title: Effects of hypoxanthine substitution in peptide nucleic acids targeting KRAS2 oncogenic mRNA molecules: theory and experiment.
abstract: Genetic disorders can arise from single base substitutions in a single gene. A single base substitution for wild type guanine in the twelfth codon of KRAS2 mRNA occurs frequently to initiate lung, pancreatic, and colon cancer. We have observed single base mismatch specificity in radioimaging of mutant KRAS2 mRNA in tumors in mice by in vivo hybridization with radiolabeled peptide nucleic acid (PNA) dodecamers. We hypothesized that multimutant specificity could be achieved with a PNA dodecamer incorporating hypoxanthine, which can form Watson-Crick base pairs with adenine, cytosine, thymine, and uracil. Using molecular dynamics simulations and free energy calculations, we show that hypoxanthine substitutions in PNAs are tolerated in KRAS2 RNA:PNA duplexes where wild type guanine is replaced by mutant uracil or adenine in RNA. To validate our predictions, we synthesized PNA dodecamers with hypoxanthine, and then measured the thermal stability of RNA:PNA duplexes. Circular dichroism thermal melting results showed that hypoxanthine-containing PNAs are more stable in duplexes where hypoxanthine-adenine and hypoxanthine-uracil base pairs are formed than single mismatch duplexes or duplexes containing hypoxanthine-guanine opposition.
authors: Departments of Biochemistry & Molecular Biology and ∥Radiology, and ⊥Kimmel Cancer Center, Thomas Jefferson University , Philadelphia, Pennsylvania 19107, United States.
authors: Jeffrey M
authors: JM
authors: Sanders
authors: Matthew E
authors: ME
authors: Wampole
authors: Chang-Po
authors: CP
authors: Chen
authors: Dalip
authors: D
authors: Sethi
authors: Amrita
authors: A
authors: Singh
authors: François-Yves
authors: FY
authors: Dupradeau
authors: Fan
authors: F
authors: Wang
authors: Brian D
authors: BD
authors: Gray
authors: Mathew L
authors: ML
authors: Thakur
authors: Eric
authors: E
authors: Wickstrom
mesh_terms: D000225:Adenine / Q000737:chemistry; D000465:Algorithms; D020029:Base Pairing; D002942:Circular Dichroism; D006147:Guanine / Q000737:chemistry; D006801:Humans; D019271:Hypoxanthine / Q000138:chemical synthesis / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009691:Nucleic Acid Denaturation; D020135:Peptide Nucleic Acids / Q000138:chemical synthesis / Q000737:chemistry*; D017354:Point Mutation; D011518:Proto-Oncogene Proteins / Q000737:chemistry / Q000235:genetics*; D016283:Proto-Oncogene Proteins p21(ras); D012333:RNA, Messenger / Q000737:chemistry*; D044366:Transition Temperature; D014498:Uracil / Q000737:chemistry; D018631:ras Proteins / Q000737:chemistry / Q000235:genetics*
chemical_list: C117307:KRAS protein, human; D020135:Peptide Nucleic Acids; D011518:Proto-Oncogene Proteins; D012333:RNA, Messenger; D019271:Hypoxanthine; D014498:Uracil; D006147:Guanine; D016283:Proto-Oncogene Proteins p21(ras); D018631:ras Proteins; D000225:Adenine
references: J Nucl Med. 2004 Dec;45(12):2070-82
references: 15585484
references: FEBS J. 2005 Aug;272(16):4055-70
references: 16098189
references: Science. 1997 Jul 18;277(5324):333-8
references: 9219684
references: Curr Opin Chem Biol. 2006 Dec;10(6):622-7
references: 17035074
references: Nat Rev Mol Cell Biol. 2008 Jul;9(7):517-31
references: 18568040
references: Phys Chem Chem Phys. 2011 Dec 7;13(45):20053-65
references: 22015376
references: Ann N Y Acad Sci. 2005 Nov;1059:106-44
references: 16382049
references: Eur J Radiol. 2009 May;70(2):265-73
references: 19264436
references: J Chem Theory Comput. 2012 May 8;8(5):1542-1555
references: 22582031
references: Chem Biodivers. 2010 Apr;7(4):786-804
references: 20397216
references: Curr Protoc Nucleic Acid Chem. 2001 May;Chapter 7:Unit 7.1
references: 18428868
references: Curr Med Chem. 2005;12(1):71-88
references: 15638731
references: J Phys Chem B. 2011 Jan 27;115(3):532-46
references: 21192664
references: Cancer Biol Ther. 2007 Jun;6(6):948-56
references: 17611392
references: Science. 1994 Aug 5;265(5173):777-80
references: 7519361
references: Biophys Chem. 1994 Aug;51(2-3):397-403; discussion 404-9
references: 7919044
references: J Phys Chem B. 2006 Nov 16;110(45):22695-701
references: 17092018
references: Nat Rev Cancer. 2011 Oct 13;11(11):761-74
references: 21993244
references: Phys Chem Chem Phys. 2012 Feb 28;14(8):2743-53
references: 22270716
references: J Cell Biol. 2012 Jan 23;196(2):189-201
references: 22270915
references: J Comput Chem. 2004 Jan 30;25(2):238-50
references: 14648622
references: Nature. 1993 Oct 7;365(6446):566-8
references: 7692304
references: J Nucl Med. 2007 Oct;48(10):1699-707
references: 17909257
references: Phys Chem Chem Phys. 2010 Jul 28;12(28):7821-39
references: 20574571
references: Nucleic Acids Res. 1985 Dec 20;13(24):8927-38
references: 4080553
references: Mol Aspects Med. 2000 Dec;21(6):167-223
references: 11173079
references: Biopolymers. 1999 Oct 5;50(4):373-80
references: 10423546
references: J Comput Chem. 2011 May;32(7):1431-40
references: 21284003
references: J Mol Graph. 1996 Feb;14(1):33-8, 27-8
references: 8744570
references: J Am Chem Soc. 2008 Oct 8;130(40):13264-73
references: 18781753
references: Proteins. 2010 May 15;78(7):1705-23
references: 20186976
references: J Chem Phys. 2004 Jun 22;120(24):11919-29
references: 15268227
references: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W511-7
references: 21609950
references: J Chem Phys. 2007 Oct 21;127(15):155102
references: 17949218
references: Cell. 1991 Jan 25;64(2):235-48
references: 1988146
references: Nucleic Acids Res. 1994 Dec 11;22(24):5218-22
references: 7816609
references: Biophys J. 2006 Oct 15;91(8):2798-814
references: 16844742
references: Bioconjug Chem. 1994 Jan-Feb;5(1):3-7
references: 8199231
references: Nucleic Acids Res. 2009 Sep;37(17):5917-29
references: 19625494
references: Ann Genet. 2004 Oct-Dec;47(4):349-58
references: 15581832
references: Q Rev Biophys. 2012 Feb;45(1):1-25
references: 22082669
references: J Mol Biol. 1966 Aug;19(2):548-55
references: 5969078
references: Nucleic Acids Res. 2005 Nov 01;33(19):6258-67
references: 16264087
references: Chem Biol. 2012 Jan 27;19(1):60-71
references: 22284355
references: Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12021-6
references: 14512516
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D360-7
references: 17962302
references: Org Biomol Chem. 2013 Apr 14;11(14):2310-7
references: 23423157
references: Biopolymers. 2007 Feb 5;85(2):169-84
references: 17080418
references: Oligonucleotides. 2003;13(6):515-37
references: 15025917
references: Org Lett. 2002 Nov 14;4(23):4013-6
references: 12423074
references: Nat Rev Genet. 2006 Dec;7(12):958-65
references: 17139327
references: J Comput Aided Mol Des. 2010 Aug;24(8):639-58
references: 20509041
references: Curr Opin Struct Biol. 2007 Apr;17(2):187-91
references: 17382533
references: Bioconjug Chem. 2010 Apr 21;21(4):731-40
references: 20232877
references: J Chem Inf Model. 2011 Jan 24;51(1):69-82
references: 21117705
references: Chem Rev. 2006 Feb;106(2):302-23
references: 16464007
references: Acc Chem Res. 2000 Dec;33(12):889-97
references: 11123888
references: Curr Pharm Des. 2010;16(28):3118-23
references: 20687874
references: Nucleic Acids Res. 1997 Oct 15;25(20):4117-22
references: 9321667
references: Biopolymers. 2000-2001;56(4):232-56
references: 11754338
references: Nat Struct Biol. 1997 Feb;4(2):98-101
references: 9033585
references: J Comput Chem. 2003 Dec;24(16):1999-2012
references: 14531054