Invader LNA: efficient targeting of short double stranded DNA.
Despite progress with triplex-forming oligonucleotides or helix-invading peptide nucleic acids (PNAs), there remains a need for probes facilitating sequence-unrestricted targeting of double stranded DNA (dsDNA) at physiologically relevant conditions. Invader LNA probes, i.e., DNA duplexes with "+1 interstrand zipper arrangements" of intercalator-functionalized 2'-amino-alpha-l-LNA monomers, are demonstrated herein to recognize short mixed sequence dsDNA targets. This approach, like pseudo-complementary PNA (pcPNA), relies on relative differences in stability between probe duplexes and the corresponding probe:target duplexes for generation of a favourable thermodynamic gradient. Unlike pcPNA, Invader LNA probes take advantage of the "nearest neighbour exclusion principle", i.e., intercalating units of Invader LNA monomers are poorly accommodated in probe duplexes but extraordinarily well tolerated in probe-target duplexes (DeltaT(m)/modification up to +11.5 degrees C). Recognition of isosequential dsDNA-targets occurs: a) at experimental temperatures much lower than the thermal denaturation temperatures (T(m)'s) of Invader LNAs or dsDNA-targets, b) at a wide range of ionic strengths, and c) with good mismatch discrimination. Recognition of dsDNA is monitored in real-time using inherent pyrene-pyrene excimer signals of Invader LNA probes, which provides insights into reaction kinetics and enables rational design of probes. These properties render Invader LNAs as promising probes for biomedical applications entailing sequence-unrestricted recognition of dsDNA.
Sau
Sujay P
SP
Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA.
Kumar
T Santhosh
TS
Hrdlicka
Patrick J
PJ
D004247:DNA / Q000737:chemistry*; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D015345:Oligonucleotide Probes / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
D015345:Oligonucleotide Probes; D009841:Oligonucleotides; C477371:locked nucleic acid; D004247:DNA
Nucleic Acids Res. 2005 Oct 04;33(17):e146
16204449
Curr Pharm Des. 2005;11(28):3671-80
16305503
Chem Biol. 2004 Jun;11(6):749-58
15217608
Org Biomol Chem. 2008 Nov 21;6(22):4212-7
18972052
Chem Commun (Camb). 2009 Nov 28;(44):6756-8
19885469
Nucleic Acids Res. 2003 Jun 15;31(12):3267-73
12799454
Chembiochem. 2007 Dec 17;8(18):2240-8
17979173
Q Rev Biophys. 2005 Nov;38(4):311-20
16737560
J Org Chem. 2006 May 26;71(11):4188-201
16709060
J Biol Chem. 2001 Jan 26;276(4):2354-60
11035027
J Mol Biol. 2000 Mar 24;297(2):511-20
10715217
J Org Chem. 2008 Sep 19;73(18):7060-6
18710289
Chem Commun (Camb). 2004 Dec 21;(24):2792-3
15599409
Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5953-8
11972051
Chem Commun (Camb). 2005 Sep 14;(34):4279-81
16113721
Chem Commun (Camb). 2004 Jul 7;(13):1478-9
15216339
Nucleic Acids Res. 2008 Sep;36(16):5123-38
18676453
Curr Med Chem Anticancer Agents. 2005 Jul;5(4):373-87
16101489
Biochemistry. 1996 Aug 27;35(34):11170-6
8780521
Proc Natl Acad Sci U S A. 1999 Oct 12;96(21):11804-8
10518531
Chembiochem. 2008 Oct 13;9(15):2388-91
18816545
Biochemistry. 2007 Jun 26;46(25):7581-9
17536840
J Am Chem Soc. 2002 Oct 30;124(43):12676-7
12392411
Nucleosides Nucleotides Nucleic Acids. 2007;26(10-12):1415-7
18066795
Chembiochem. 2007 Jul 9;8(10):1122-5
17551917
Nucleic Acids Res. 2007;35(22):7604-13
17977869
Nucleic Acids Res. 2005 May 23;33(9):3025-32
15911633
Curr Med Chem Anticancer Agents. 2005 Jul;5(4):319-26
16101484
Chem Commun (Camb). 2004 May 7;(9):1064-5
15116186
Biochemistry. 2000 Sep 5;39(35):10908-13
10978178
Biochimie. 2008 Aug;90(8):1109-16
18460344
J Am Chem Soc. 2008 Jun 4;130(22):6904-5
18473465
J Am Chem Soc. 2007 Dec 19;129(50):15596-600
18027941
Biochemistry. 2004 Apr 13;43(14):4160-9
15065859
J Am Chem Soc. 2005 Oct 26;127(42):14849-58
16231939
Nucleic Acids Res. 2005 Mar 03;33(4):1362-71
15745996
Biopolymers. 1968 Apr;6(4):575-84
5644787
Chembiochem. 2003 Sep 5;4(9):841-7
12964158
Biochemistry. 2007 Jun 26;46(25):7572-80
17536839
Nucleic Acids Res. 1996 Jul 1;24(13):2470-5
8692683
Curr Drug Targets. 2004 Nov;5(8):691-703
15578950
J Biol Chem. 2005 May 20;280(20):20076-85
15760901
J Am Chem Soc. 2008 Apr 9;130(14):4886-96
18341342
Chem Commun (Camb). 2005 May 21;(19):2509-11
15886787
Mol Biosyst. 2006 Nov;2(11):551-60
17216036
Chembiochem. 2004 Dec 3;5(12):1673-9
15532065
Oligonucleotides. 2003;13(6):515-37
15025917
Nat Chem Biol. 2005 Sep;1(4):210-5
16408037
Nucleic Acids Res. 1993 Dec 11;21(24):5630-5
8284208
J Org Chem. 2009 Feb 6;74(3):1070-81
19108636
Nucleic Acids Res. 2008 Mar;36(5):1464-71
18203747
Nucleic Acids Res. 2005 Dec 23;33(22):7129-37
16377781
Nucleic Acids Res. 1996 Jun 1;24(11):2143-9
8668547
Nucleic Acids Res. 1999 Apr 15;27(8):1802-9
10101187
FASEB J. 2007 Jun;21(8):1902-14
17314142
Biochemistry. 2008 Dec 16;47(50):13147-9
19053275
J Am Chem Soc. 2006 Jan 11;128(1):14-5
16390098