Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases

Topham, Christopher M.; Smith, Jeremy C.

doi:10.1007/s10822-021-00375-9

Title: Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases

Journal Article · Wed Feb 24 00:00:00 EST 2021 · Journal of Computer-Aided Molecular Design

DOI:https://doi.org/10.1007/s10822-021-00375-9· OSTI ID:1820850

^[1];

^[2]

Molecular Forces Consulting, Lavaur (France); Univ. Heidelberg (Germany); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Molecular Biophysics; Univ. of Tennessee, Knoxville, TN (United States)
Univ. Heidelberg (Germany); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Molecular Biophysics; Univ. of Tennessee, Knoxville, TN (United States)

Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. Additionally, in geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T–A and U–A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1820850

Journal Information:: Journal of Computer-Aided Molecular Design, Vol. 35, Issue 3; ISSN 0920-654X

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

References (109)

Mechanisms of triplex DNA-mediated inhibition of transcription initiation in cells Jain, Aklank; Magistri, Marco; Napoli, Sara Biochimie, Vol. 92, Issue 3 https://doi.org/10.1016/j.biochi.2009.12.012	journal	March 2010
Kinetic analysis of specificity of duplex DNA targeting by homopyrimidine peptide nucleic acids Demidov, V. V.; Yavnilovich, M. V.; Frank-Kamenetskii, M. D. Biophysical Journal, Vol. 72, Issue 6 https://doi.org/10.1016/S0006-3495(97)78918-5	journal	June 1997
Kinetic sequence discrimination of cationic bis-PNAs upon targeting of double-stranded DNA Kuhn, H.; Demidov, V. V.; Frank-Kamenetskii, M. D. Nucleic Acids Research, Vol. 26, Issue 2 https://doi.org/10.1093/nar/26.2.582	journal	January 1998
Triple-Helical Recognition of RNA Using 2-Aminopyridine-Modified PNA at Physiologically Relevant Conditions Zengeya, Thomas; Gupta, Pankaj; Rozners, Eriks Angewandte Chemie International Edition, Vol. 51, Issue 50 https://doi.org/10.1002/anie.201207925	journal	November 2012
γ‐( S )‐Guanidinylmethyl‐Modified Triplex‐Forming Peptide Nucleic Acids Increase Hoogsteen‐Face Affinity for a MicroRNA and Enhance Cellular Uptake Tähtinen, Ville; Verhassel, Alejandra; Tuomela, Johanna ChemBioChem, Vol. 20, Issue 24 https://doi.org/10.1002/cbic.201900393	journal	September 2019
High-affinity triplex targeting of double stranded DNA using chemically modified peptide nucleic acid oligomers Hansen, Mads E.; Bentin, Thomas; Nielsen, Peter E. Nucleic Acids Research, Vol. 37, Issue 13 https://doi.org/10.1093/nar/gkp437	journal	May 2009
An extra dimension in nucleic acid sequence recognition Fox, Keith R.; Brown, Tom Quarterly Reviews of Biophysics, Vol. 38, Issue 4 https://doi.org/10.1017/S0033583506004197	journal	November 2005
Chiral Peptide Nucleic Acids with a Substituent in the N-(2-Aminoethy)glycine Backbone Sugiyama, Toru; Kittaka, Atsushi Molecules, Vol. 18, Issue 1 https://doi.org/10.3390/molecules18010287	journal	December 2012
A 4-[(3R,4R)-dihydroxypyrrolidino]pyrimidin-2-one nucleobase for a CG base pair in triplex DNA Hari, Yoshiyuki; Akabane, Masaaki; Hatanaka, Yuri Chemical Communications, Vol. 47, Issue 15 https://doi.org/10.1039/c1cc10138b	journal	January 2011
A Nucleic Acid Triple Helix Formed by a Peptide Nucleic Acid-DNA Complex Betts, L.; Josey, J. A.; Veal, J. M. Science, Vol. 270, Issue 5243 https://doi.org/10.1126/science.270.5243.1838	journal	December 1995
Improvement of sequence selectivity in triple helical recognition of RNA by phenylalanine-derived PNA Zengeya, Thomas; Gindin, Artem; Rozners, Eriks Artificial DNA: PNA & XNA, Vol. 4, Issue 3 https://doi.org/10.4161/adna.26599	journal	July 2013
The triple helix: 50 years later, the outcome Duca, M.; Vekhoff, P.; Oussedik, K. Nucleic Acids Research, Vol. 36, Issue 16 https://doi.org/10.1093/nar/gkn493	journal	August 2008
Extended DNA-Recognition Repertoire of Peptide Nucleic Acid (PNA): PNA−dsDNA Triplex Formed with Cytosine-Rich Homopyrimidine PNA Wittung, Pernilla; Nielsen, Peter; Nordén, Bengt Biochemistry, Vol. 36, Issue 26 https://doi.org/10.1021/bi963136b	journal	July 1997
A Novel PNA-Monomer for Recognition of Thymine in Triple-Helix Structures Goldbech Olsen, Anne; Dahl, Otto; Nielsen, Peter E. Nucleosides, Nucleotides and Nucleic Acids, Vol. 22, Issue 5-8 https://doi.org/10.1081/NCN-120022958	journal	October 2003
Strand Invasion of Extended, Mixed-Sequence B-DNA by γPNAs He, Gaofei; Rapireddy, Srinivas; Bahal, Raman Journal of the American Chemical Society, Vol. 131, Issue 34 https://doi.org/10.1021/ja900228j	journal	August 2009
Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions Marenich, Aleksandr V.; Cramer, Christopher J.; Truhlar, Donald G. The Journal of Physical Chemistry B, Vol. 113, Issue 18, p. 6378-6396 https://doi.org/10.1021/jp810292n	journal	May 2009
Solution structure of a peptide nucleic acid–DNA duplex Eriksson, Magdalena; Nielsen, Peter E. Nature Structural Biology, Vol. 3, Issue 5 https://doi.org/10.1038/nsb0596-410	journal	May 1996
Stable and Selective Recognition of Three Base Pairs in the Parallel Triple-Helical DNA Binding Motif Buchini, Sabrina; Leumann, Christian J. Angewandte Chemie International Edition, Vol. 43, Issue 30 https://doi.org/10.1002/anie.200460159	journal	July 2004
PNA hybridizes to complementary oligonucleotides obeying the Watson–Crick hydrogen-bonding rules Egholm, Michael; Buchardt, Ole; Christensen, Leif Nature, Vol. 365, Issue 6446 https://doi.org/10.1038/365566a0	journal	October 1993
Benchmarking Quantum Chemical Methods: Are We Heading in the Right Direction? Mata, Ricardo A.; Suhm, Martin A. Angewandte Chemie International Edition, Vol. 56, Issue 37 https://doi.org/10.1002/anie.201611308	journal	April 2017
Molecular Dynamics Simulations of PNA·DNA and PNA·RNA Duplexes in Aqueous Solution Soliva, Robert; Sherer, Edward; Luque, F. Javier Journal of the American Chemical Society, Vol. 122, Issue 25 https://doi.org/10.1021/ja000259h	journal	June 2000
Targeting DNA with triplex-forming oligonucleotides to modify gene sequence Simon, Philippe; Cannata, Fabio; Concordet, Jean-Paul Biochimie, Vol. 90, Issue 8 https://doi.org/10.1016/j.biochi.2008.04.004	journal	August 2008
Synthesis and triplex-forming properties of oligonucleotides capable of recognizing corresponding DNA duplexes containing four base pairs Ohkubo, Akihiro; Yamada, Kenji; Ito, Yu Nucleic Acids Research, Vol. 43, Issue 12 https://doi.org/10.1093/nar/gkv496	journal	May 2015
Orientation Preferences of Backbone Secondary Amide Functional Groups in Peptide Nucleic Acid Complexes: Quantum Chemical Calculations Reveal an Intrinsic Preference of Cationic D-Amino Acid-Based Chiral PNA Analogues for the P-form Topham, Christopher M.; Smith, Jeremy C. Biophysical Journal, Vol. 92, Issue 3 https://doi.org/10.1529/biophysj.105.079723	journal	February 2007
The first crystal structures of RNA–PNA duplexes and a PNA-PNA duplex containing mismatches—toward anti-sense therapy against TREDs Kiliszek, Agnieszka; Banaszak, Katarzyna; Dauter, Zbigniew Nucleic Acids Research, Vol. 44, Issue 4 https://doi.org/10.1093/nar/gkv1513	journal	December 2015
Incorporation of thio-pseudoisocytosine into triplex-forming peptide nucleic acids for enhanced recognition of RNA duplexes Devi, Gitali; Yuan, Zhen; Lu, Yunpeng Nucleic Acids Research, Vol. 42, Issue 6 https://doi.org/10.1093/nar/gkt1367	journal	January 2014
Recognition of Chromosomal DNA by PNAs Kaihatsu, Kunihiro; Janowski, Bethany A.; Corey, David R. Chemistry & Biology, Vol. 11, Issue 6 https://doi.org/10.1016/j.chembiol.2003.09.014	journal	June 2004
Strand Invasion of Mixed-Sequence, Double-Helical B-DNA by γ-Peptide Nucleic Acids Containing G-Clamp Nucleobases under Physiological Conditions Rapireddy, Srinivas; Bahal, Raman; Ly, Danith H. Biochemistry, Vol. 50, Issue 19 https://doi.org/10.1021/bi2002554	journal	April 2011
Focus on PNA Flexibility and RNA Binding using Molecular Dynamics and Metadynamics Verona, Massimiliano Donato; Verdolino, Vincenzo; Palazzesi, Ferruccio Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep42799	journal	February 2017
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu Grimme, Stefan; Antony, Jens; Ehrlich, Stephan The Journal of Chemical Physics, Vol. 132, Issue 15 https://doi.org/10.1063/1.3382344	journal	April 2010
JUMNA (junction minimisation of nucleic acids) Lavery, R.; Zakrzewska, K.; Sklenar, H. Computer Physics Communications, Vol. 91, Issue 1-3 https://doi.org/10.1016/0010-4655(95)00046-I	journal	September 1995
Targeting of an Interrupted Polypurine:Polypyrimidine Sequence in Mammalian Cells by a Triplex-Forming Oligonucleotide Containing a Novel Base Analogue Semenyuk, A.; Darian, E.; Liu, J. Biochemistry, Vol. 49, Issue 36 https://doi.org/10.1021/bi100797z	journal	August 2010
Superior Duplex DNA Strand Invasion by Acridine Conjugated Peptide Nucleic Acids Bentin, Thomas; Nielsen, Peter E. Journal of the American Chemical Society, Vol. 125, Issue 21 https://doi.org/10.1021/ja029936t	journal	May 2003
Double duplex invasion by peptide nucleic acid: A general principle for sequence-specific targeting of double-stranded DNA Lohse, J.; Dahl, O.; Nielsen, P. E. Proceedings of the National Academy of Sciences, Vol. 96, Issue 21 https://doi.org/10.1073/pnas.96.21.11804	journal	October 1999
Recognition of GC base pairs by triplex forming oligonucleotides containing nucleosides derived from 2-aminopyridine Cassidy, S. Nucleic Acids Research, Vol. 25, Issue 24 https://doi.org/10.1093/nar/25.24.4891	journal	December 1997
A Simple γ-Backbone Modification Preorganizes Peptide Nucleic Acid into a Helical Structure Dragulescu-Andrasi, Anca; Rapireddy, Srinivas; Frezza, Brian M. Journal of the American Chemical Society, Vol. 128, Issue 31 https://doi.org/10.1021/ja0625576	journal	August 2006
Crystal Structure of Chiral γPNA with Complementary DNA Strand: Insights into the Stability and Specificity of Recognition and Conformational Preorganization Yeh, Joanne I.; Shivachev, Boris; Rapireddy, Srinivas Journal of the American Chemical Society, Vol. 132, Issue 31 https://doi.org/10.1021/ja907225d	journal	August 2010
Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model Barone, Vincenzo; Cossi, Maurizio The Journal of Physical Chemistry A, Vol. 102, Issue 11 https://doi.org/10.1021/jp9716997	journal	March 1998
Sequence Selective Recognition of Double-Stranded RNA at Physiologically Relevant Conditions Using PNA-Peptide Conjugates Muse, Oluwatoyosi; Zengeya, Thomas; Mwaura, Juddy ACS Chemical Biology, Vol. 8, Issue 8 https://doi.org/10.1021/cb400144x	journal	June 2013
Versatility of peptide nucleic acids (PNAs): role in chemical biology, drug discovery, and origins of life Sharma, Chiranjeev; Awasthi, Satish Kumar Chemical Biology & Drug Design, Vol. 89, Issue 1 https://doi.org/10.1111/cbdd.12833	journal	September 2016
Recent advances in peptide nucleic acid for cancer bionanotechnology Wu, Jun-chen; Meng, Qing-chun; Ren, Hong-mei Acta Pharmacologica Sinica, Vol. 38, Issue 6 https://doi.org/10.1038/aps.2017.33	journal	April 2017
Conformationally Constrained PNA Analogues: Structural Evolution toward DNA/RNA Binding Selectivity Kumar, Vaijayanti A.; Ganesh, Krishna N. Accounts of Chemical Research, Vol. 38, Issue 5 https://doi.org/10.1021/ar030277e	journal	February 2005
Sequence-Specific Targeting of Duplex DNA by Peptide Nucleic Acids via Triplex Strand Invasion Demidov, Vadim V.; Frank-Kamenetskii, Maxim D. Methods, Vol. 23, Issue 2 https://doi.org/10.1006/meth.2000.1112	journal	February 2001
Synthesis and evaluation of a conformationally constrained pyridazinone PNA-monomer for recognition of thymine in triple-helix structures Olsen, Anne Goldbech; Dahl, Otto; Nielsen, Peter E. Bioorganic & Medicinal Chemistry Letters, Vol. 14, Issue 6 https://doi.org/10.1016/j.bmcl.2003.12.093	journal	March 2004
NMR solution structure of a peptide nucleic acid complexed with RNA Brown, S.; Thomson, S.; Veal, J. Science, Vol. 265, Issue 5173 https://doi.org/10.1126/science.7519361	journal	August 1994
Peptide Nucleic Acids with a Structurally Biased Backbone. Updated Review and Emerging Challenges Corradini, Roberto; Sforza, Stefano; Tedeschi, Tullia Current Topics in Medicinal Chemistry, Vol. 11, Issue 12 https://doi.org/10.2174/156802611795860979	journal	June 2011
Peptide Nucleic Acids(PNAs) Containing Thymine Monomers Derived from Chiral Amino Acids: Hybridization and Solubility Properties ofD-Lysine PNA Nielsen, Peter E.; Haaima, Gerald; Lohse, Anders Angewandte Chemie International Edition in English, Vol. 35, Issue 17 https://doi.org/10.1002/anie.199619391	journal	September 1996
Incorporation of a novel nucleobase allows stable oligonucleotide-directed triple helix formation at the target sequence containing a purine·pyrimidine interruption Guianvarc’h, Dominique; Benhida, Rachid; Fourrey, Jean-Louis Chemical Communications, Issue 18 https://doi.org/10.1039/b103743a	journal	January 2001
1,8-Naphthyridin-2,7-(1,8H)-dione is an effective mimic of protonated cytosine in peptide nucleic acid triplex recognition systems Christensen, Caspar; Eldrup, Anne B.; Haaima, Gerald Bioorganic & Medicinal Chemistry Letters, Vol. 12, Issue 21 https://doi.org/10.1016/S0960-894X(02)00658-3	journal	November 2002
Two sides of the coin: affinity and specificity of nucleic acid interactions Demidov, Vadim V.; Frank-Kamenetskii, Maxim D. Trends in Biochemical Sciences, Vol. 29, Issue 2 https://doi.org/10.1016/j.tibs.2003.12.007	journal	February 2004
The influence of helix morphology on co-operative polyamide backbone conformational flexibility in peptide nucleic acid complexes 1 1Edited by I. Tinoco Topham, Christopher M.; Smith, Jeremy C. Journal of Molecular Biology, Vol. 292, Issue 5 https://doi.org/10.1006/jmbi.1999.3131	journal	October 1999
Extending Recognition by Peptide Nucleic Acids (PNAs): Binding to Duplex DNA and Inhibition of Transcription by Tail-Clamp PNA−Peptide Conjugates Kaihatsu, Kunihiro; Shah, Rahul H.; Zhao, Xin Biochemistry, Vol. 42, Issue 47 https://doi.org/10.1021/bi035194k	journal	November 2003
Perspective on density functional theory Burke, Kieron The Journal of Chemical Physics, Vol. 136, Issue 15 https://doi.org/10.1063/1.4704546	journal	April 2012
VMD: Visual molecular dynamics Humphrey, William; Dalke, Andrew; Schulten, Klaus Journal of Molecular Graphics, Vol. 14, Issue 1 https://doi.org/10.1016/0263-7855(96)00018-5	journal	February 1996
Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model Cossi, Maurizio; Rega, Nadia; Scalmani, Giovanni Journal of Computational Chemistry, Vol. 24, Issue 6 https://doi.org/10.1002/jcc.10189	journal	April 2003
Formation of stable DNA triplexes Fox, Keith R.; Brown, Tom Biochemical Society Transactions, Vol. 39, Issue 2 https://doi.org/10.1042/BST0390629	journal	March 2011
Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters Jasiński, Maciej; Feig, Michael; Trylska, Joanna Journal of Chemical Theory and Computation, Vol. 14, Issue 7 https://doi.org/10.1021/acs.jctc.8b00291	journal	May 2018
Triplex-Forming Oligonucleotides - Sequence-Specific DNA Ligands as Tools for Gene Inhibition and for Modulation of DNA-Associated Functions Besch, Robert; Giovannangeli, Carine; Degitz, Klaus Current Drug Targets, Vol. 5, Issue 8 https://doi.org/10.2174/1389450043345100	journal	November 2004
Triple helical recognition of pyrimidine inversions in polypurine tracts of RNA by nucleobase-modified PNA Gupta, Pankaj; Zengeya, Thomas; Rozners, Eriks Chemical Communications, Vol. 47, Issue 39 https://doi.org/10.1039/c1cc14706d	journal	January 2011
CG base pair recognition within DNA triple helices by modified N-methylpyrrolo-dC nucleosides Gerrard, Simon R.; Edrees, Mastoura M.; Bouamaied, Imenne Organic & Biomolecular Chemistry, Vol. 8, Issue 22 https://doi.org/10.1039/c0ob00119h	journal	January 2010
Cg Base Pair Recognition Within Dna Triple Helices Using N -Methyl-3 H -Pyrrolo[2,3- d ]Pyrimidin-2(7 H )-One Nucleoside Analogues Gerrard, Simon R.; Srinivasan, Natarajan; Fox, Keith R. Nucleosides, Nucleotides and Nucleic Acids, Vol. 26, Issue 10-12 https://doi.org/10.1080/15257770701533958	journal	November 2007
Triplex-forming oligonucleotides: principles and applications Vasquez, Karen M.; Glazer, Peter M. Quarterly Reviews of Biophysics, Vol. 35, Issue 1 https://doi.org/10.1017/S0033583502003773	journal	February 2002
Towards the Sequence-Selective Recognition of Double-Stranded DNA Containing Pyrimidine-Purine Interruptions by Triplex-Forming Oligonucleotides Hari, Yoshiyuki; Obika, Satoshi; Imanishi, Takeshi European Journal of Organic Chemistry, Vol. 2012, Issue 15 https://doi.org/10.1002/ejoc.201101821	journal	March 2012
Strand invasion by mixed base PNAs and a PNA-peptide chimera Zhang, X. Nucleic Acids Research, Vol. 28, Issue 17 https://doi.org/10.1093/nar/28.17.3332	journal	September 2000
Optimization of the Alkyl Linker of TO Base Surrogate in Triplex-Forming PNA for Enhanced Binding to Double-Stranded RNA Sato, Takaya; Sato, Yusuke; Nishizawa, Seiichi Chemistry - A European Journal, Vol. 23, Issue 17 https://doi.org/10.1002/chem.201604676	journal	January 2017
Kinetics and mechanism of polyamide ("peptide") nucleic acid binding to duplex DNA. Demidov, V. V.; Yavnilovich, M. V.; Belotserkovskii, B. P. Proceedings of the National Academy of Sciences, Vol. 92, Issue 7 https://doi.org/10.1073/pnas.92.7.2637	journal	March 1995
Triplex technology in studies of DNA damage, DNA repair, and mutagenesis Mukherjee, Anirban; Vasquez, Karen M. Biochimie, Vol. 93, Issue 8 https://doi.org/10.1016/j.biochi.2011.04.001	journal	August 2011
Sequence-Unrestricted, Watson-Crick Recognition of Double Helical B-DNA by (R)-MiniPEG-γPNAs Bahal, Raman; Sahu, Bichismita; Rapireddy, Srinivas ChemBioChem, Vol. 13, Issue 1 https://doi.org/10.1002/cbic.201100646	journal	December 2011
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank Westbrook, John D.; Shao, Chenghua; Feng, Zukang Bioinformatics, Vol. 31, Issue 8 https://doi.org/10.1093/bioinformatics/btu789	journal	December 2014
Toward accurate relative energy predictions of the bioactive conformation of drugs Butler, Keith T.; Luque, F. Javier; Barril, Xavier Journal of Computational Chemistry, Vol. 30, Issue 4 https://doi.org/10.1002/jcc.21087	journal	March 2009
PNA2/DNA Triplexes: Stability and Specificity Krupnik, O. V.; Lazurkin, Yu. S. Russian Journal of Genetics, Vol. 41, Issue 7 https://doi.org/10.1007/s11177-005-0150-5	journal	July 2005
Single and Bis Peptide Nucleic Acids as Triplexing Agents: Binding and Stoichiometry Griffith, Michael C.; Risen, Lisa M.; Greig, Michael J. Journal of the American Chemical Society, Vol. 117, Issue 2 https://doi.org/10.1021/ja00107a033	journal	January 1995
Defining the Structure of Irregular Nucleic Acids: Conventions and Principles Lavery, Richard; Sklenar, Heinz Journal of Biomolecular Structure and Dynamics, Vol. 6, Issue 4 https://doi.org/10.1080/07391102.1989.10507728	journal	February 1989
Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide Nielsen, P.; Egholm, M.; Berg, R. Science, Vol. 254, Issue 5037 https://doi.org/10.1126/science.1962210	journal	December 1991
Gene Targeting and Expression Modulation by Peptide Nucleic Acids (PNA) E. Nielsen, Peter Current Pharmaceutical Design, Vol. 16, Issue 28 https://doi.org/10.2174/138161210793292546	journal	September 2010
Synthetic, Structural, and RNA Binding Studies on 2‐Aminopyridine‐Modified Triplex‐Forming Peptide Nucleic Acids Kotikam, Venubabu; Kennedy, Scott D.; MacKay, James A. Chemistry – A European Journal, Vol. 25, Issue 17 https://doi.org/10.1002/chem.201806293	journal	March 2019
Effect of Temperature and Ionic Strength on the Dissociation Kinetics and Lifetime of PNA−DNA Triplexes ^† Kosaganov, Yurii N.; Stetsenko, Dmitrii A.; Lubyako, Elena N. Biochemistry, Vol. 39, Issue 38 https://doi.org/10.1021/bi0006417	journal	September 2000
Structural diversity of target-specific homopyrimidine peptide nucleic acid–dsDNA complexes Bentin, Thomas; Hansen, Georg I.; Nielsen, Peter E. Nucleic Acids Research, Vol. 34, Issue 20 https://doi.org/10.1093/nar/gkl736	journal	November 2006
A theoretical analysis of specificity of nucleic acid interactions with oligonucleotides and peptide nucleic acids (PNAs) Lomakin, Aleksey; Frank-Kamenetskii, Maxim D. Journal of Molecular Biology, Vol. 276, Issue 1 https://doi.org/10.1006/jmbi.1997.1497	journal	February 1998
Four base recognition by triplex-forming oligonucleotides at physiological pH Rusling, D. A. Nucleic Acids Research, Vol. 33, Issue 9 https://doi.org/10.1093/nar/gki625	journal	May 2005
Effect of chirality in gamma-PNA: PNA interaction, another piece in the picture Manicardi, Alex; Corradini, Roberto Artificial DNA: PNA & XNA, Vol. 5, Issue 3 https://doi.org/10.1080/1949095X.2015.1131801	journal	December 2014
Efficient triple helix formation by oligodeoxyribonucleotides containing alpha- or beta-2-amino-5-(2-deoxy-D-ribofuranosyl) pyridine residues Bates, P. Nucleic Acids Research, Vol. 24, Issue 21 https://doi.org/10.1093/nar/24.21.4176	journal	November 1996
Strand-invasion of duplex DNA by peptide nucleic acid oligomers. Peffer, N. J.; Hanvey, J. C.; Bisi, J. E. Proceedings of the National Academy of Sciences, Vol. 90, Issue 22 https://doi.org/10.1073/pnas.90.22.10648	journal	November 1993
PDB Ligand Conformational Energies Calculated Quantum-Mechanically Sitzmann, Markus; Weidlich, Iwona E.; Filippov, Igor V. Journal of Chemical Information and Modeling, Vol. 52, Issue 3 https://doi.org/10.1021/ci200595n	journal	February 2012
General atomic and molecular electronic structure system Schmidt, Michael W.; Baldridge, Kim K.; Boatz, Jerry A. Journal of Computational Chemistry, Vol. 14, Issue 11, p. 1347-1363 https://doi.org/10.1002/jcc.540141112	journal	November 1993
¹⁹ F NMR Spectroscopic Analysis of the Binding Modes in Triple-Helical Peptide Nucleic Acid (PNA)/MicroRNA Complexes Tähtinen, Ville; Granqvist, Lotta; Murtola, Merita Chemistry - A European Journal, Vol. 23, Issue 29 https://doi.org/10.1002/chem.201700601	journal	April 2017
Affinity and selectivity of C2- and C5-substituted “chiral-box” PNA in solution and on microarrays Manicardi, Alex; Calabretta, Alessandro; Bencivenni, Mariangela Chirality, Vol. 22, Issue 1E https://doi.org/10.1002/chir.20865	journal	January 2010
Recognition of CG inversions in DNA triple helices by methylated 3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one nucleoside analogues Ranasinghe, Rohan T.; Rusling, David A.; Powers, Vicki E. C. Chemical Communications, Issue 20 https://doi.org/10.1039/b502325d	journal	January 2005
The Definition of Generalized Helicoidal Parameters and of Axis Curvature for Irregular Nucleic Acids Lavery, Richard; Sklenar, Heinz Journal of Biomolecular Structure and Dynamics, Vol. 6, Issue 1 https://doi.org/10.1080/07391102.1988.10506483	journal	August 1988
Enhanced Strand Invasion by Peptide Nucleic Acid−Peptide Conjugates Kaihatsu, Kunihiro; Braasch, Dwaine A.; Cansizoglu, Ahmet Biochemistry, Vol. 41, Issue 37 https://doi.org/10.1021/bi0263659	journal	August 2002
Triplex-forming oligonucleotides: a third strand for DNA nanotechnology Chandrasekaran, Arun Richard; Rusling, David A. Nucleic Acids Research, Vol. 46, Issue 3 https://doi.org/10.1093/nar/gkx1230	journal	December 2017
RNA triplexes: from structural principles to biological and biotech applications: RNA triplexes Devi, Gitali; Zhou, Yuan; Zhong, Zhensheng Wiley Interdisciplinary Reviews: RNA, Vol. 6, Issue 1 https://doi.org/10.1002/wrna.1261	journal	August 2014
Biophysics of the DNA molecule Frank-Kamenetskii, Maxim D. Physics Reports, Vol. 288, Issue 1-6 https://doi.org/10.1016/S0370-1573(97)00020-3	journal	September 1997
Efficient pH-independent sequence-specific DNA binding by pseudoisocytosine-containing bis-PNA Egholm, Michael; Christensen, Leif; Deuholm, Kim L. Nucleic Acids Research, Vol. 23, Issue 2 https://doi.org/10.1093/nar/23.2.217	journal	January 1995
Stable Recognition of TA Interruptions by Triplex Forming Oligonucleotides Containing a Novel Nucleoside Wang, Yang; Rusling, David A.; Powers, Vicki E. C. Biochemistry, Vol. 44, Issue 15 https://doi.org/10.1021/bi050013v	journal	March 2005
A Novel Peptide Nucleic Acid Monomer for Recognition of Thymine in Triple-Helix Structures Eldrup, Anne B.; Dahl, Otto; Nielsen, Peter E. Journal of the American Chemical Society, Vol. 119, Issue 45 https://doi.org/10.1021/ja9717424	journal	November 1997
A Simple Cytosine to G-Clamp Nucleobase Substitution Enables Chiral γ-PNAs to Invade Mixed-Sequence Double-Helical B-form DNA Chenna, Venugopal; Rapireddy, Srinivas; Sahu, Bichismita ChemBioChem, Vol. 9, Issue 15 https://doi.org/10.1002/cbic.200800441	journal	October 2008
Insights into peptide nucleic acid (PNA) structural features: The crystal structure of a D-lysine-based chiral PNA-DNA duplex Menchise, V.; De Simone, G.; Tedeschi, T. Proceedings of the National Academy of Sciences, Vol. 100, Issue 21 https://doi.org/10.1073/pnas.2034746100	journal	September 2003
Peptide Nucleic Acids (PNA) in Chemical Biology and Drug Discovery Nielsen, Peter E. Chemistry & Biodiversity, Vol. 7, Issue 4 https://doi.org/10.1002/cbdv.201000005	journal	April 2010
Combined Triplex/Duplex Invasion of Double-Stranded DNA by “Tail-Clamp” Peptide Nucleic Acid Bentin, Thomas; Larsen, H. Jakob; Nielsen, Peter E. Biochemistry, Vol. 42, Issue 47 https://doi.org/10.1021/bi0351918	journal	November 2003
Triplex-Forming Oligonucleotides as Potential Tools for Modulation of Gene Expression Rogers, F.; Lloyd, J.; Glazer, P. Current Medicinal Chemistry-Anti-Cancer Agents, Vol. 5, Issue 4 https://doi.org/10.2174/1568011054222300	journal	July 2005
Recognition of Double-Stranded RNA by Guanidine-Modified Peptide Nucleic Acids Gupta, Pankaj; Muse, Oluwatoyosi; Rozners, Eriks Biochemistry, Vol. 51, Issue 1 https://doi.org/10.1021/bi201570a	journal	December 2011
DNA unwinding upon strand-displacement binding of a thymine-substituted polyamide to double-stranded DNA. Cherny, D. Y.; Belotserkovskii, B. P.; Frank-Kamenetskii, M. D. Proceedings of the National Academy of Sciences, Vol. 90, Issue 5 https://doi.org/10.1073/pnas.90.5.1667	journal	March 1993
Duplex formation and secondary structure of γ-PNA observed by NMR and CD Viéville, J. M. P.; Barluenga, S.; Winssinger, N. Biophysical Chemistry, Vol. 210 https://doi.org/10.1016/j.bpc.2015.09.002	journal	March 2016
Direct Observation of Strand Invasion by Peptide Nucleic Acid (PNA) into Double-Stranded DNA Wittung, Pernilla; Nielsen, Peter; Nordén, Bengt Journal of the American Chemical Society, Vol. 118, Issue 30 https://doi.org/10.1021/ja960521f	journal	January 1996
Evidence for (PNA)2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement Nielsen, Peter E.; Egholm, Michael; Buchardt, Ole Journal of Molecular Recognition, Vol. 7, Issue 3 https://doi.org/10.1002/jmr.300070303	journal	September 1994
5-Substituted 2-Aminopyridine C -Nucleosides as Protonated Cytidine Equivalents: Increasing Efficiency and Selectivity in DNA Triple-Helix Formation Hildbrand, Stefan; Blaser, Adrian; Parel, Serge P. Journal of the American Chemical Society, Vol. 119, Issue 24 https://doi.org/10.1021/ja9704904	journal	June 1997
The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies Šponer, Jiří; Mládek, Arnošt; Šponer, Judit E. Physical Chemistry Chemical Physics, Vol. 14, Issue 44 https://doi.org/10.1039/c2cp41987d	journal	January 2012
2′,4′-BNA bearing a chiral guanidinopyrrolidine-containing nucleobase with potent ability to recognize the CG base pair in a parallel-motif DNA triplex Hari, Yoshiyuki; Akabane, Masaaki; Obika, Satoshi Chemical Communications, Vol. 49, Issue 67 https://doi.org/10.1039/c3cc44030c	journal	January 2013

Similar Records

Orientation Preferences of Backbone Secondary Amide Functional Groups in Peptide Nucleic Acid Complexes: Quantum Chemical Calculations Reveal an Intrinsic Preference of Cationic D-Amino Acid-Based Chiral PNA Analogues for the P-form

Journal Article · Mon Jan 01 00:00:00 EST 2007 · Biophysical Journal · OSTI ID:1820850

Smith, Jeremy C; Topham, Christopher

Triplex formation at single-stranded nucleic acid target sites of unrestricted sequence by two added strands of oligonucleotides: A proposed model

Journal Article · Wed Nov 16 00:00:00 EST 1994 · Journal of the American Chemical Society; (United States) · OSTI ID:1820850

Trapane, T L; Ts'o, P O.P.

DNA triplex formation of oligonucleotide analogues consisting of linker groups and octamer segments that have opposite sugar-phosphate backbone polarities

Journal Article · Tue Oct 15 00:00:00 EDT 1991 · Biochemistry; (United States) · OSTI ID:1820850

Ono, A; Kan, Lousing; Chen, Chingnien

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Double-stranded DNA-targeted drug design
PNA-peptide nucleic acid
Triplex
Pyrimidine base recognition
Quantum chemical modelling

Title: Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases

Citation Formats

References (109)

Similar Records

Related Subjects