) NMR solution structure of a peptide nucleic-acid complexed with RNA. Science 265(5173):777–780. doi:10.1126/science.7519361
Rasmussen H, Sandholm J (1997) Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 angstrom resolution. Nat Struct Biol 4(2):98–101. doi:10.1038/nsb0297-98
Demidov VV, Protozanova E, Izvolsky KI, Price C, Nielsen PE, Frank-Kamenetskii MD (2002) Kinetics and mechanism of the DNA double helix invasion by pseudocomplementary peptide nucleic acids. Proc Natl Acad Sci U S A 99(9):5953–5958. doi:10.1073/pnas.092127999
Demidov V, Frankkamenetskii MD, Egholm M, Buchardt O, Nielsen PE (1993) Sequence selective double-strand DNA cleavage by peptide nucleic-acid (PNA) targeting using nuclease s1. Nucleic Acids Res 21(9):2103–2107. doi:10.1093/nar/21.9.2103
Nielsen PE (1999) Applications of peptide nucleic acids. Curr Opin Biotechnol 10(1):71–75
Briones C, Mateo-Marti E, Gomez-Navarro C, Parro V, Roman E, Martin-Gago JA (2004) Ordered self-assembled monolayers of peptide nucleic acids with DNA recognition capability. Phys Rev Lett 93(20). doi:10.1103/PhysRevLett.93.208103
Briones C, Mateo-Marti E, Gomez-Navarro C, Parro V, Roman E, Martin-Gago JA (2005) Structural and functional characterization of self-assembled monolayers of peptide nucleic acids and its interaction with complementary DNA. J Mol Catal -Chem 228(1–2):131–136. doi:10.1016/j.molcata.2004.09.076
Mateo-Martí E, Briones C, Román E, Briand E, Pradier CM, Martín-Gago JA (2005) Self-assembled monolayers of peptide nucleic acids on gold surfaces: a spectroscopic study. Langmuir 21(21):9510–9517. doi:10.1021/la050366v
Briones C, Martin-Gago JA (2006) Nucleic acids and their analogs as nanomaterials for biosensor development. Curr Nanosci 2(3):257–273
Rogero C, Chaffey BT, Mateo-Marti E, Sobrado JM, Horrocks BR, Houlton A, Lakey JH, Briones C, Martin-Gago JA (2008) Silicon surface nanostructuring for covalent immobilization of biomolecules. J Phys Chem C 112(25):9308–9314. doi:10.1021/jp801543p
Singh RP, Oh BK, Choi JW (2010) Application of peptide nucleic acid towards development of nanobiosensor arrays. Bioelectrochemistry 79(2):153–161. doi:10.1016/j.bioelechem.2010.02.004
Wang J, Palecek E, Nielsen PE, Rivas G, Cai X, Shiraishi H, Dontha N, Luo D, Farias PAM (1996) Peptide nucleic acid probes for sequence-specific DNA biosensors. J Am Chem Soc 118(33):7667–7670. doi:10.1021/ja9608050
Wang J, Rivas G, Cai X, Chicharro M, Parrado C, Dontha N, Begleiter A, Mowat M, Palecek E, Nielsen PE (1997) Detection of point mutation in the p53 gene using a peptide nucleic acid biosensor. Anal Chim Acta 344(1–2):111–118
Raoof JB, Ojani R, Golabi SM, Hamidi-Asl E, Hejazi MS (2011) Preparation of an electrochemical PNA biosensor for detection of target DNA sequence and single nucleotide mutation on p53 tumor suppressor gene corresponding oligonucleotide. Sens Actuators B-Chem 157(1):195–201. doi:10.1016/j.snb.2011.03.049
Hejazi MS, Pournaghi-Azar MH, Ahour F (2010) Electrochemical detection of short sequences of hepatitis C 3a virus using a peptide nucleic acid-assembled gold electrode. Anal Biochem 399(1):118–124
Pournaghi-Azar M, Ahour F, Hejazi M (2010) Direct detection and discrimination of double-stranded oligonucleotide corresponding to hepatitis C virus genotype 3a using an electrochemical DNA biosensor based on peptide nucleic acid and double-stranded DNA hybridization. Anal Bioanal Chem 397(8):3581–3587. doi:10.1007/s00216-010-3875-5
Hejazi MS, Pournaghi-Azar MH, Alipour E, Abdolahinia ED, Arami S, Navvah H (2011) Development of a novel electrochemical biosensor for detection and discrimination of dna sequence and single base mutation in dsDNA samples based on PNA-dsDNA hybridization - a new platform technology. Electroanalysis 23(2):503–511. doi:10.1002/elan.201000413
Luo XT, Hsing IM (2009) Immobilization-free multiplex electrochemical DNA and SNP detection. Biosens Bioelectron 25(4):803–808. doi:10.1016/j.bios.2009.08.034
Luo X, Hsing IM (2009) Real time electrochemical monitoring of DNA/PNA dissociation by melting curve analysis. Electroanalysis 21(14):1557–1561. doi:10.1002/elan.200904592
Husken N, Gebala M, Schuhmann W, Metzler-Nolte N (2010) A single-electrode, dual-potential ferrocene-PNA biosensor for the detection of DNA. ChemBioChem 11(12):1754–1761. doi:10.1002/cbic.200900748
Kerman K, Vestergaard M, Nagatani N, Takamura Y, Tamiya E (2006) Electrochemical genosensor based on peptide nucleic acid-mediated PCR and asymmetric PCR techniques: electrostatic interactions with a metal cation. Anal Chem 78(7):2182–2189. doi:10.1021/ac051526a
Fang ZC, Kelley SO (2009) Direct electrocatalytic mRNA detection using PNA-nanowire sensors. Anal Chem 81(2):612–617. doi:10.1021/ac801890f
Wu W, Zhang G-J (2011) Silicon nanowire biosensor for ultrasensitive and label-free direct detection of miRNAs. In: MicroRNA and cancer, vol 676. Methods in molecular biology. Humana Press, pp 111-121. doi:10.1007/978-1-60761-863-8_9
Gao Z, Peng Y (2011) A highly sensitive and specific biosensor for ligation- and PCR-free detection of MicroRNAs. Biosens Bioelectron 26(9):3768–3773
Nelson PT, Baldwin DA, Scearce LM, Oberholtzer JC, Tobias JW, Mourelatos Z (2004) Microarray-based, high-throughput gene expression profiling of microRNAs. Nat Meth 1(2):155–161
Le Floch F, Ho HA, Leclerc M (2006) Label-free electrochemical detection of protein based on a ferrocene-bearing cationic polythiophene and aptamer. Anal Chem 78(13):4727–4731. doi:10.1021/ac0521955
Kong J, Ferhan AR, Chen X, Zhang L, Balasubramanian N (2008) Polysaccharide templated silver nanowire for ultrasensitive electrical detection of nucleic acids. Anal Chem 80(19):7213–7217. doi:10.1021/ac800334y
Kong JM, Zhang H, Chen XT, Balasubramanian N, Kwong DL (2008) Ultrasensitive electrical detection of nucleic acids by haematin catalysed silver nanoparticle formation in sub-microgapped biosensors. Biosens Bioelectron 24(4):787–791. doi:10.1016/j.bios.2008.06.047
Fang C, Fan Y, Kong J, Gao Z, Balasubramanian N (2008) Electrical detection of oligonucleotide using an aggregate of gold nanoparticles as a conductive tag. Anal Chem 80(24):9387–9394. doi:10.1021/ac801433z
Ferreira GNM, da-Silva A-C, Tomé B (2009) Acoustic wave biosensors: physical models and biological applications of quartz crystal microbalance. Trends Biotechnol 27(12):689–697. doi:10.1016/j.tibtech.2009.09.003
Wittung-Stafshede P, Rodahl M, Kasemo B, Nielsen P, Norden B (2000) Detection of point mutations in DNA by PNA-based quartz-crystal biosensor. Colloids Surf -Physicochem Eng Aspects 174(1–2):269–273. doi:10.1016/s0927-7757(00)00537-9
Yao C, Zhu T, Tang J, Wu R, Chen Q, Chen M, Zhang B, Huang J, Fu W (2008) Hybridization assay of hepatitis B virus by QCM peptide nucleic acid biosensor. Biosens Bioelectron 23(6):879–885
Lao AIK, Su X, Aung KMM (2009) SPR study of DNA hybridization with DNA and PNA probes under stringent conditions. Biosens Bioelectron 24(6):1717–1722. doi:10.1016/j.bios.2008.08.054
Carrascosa LG, Calle A, Lechuga LM (2009) Label-free detection of DNA mutations by SPR: application to the early detection of inherited breast cancer. Anal Bioanal Chem 393(4):1173–1182. doi:10.1007/s00216-008-2555-1
Sepulveda B, Carrascosa LG, Regatos D, Otte MA, Farina D, Lechuga LM (2009) Surface plasmon resonance biosensors for highly sensitive detection in real samples. In: Razeghi MMH (ed) Biosensing Ii, vol 7397. Proceedings of SPIE. doi:10.1117/12.827062
Sawata S, Kai E, Ikebukuro K, Iida T, Honda T, Karube I (1999) Application of peptide nucleic acid to the direct detection of deoxyribonucleic acid amplified by polymerase chain reaction. Biosens Bioelectron 14(4):397–404. doi:10.1016/s0956-5663(99)00018-4
Prabhakar N, Arora K, Arya SK, Solanki PR, Iwamoto M, Singh H, Malhotra BD (2008) Nucleic acid sensor for M-tuberculosis detection based on surface plasmon resonance. Analyst 133(11):1587–1592. doi:10.1039/b808225a
Ananthanawat C, Vilaivan T, Mekboonsonglarp W, Hoven VP (2009) Thiolated pyrrolidinyl peptide nucleic acids for the detection of DNA hybridization using surface plasmon resonance. Biosens Bioelectron 24(12):3544–3549. doi:10.1016/j.bios.2009.05.011
Ananthanawat C, Vilaivan T, Hoven VP, Su X (2010) Comparison of DNA, aminoethylglycyl PNA and pyrrolidinyl PNA as probes for detection of DNA hybridization using surface plasmon resonance technique. Biosens Bioelectron 25(5):1064–1069. doi:10.1016/j.bios.2009.09.028
Ananthanawat C, Hoven VP, Vilaivan T, Su X (2011) Surface plasmon resonance study of PNA interactions with double-stranded DNA. Biosens Bioelectron 26(5):1918–1923. doi:10.1016/j.bios.2010.05.027
Endo T, Kerman K, Nagatani N, Takamura Y, Tamiya E (2005) Label-free detection of peptide nucleic acid-DNA hybridization using localized surface plasmon resonance based optical biosensor. Anal Chem 77(21):6976–6984. doi:10.1021/ac0513459
Joung H-A, Lee N-R, Lee SK, Ahn J, Shin YB, Choi H-S, Lee C-S, Kim S, Kim M-G (2008) High sensitivity detection of 16 s rRNA using peptide nucleic acid probes and a surface plasmon resonance biosensor. Anal Chim Acta 630(2):168–173
Su X, Teh HF, Aung KMM, Zong Y, Gao Z (2008) Femtomol SPR detection of DNA-PNA hybridization with the assistance of DNA-guided polyaniline deposition. Biosens Bioelectron 23(11):1715–1720
D'Agata R, Corradini R, Grasso G, Marchelli R, Spoto G (2008) Ultrasensitive detection of DNA by PNA and nanoparticle-enhanced surface plasmon resonance imaging. ChemBioChem 9(13):2067–2070. doi:10.1002/cbic.200800310
Pita M, Abad JM, Vaz-Dominguez C, Briones C, Mateo-Marti E, Martin-Gago JA, Morales MDP, Fernandez VM (2008) Synthesis of cobalt ferrite core/metallic shell nanoparticles for the development of a specific PNA/DNA biosensor. J Colloid Interface Sci 321(2):484–492. doi:10.1016/j.jcis.2008.02.010
Southern EM (2001) DNA Microarrays. In, vol 170. pp 1-15
Stoughton RB (2005) Applications of DNA microarrays in biology. In: Annual review of biochemistry, vol 74. Annual review of biochemistry. pp 53-82. doi:10.1146/annurev.biochem.74.082803.133212
Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray. Science 270(5235):467–470. doi:10.1126/science.270.5235.467
Dufva M (2009) Introduction to microarray technology DNA microarrays for biomedical research. In: Dufva M (ed), vol 529. Methods in molecular biology. Humana Press, pp 1-22. doi:10.1007/978-1-59745-538-1_1
Brandt O, Hoheisel JD (2004) Peptide nucleic acids on microarrays and other biosensors. Trends Biotechnol 22(12):617–622. doi:10.1016/j.tibtech.2004.10.003
Liu B, Bazan GC (2005) Methods for strand-specific DNA detection with cationic conjugated polymers suitable for incorporation into DNA chips and microarrays. Proc Natl Acad Sci U S A 102(3):589–593. doi:10.1073/pnas.0408561102
Weiler J, Gausepohl H, Hauser N, Jensen ON, Hoheisel JD (1997) Hybridisation based DNA screening on peptide nucleic acid (PNA) oligomer arrays. Nucleic Acids Res 25(14):2792–2799. doi:10.1093/nar/25.14.2792
Matysiak S, Reuthner F, Hoheisel JD (2001) Automating parallel peptide synthesis for the production of PNA library arrays. Biotechniques 31(4):896, 898, 900–2, 904. http://www.ncbi.nlm.nih.gov/pubmed/11680721
Jacob A, Brandt O, Stephan A, Hoheisel JD (2004) Peptide nucleic acid microarrays bioconjugation protocols. In: Niemeyer CM (ed), vol 283. Methods in molecular biology. Humana Press, pp 283-293. doi:10.1385/1-59259-813-7:283
Brandt O, Feldner J, Stephan A, Schröder M, Schnölzer M, Arlinghaus HF, JrD H, Jacob A (2003) PNA microarrays for hybridisation of unlabelled DNA samples. Nucleic Acids Res 31(19):e119. doi:10.1093/nar/gng120
Song HJ, Lee JW, Kim BG, Song SY, Bae DS, Kim DS (2010) Comparison of the performance of the PANArray (TM) HPV test and DNA chip test for genotyping of human papillomavirus in cervical swabs. Biochip J 4(3):167–172. doi:10.1007/s13206-010-4301-y
J-j C, Kim C, Park H (2009) Peptide nucleic acid-based array for detecting and genotyping human papillomaviruses. J Clin Microbiol 47(6):1785–1790. doi:10.1128/jcm.01398-08
Jang H, Kim J, Choi J-J, Son Y, Park H (2010) Peptide nucleic acid array for detection of point mutations in Hepatitis B virus associated with antiviral resistance. J Clin Microbiol 48(9):3127–3131. doi:10.1128/jcm.02058-09
Calabretta A, Wasserberg D, Posthuma-Trumpie GA, Subramaniam V, van Amerongen A, Corradini R, Tedeschi T, Sforza S, Reinhoudt DN, Marchelli R, Huskens J, Jonkheijm P (2011) Patterning of peptide nucleic acids using reactive microcontact printing. Langmuir 27(4):1536–1542. doi:10.1021/la102756k
Cretich M, Chiari M, Debaene F, Winssinger N (2009) Self-assembly of PNA-encoded peptides into microarrays. In: Peptide microarrays, vol 570. Methods in molecular biology. Humana Press, pp 299-307. doi:10.1007/978-1-60327-394-7_15
Ragoussis J, Elvidge GP, Kaur K, Colella S (2006) Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research. Plos Genet 2(7):920–929. doi:10.1371/journal.pgen.0020100
Ross PL, Lee K, Belgrader P (1997) Discrimination of single-nucleotide polymorphisms in human DNA using peptide nucleic acid probes detected by MALDI-TOF mass spectrometry. Anal Chem 69(20):4197–4202. doi:10.1021/ac9703966
Schatz P, Distler J, Berlin K, Schuster M (2006) Novel method for high throughput DNA methylation marker evaluation using PNA-probe library hybridization and MALDI-TOF detection. Nucleic Acids Res 34(8). doi:10.1093/nar/gkl218
Arlinghaus HF, Schroder M, Feldner JC, Brandt O, Hoheisel JD, Lipinsky D (2004) Development of PNA microarrays for gene diagnostics with TOF-SIMS. Appl Surf Sci 231:392–396. doi:10.1016/j.apsusc.2004.03.145
Winssinger N, Harris JL (2005) Microarray-based functional protein profiling using peptide nucleic acid-encoded libraries. Expert Rev Proteomics 2(6):937–947. doi:10.1586/14789450.2.6.937
Oura K, Lifshits VG, Saranin AA, Zotov AV, Katayama M, Yates JT (2004) Surface science: an introduction, vol 57. vol 10. AIP
Poling GW (1970) Infrared reflection studies of metal surfaces. J Colloid Interface Sci 34(3):365. doi:10.1016/0021-9797(70)90195-5
Mateo-Marti E, Briones C, Pradier CM, Martin-Gago JA (2007) A DNA biosensor based on peptide nucleic acids on gold surfaces. Biosens Bioelectron 22(9–10):1926–1932. doi:10.1016/j.bios.2006.08.012
Mertens J, Rogero C, Calleja M, Ramos D, Martin-Gago JA, Briones C, Tamayo J (2008) Label-free detection of DNA hybridization based on hydration-induced tension in nucleic acid films. Nat Nanotechnol 3(5):301–307. doi:10.1038/nnano.2008.91
Obika S, Nanbu D, Hari Y, Morio K-i, In Y, Ishida T, Imanishi T (1997) Synthesis of 2′-O,4′-C-methyleneuridine and -cytidine. Novel bicyclic nucleosides having a fixed C3, -endo sugar puckering. Tetrahedron Lett 38(50):8735–8738
Koshkin AA, Rajwanshi VK, Wengel J (1998) Novel convenient syntheses of LNA [2.2.1]bicyclo nucleosides. Tetrahedron Lett 39(24):4381–4384
Natsume T, Ishikawa Y, Dedachi K, Tsukamoto T, Kurita N (2007) Effect of base mismatch on the electronic properties of DNA-DNA and LNA-DNA double strands: density-functional theoretical calculations. Chem Phys Lett 446(1–3):151–158
Størling ZM, Koch T, Begley TP (2007) Locked nucleic acids. In: Wiley encyclopedia of chemical biology. John Wiley & Sons, Inc. doi:10.1002/9780470048672.wecb516
Vester B, Wengel J (2004) LNA (Locked Nucleic Acid): high-affinity targeting of complementary RNA and DNA. Biochemistry 43(42):13233–13241. doi:10.1021/bi0485732
Fang S, Lee HJ, Wark AW, Corn RM (2006) Attomole microarray detection of MicroRNAs by nanoparticle-amplified SPR imaging measurements of surface polyadenylation reactions. J Am Chem Soc 128(43):14044–14046. doi:10.1021/ja065223p
Diercks S, Gescher C, Metfies K, Medlin LK (2009) Evaluation of locked nucleic acids for signal enhancement of oligonucleotide probes for microalgae immobilised on solid surfaces. J Appl Phycol 21(6):657–668. doi:10.1007/s10811-008-9399-0
Orum H, Jakobsen MH, Koch T, Vuust J, Borre MB (1999) Detection of the factor V Leiden mutation by direct allele-specific hybridization of PCR amplicons to photoimmobilized locked nucleic acids. Clin Chem 45(11):1898–1905
Simeonov A, Nikiforov TT (2002) Single nucleotide polymorphism genotyping using short, fluorescently labeled locked nucleic acid (LNA) probes and fluorescence polarization detection. Nucleic Acids Res 30(17):e91. doi:10.1093/nar/gnf090
Wang L, Yang CJ, Medley CD, Benner SA, Tan W (2005) Locked nucleic acid molecular beacons. J Am Chem Soc 127(45):15664–15665. doi:10.1021/ja052498g
Martinez K, Estevez MC, Wu YR, Phillips JA, Medley CD, Tan WH (2009) Locked nucleic acid based beacons for surface interaction studies and biosensor development. Anal Chem 81(9):3448–3454. doi:10.1021/ac8027239
Han WH, Liao JM, Chen KL, Wu SM, Chiang YW, Lo ST, Chen CL, Chiang CM (2010) Enhanced recognition of single-base mismatch using locked nucleic acid-integrated hairpin DNA probes revealed by atomic force microscopy nanolithography. Anal Chem 82(6):2395–2400. doi:10.1021/ac902665c
Chen J, Zhang J, Wang K, Lin X, Huang L, Chen G (2008) Electrochemical biosensor for detection of BCR/ABL fusion gene using locked nucleic acids on 4-aminobenzenesulfonic acid-modified glassy carbon electrode. Anal Chem 80(21):8028–8034. doi:10.1021/ac801040e
Lin LQ, Lin XH, Chen JH, Chen W, He M, Chen YZ (2009) Electrochemical biosensor for detection of BCR/ABL fusion gene based on hairpin locked nucleic acids probe. Electrochem Commun 11(8):1650–1653. doi:10.1016/j.elecom.2009.06.015
Wang K, Sun ZL, Feng MJ, Liu AL, Yang SY, Chen YZ, Lin XH (2011) Design of a sandwich-mode amperometric biosensor for detection of PML/RAR alpha fusion gene using locked nucleic acids on gold electrode. Biosens Bioelectron 26(6):2870–2876. doi:10.1016/j.bios.2010.11.030
Lin L, Liu Q, Wang L, Liu A, Weng S, Lei Y, Chen W, Lin X, Chen Y (2011) Enzyme-amplified electrochemical biosensor for detection of PML-RAR alpha fusion gene based on hairpin LNA probe. Biosens Bioelectron 28(1):277–283. doi:10.1016/j.bios.2011.07.032
Berti F, Eisenkolbl C, Minocci D, Nieri P, Rossi AM, Mascini M, Marrazza G (2011) Cannabinoid receptor gene detection by electrochemical genosensor. J Electroanal Chem 656(1–2):55–60. doi:10.1016/j.jelechem.2011.01.021
Laschi S, Palchetti I, Marrazza G, Mascini M (2009) Enzyme-amplified electrochemical hybridization assay based on PNA, LNA and DNA probe-modified micro-magnetic beads. Bioelectrochemistry 76(1–2):214–220
Darfeuille F, Hansen JB, Orum H, Primo CD, Toulme JJ (2004) LNA/DNA chimeric oligomers mimic RNA aptamers targeted to the TAR RNA element of HIV-1. Nucleic Acids Res 32(10):3101–3107. doi:10.1093/nar/gkh636
Virno A, Randazzo A, Giancola C, Bucci M, Cirino G, Mayol L (2007) A novel thrombin binding aptamer containing a G-LNA residue. Bioorg Med Chem 15(17):5710–5718. doi:10.1016/j.bmc.2007.06.008
Hernandez FJ, Kalra N, Wengel J, Vester B (2009) Aptamers as a model for functional evaluation of LNA and 2′-amino LNA. Bioorganic Med Chem Lett 19(23):6585–6587. doi:10.1016/j.bmcl.2009.10.039
McTigue PM, Peterson RJ, Kahn JD (2004) Sequence-dependent thermodynamic parameters; for locked nucleic acid (LNA)-DNA duplex formation. Biochemistry 43(18):5388–5405. doi:10.1021/bi035976d
Kaur H, Arora A, Wengel J, Maiti S (2006) Thermodynamic, counterion, and hydration effects for the incorporation of locked nucleic acid nucleotides into DNA duplexes. Biochemistry 45(23):7347–7355. doi:10.1021/bi060307w
Singh SK, Nielsen P, Koshkin AA, Wengel J (1998) LNA (locked nucleic acids): synthesis and high-affinity nucleic acid recognition. Chem Commun 4:455–456. doi:10.1039/a708608c
Breslauer KJ, Frank R, Blocker H, Marky LA (1986) Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A 83(11):3746–3750
SantaLucia J Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A 95(4):1460–1465
Sugimoto N, S-i N, Yoneyama M, K-i H (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res 24(22):4501–4505. doi:10.1093/nar/24.22.4501
Kim D-K, Kwon Y-S, Takamura Y, Tamiya E (2006) Detection of DNA Hybridization Properties Using Thermodynamic Method. Japanese Journal of Applied Physics 45 (Copyright (C) 2006 The Japan Society of Applied Physics):509
Acknowledgements
This work was supported by MICINN (grants EUI2008-00158 and BIO2010-20696) and CSIC (grant 200920I040). CIBERehd is funded by the Instituto de Salud Carlos III.
Author information
Authors and Affiliations
Corresponding author
Additional information
Published in the topical collection Biomimetic Recognition Elements for Sensing Applications with guest editor María Cruz Moreno-Bondi.
Rights and permissions
About this article
Cite this article
Briones, C., Moreno, M. Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development. Anal Bioanal Chem 402, 3071–3089 (2012). https://doi.org/10.1007/s00216-012-5742-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00216-012-5742-z