NMR Studies of DNA Duplexes Singly Cross-linked by Different Synthetic Linkers

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1995 Dec 11

PMID 8532525

Citations 10

Authors

S Altmann

A M Labhardt

D Bur

C Lehmann

W Bannwarth

M Billeter

K Wuthrich

W Leupin

Affiliations

Soon will be listed here.

Abstract

Molecular modelling studies resulted in the design of a variety of non-nucleotidic covalent linkers to bridge the 3'-end of the (+)-strand and the 5'-end of the (-)-strand in DNA duplexes. Three of these linkers were synthesized and used to prepare singly cross-linked duplexes d(GTGGAATTC)-linker-d(GAATTCCAC). Linker I is an assembly of a propylene-, a phosphate- and a second propylene-group and is thought to mimic the backbone of two nucleotides. Linkers II and III consist of five and six ethyleneglycol units, respectively. The melting temperatures of the cross-linked duplexes are 65 degrees C for I and 73 degrees C for II and III, as compared with 36 degrees C for the corresponding non-linked nonadeoxynucleotide duplex. The three cross-linked duplexes were structurally characterized by nuclear magnetic resonance spectroscopy. The 1H and 31P resonance assignments in the DNA stem were obtained using standard methods. For the resonance assignment of the linker protons, two-dimensional 1H-31P heteronuclear COSY and two-quantum-experiments were used. Distance geometry calculations with NOE-derived distance constraints were performed and the resulting structures were energy-minimized. In duplex I, the nucleotides flanking the propylene-phosphate-propylene-linker do not form a Watson-Crick base pair, whereas in duplexes II and III the entire DNA stem is in a B-type double helix conformation.

Citing Articles

Enzyme-free ligation of dimers and trimers to RNA primers.

Sosson M, Pfeffer D, Richert C Nucleic Acids Res. 2019; 47(8):3836-3845.

PMID: 30869145 PMC: 6486630. DOI: 10.1093/nar/gkz160.

Enzyme-free genetic copying of DNA and RNA sequences.

Sosson M, Richert C Beilstein J Org Chem. 2018; 14:603-617.

PMID: 29623122 PMC: 5870163. DOI: 10.3762/bjoc.14.47.

Stabilization of RNA hairpins using non-nucleotide linkers and circularization.

Kiliszek A, Blaszczyk L, Kierzek R, Rypniewski W Nucleic Acids Res. 2017; 45(10):e92.

PMID: 28334744 PMC: 5449636. DOI: 10.1093/nar/gkx122.

Characterization of Interstrand DNA-DNA Cross-Links Using the α-Hemolysin Protein Nanopore.

Zhang X, Price N, Fang X, Yang Z, Gu L, Gates K ACS Nano. 2015; 9(12):11812-9.

PMID: 26563913 PMC: 4826734. DOI: 10.1021/acsnano.5b03923.

A simple, high-yield synthesis of DNA duplexes containing a covalent, thermally cleavable interstrand cross-link at a defined location.

Gamboa Varela J, Gates K Angew Chem Int Ed Engl. 2015; 54(26):7666-9.

PMID: 25967397 PMC: 4532324. DOI: 10.1002/anie.201502566.

References

Guntert P, Braun W, Wuthrich K . Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J Mol Biol. 1991; 217(3):517-30. DOI: 10.1016/0022-2836(91)90754-t. View

Cowart M, Benkovic S . A novel combined chemical-enzymatic synthesis of cross-linked DNA using a nucleoside triphosphate analogue. Biochemistry. 1991; 30(3):788-96. DOI: 10.1021/bi00217a032. View

Maurizot J, Chevrie K, Durand M, Thuong N . The lac repressor and its N-terminal headpiece can bind a mini-operator containing a hairpin loop made of a hexaethylene glycol chain. FEBS Lett. 1991; 288(1-2):101-4. DOI: 10.1016/0014-5793(91)81012-w. View

Blommers M, van de Ven F, van der Marel G, VAN Boom J, Hilbers C . The three-dimensional structure of a DNA hairpin in solution two-dimensional NMR studies and structural analysis of d(ATCCTATTTATAGGAT). Eur J Biochem. 1991; 201(1):33-51. DOI: 10.1111/j.1432-1033.1991.tb16253.x. View

Antao V, Lai S, Tinoco Jr I . A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res. 1991; 19(21):5901-5. PMC: 329045. DOI: 10.1093/nar/19.21.5901. View

Fede A, LABHARDT A, Bannwarth W, Leupin W . Dynamics and binding mode of Hoechst 33258 to d(GTGGAATTCCAC)2 in the 1:1 solution complex as determined by two-dimensional 1H NMR. Biochemistry. 1991; 30(48):11377-88. DOI: 10.1021/bi00112a004. View

Berman H, Olson W, Beveridge D, Westbrook J, Gelbin A, Demeny T . The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J. 1992; 63(3):751-9. PMC: 1262208. DOI: 10.1016/S0006-3495(92)81649-1. View

Ma M, Reid L, Climie S, Lin W, Kuperman R, Barnett R . Design and synthesis of RNA miniduplexes via a synthetic linker approach. Biochemistry. 1993; 32(7):1751-8. DOI: 10.1021/bi00058a008. View

Doktycz M, Paner T, Benight A . Studies of DNA dumbbells. IV. Preparation and melting of a DNA dumbbell with the 16 base-pair sequence 5'G-T-A-T-C-C-C-T-C-T-G-G-A-T-A-C3' linked on the ends by dodecyl chains. Biopolymers. 1993; 33(12):1765-77. DOI: 10.1002/bip.360331203. View

10.

Mooren M, Pulleyblank D, Wijmenga S, van de Ven F, Hilbers C . The solution structure of the hairpin formed by d(TCTCTC-TTT-GAGAGA). Biochemistry. 1994; 33(23):7315-25. DOI: 10.1021/bi00189a037. View

11.

Cain R, Zuiderweg E, Glick G . Solution structure of a DNA hairpin and its disulfide cross-linked analog. Nucleic Acids Res. 1995; 23(12):2153-60. PMC: 307002. DOI: 10.1093/nar/23.12.2153. View

12.

Gerber P, Muller K . MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry. J Comput Aided Mol Des. 1995; 9(3):251-68. DOI: 10.1007/BF00124456. View

13.

Hare D, Wemmer D, Chou S, Drobny G, Reid B . Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) using two-dimensional nuclear magnetic resonance methods. J Mol Biol. 1983; 171(3):319-36. DOI: 10.1016/0022-2836(83)90096-7. View

14.

Rance M, Sorensen O, Bodenhausen G, Wagner G, Ernst R, Wuthrich K . Improved spectral resolution in cosy 1H NMR spectra of proteins via double quantum filtering. Biochem Biophys Res Commun. 1983; 117(2):479-85. DOI: 10.1016/0006-291x(83)91225-1. View

15.

Feigon J, Leupin W, Denny W, Kearns D . Two-dimensional proton nuclear magnetic resonance investigation of the synthetic deoxyribonucleic acid decamer d(ATATCGATAT)2. Biochemistry. 1983; 22(25):5943-51. DOI: 10.1021/bi00294a038. View

16.

SKLENAR V, Miyashiro H, Zon G, Miles H, Bax A . Assignment of the 31P and 1H resonances in oligonucleotides by two-dimensional NMR spectroscopy. FEBS Lett. 1986; 208(1):94-8. DOI: 10.1016/0014-5793(86)81539-3. View

17.

Otting G, Grutter R, Leupin W, Minganti C, Ganesh K, Sproat B . Sequential NMR assignments of labile protons in DNA using two-dimensional nuclear-Overhauser-enhancement spectroscopy with three jump-and-return pulse sequences. Eur J Biochem. 1987; 166(1):215-20. DOI: 10.1111/j.1432-1033.1987.tb13504.x. View

18.

Grutter R, Otting G, Wuthrich K, Leupin W . OR3 operator of bacteriophage lambda in a 23 base-pair DNA fragment: sequence-specific 1H NMR assignments for the non-labile protons and comparison with the isolated 17 base-pair operator. Eur Biophys J. 1988; 16(5):279-86. DOI: 10.1007/BF00254064. View

19.

Billeter M, Kline A, Braun W, Huber R, Wuthrich K . Comparison of the high-resolution structures of the alpha-amylase inhibitor tendamistat determined by nuclear magnetic resonance in solution and by X-ray diffraction in single crystals. J Mol Biol. 1989; 206(4):677-87. DOI: 10.1016/0022-2836(89)90575-5. View

20.

Rinkel L, Altona C . Conformational analysis of the deoxyribofuranose ring in DNA by means of sums of proton-proton coupling constants: a graphical method. J Biomol Struct Dyn. 1987; 4(4):621-49. DOI: 10.1080/07391102.1987.10507665. View