Abstract
In addition to noncovalent interactions, metal ligation and disulfide cross-linking are often used by proteins to achieve and maintain their three-dimensional structure. Another class of biologically important macro-molecules, nucleic acids, possess the functionality required for hydrophobic packing and metal chelation, but lack the sulfhydryl groups that are necessary for disculfide cross-linking. Hence, the limited repertoire of atoms in nucleic acids deprives them of a molecular device — the disulfide cross-link — that is widely employed by proteins to control macromolecular structure, dynamics, stability, and perhaps folding. Nonetheless, recent advances in the chemical synthesis of modified nucleic acids have made it possible to overcome this deficiency by allowing attachment of sulfhydryl groups to specific bases in DNA and RNA. Having surmounted the initial obstacle imposed by nature, we have begun to explore the structure and applications of disulfide cross-linked nucleic acids. This new field is just now taking its first, halting steps, as reviewed here, but the results thus far point toward a rich and exciting future.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Anderson JE, Ptashne M, Harrison SC (1987) Structure of the repressor-operator complex of bacteriophage 434. Nature 326:846–852
Beaucage SL, Iyer RP (1993) The synthesis of modified oligonucleotides by the phosphoramidite approach and their applications. Tetrahedron 49:6123–6194
Bracco L, Kotlarz D, Kolb A, Diekmann S, Bue H (1989) Synthetic curved sequences can act as transcriptional activators in Escherichia coli. EMBO J 8:4289–4296
Brünger AT (1992) X-PLOR (Version 3.0) Manual, Yale University, New Haven
Chen L, MacMillan AM, Chang W, Ezaz-Nikpay K, Lane WS, Verdine GL (1991) Direct identification of the active-site nucleophile in a DNA (cytosine-5)-methyltransferase. Biochemistry 30:11018–11025
Connolly BA, Rider P (1985) Chemical synthesis of oligonucleotides containing a free sulphydryl group and subsequent attachment of thiol specific probes. Nucleic Acids Res 13:4485–4502
Cowart M, Benkovic SJ (1991) A novel combined chemical-enzymatic synthesis of cross-linked DNA using a nucleoside triphosphate analogue. Biochemistry 30:788–796
Cowart M, Gibson KJ, Allen CJ, Benkovic SJ (1989) DNA substrate structural requirements for the exonuclease and polymerase activities of procaryotic and phage DNA polymerases. Biochemistry 28:1975–1983
Cox MM, Lehman IR (1987) Enzymes of general recombination. Annu Rev Biochem 56:229–262
Engel JD, von Hippel PH (1974) Effects of methylation on the stability of nucleic acid conformations: studies at the monomer level. Biochemistry 13:4143–4158
Engel JD, von Hippel PH (1978) Effects of methylation on the stability of nucleic acid conformations. J Biol Chem 253:927–934
Erlanson DA, Chen L, Verdine GL (1993) Allosteric effects on enzyme action in disulfide cross-linked DNA. J Am Chem Soc (in press)
Farrell N, Qu Y, Feng L, Van Houten B (1990) Comparison of chemical reactivity, cytotoxicity, interstrand cross-linking and DNA sequence specificity of bis(platinum) complexes containing monodentate or bidentate coordination spheres with their monomeric analogues. Biochemistry 29:9522–9531
Ferentz AE, Verdine GL (1991) Disulfide cross-linked oligonucleotides. J Am Chem Soc 113:4000–4002
Ferentz AE, Verdine GL (1992) Aminoiysis of 2′-deoxyinosine aryl ethers: nucleoside model studies for the synthesis of functionally tethered oligonucleotides. Nucleosides Nucleotides 11:1749–1763
Ferentz AE, Wiorkiewicz-Kuczera J, Karplus M, Verdine GL (1993a) Molecular dynamics simulations of disulfide cross-linked DNA decamers. J Am Chem Soc 115:7569–7583
Ferentz AE, Keating TA, Verdine GL (1993b) Synthesis and characterization of disulfide cross-linked oligonucleotides. J Am Chem Soc 115:9006–9014
Fidanza JA, McLaughlin LW (1992) Use of a thiol tether for the site-specific attachment of reporter groups to DNA. J Org Chem 57:2340–2346
Frederick CA, Quigley GJ, van der Marel GA, van Boom JH, Wang AH-J, Rich A (1988) Methylation of the Eco RI recognition site does not alter DNA conformation: the crystal structure of d(CGCGAm6ATTCGCG) at 2.0 Å resolution. J Biol Chem 263:17872–17879
Gamper H, Piette J, Hearst JE (1984) Efficient formation of a cross-linkable HMT monoadduct at the Kpn I recognition site. Photochem Photobiol 40:29–34
Gartenberg MR, Crothers DM (1991) Synthetic DNA bending sequences increase the rate of in vitro transcription initiation at the Escherichia coli lac promoter. J Mol Biol 219:217–230
Glick GD (1991) Synthesis of a conformationally restricted DNA hairpin. J Org Chem 56:6746–6747
Glick GD, Osborne SE, Knitt DS, Marino JP Jr (1992) Trapping and isolation of an alternate DNA conformation. J Am Chem Soc 114:5447–5448
Glück A, Endo Y, Wool IR (1992) Ribosomal RNA identity elements for ricin A-chain analysis with tetraloop mutants. J Mol Biol 226:411–426
Goodchild J (1990) Conjugates of oligonucleotides and modified oligonucleotides: a review of their synthesis and properties. Bioconj Chem 1:165–187
Goodman SD, Nash H (1989) Functional replacement of a protein-induced bend in a DNA recombination site. Nature 341:251–254
Harris CM, Zhou L, Strand EA, Harris TM (1991) New strategy for the synthesis of oligodeoxynucleotides bearing adducts at exocyclic amine sites of purine nucleosides. J Am Chem Soc 113:4328–4329
Huang H, Solomon MS, Hopkins PB (1992) Formaldehyde preferentially interstrand cross-links duplex DNA through deoxyadenosine residues at the sequence 5′-d(AT). J Am Chem Soc 114:9240–9241
Kirchner JJ, Sigurdsson ST, Hopkins PB (1992) Interstrand cross-linking of duplex DNA by nitrous acid: covalent structure of the dG-to-dG cross-link at the sequence 5′-CG. J Am Chem Soc 114:4012–4027
Koo H-S, Wu H-M, Crothers DM (1986) DNA bending at adenine thymine tracts. Nature 320:501–506
Larson CJ, Verdine GL (1992) A high-capacity column for affinity purification of sequence-specific DNA-binding proteins. Nucleic Acids Res 20:3525
Lavery R, Sklenar H (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J Biomol Str Dyn 6:63–91
Lemaire M-A, Schwartz A, Rahmouni AR, Leng M (1991) Proc Natl Acad Sci USA 88:1982–1985
Lesser DR, Kurpiewski MR, Jen-Jacobson L (1990) The energetic basis of specificity in the Eco RI endonuclease-DNA interaction. Science 250:776–786
MacMillan AM, Verdine GL (1990) Synthesis of functionally tethered oligodeoxynucleotides by the convertible nucleoside approach. J Org Chem 55:5931–5933
MacMillan AM, Verdine GL (1991) Engineering tethered DNA molecules by the convertible nucleoside approach. Tetrahedron 47:2603–2616
MacMillan AM, Lee RJ, Verdine GL (1993) Direct observation of a specific contact in the λ repressor-OL1 complex by isotope-edited NMR. J Am Chem Soc 115:4921–4922
Matteucci MD, Webb TR (1987) Synthesis and crosslinking properties of a deoxyoligonucleotide containing N 6,N 6-ethanodeoxyadenosine. Tetrahedron Lett 28:2469–2472
McClure WR (1985) Mechanism and control of transcription initiation in prokaryotes. Annu Rev Biochem 54:171–204
Meyer RB Jr, Tabone JC, Hurst GD, Smith TM, Gamper HJ (1989) Efficient specific cross-linking and cleavage of DNA by stable, synthetic complementary oligodeoxynucleotides. J Am Chem Soc 111:8517–8519
Millard JT, White MM (1993) Diepoxybutane cross-links DNA at 5′-GNC sequences. Biochemistry 32:2120–2124
Millard JT, Raucher S, Hopkins PB (1990) Mechlorethamine cross-links deoxyguanosine residues at 5′-GNC sequences in duplex DNA fragments. J Am Chem Soc 112: 2459–2460
Milton J, Connolly B, Nikiforov TT, Cosstick R (1993) Site-specific disulfide bridges in oligodeoxynucleotide duplexes containing 6-mercaptopurine and 4-thiothymidine bases. J Chem Soc Chem Commun 779–780
Nossal NG (1983) Procaryotic DNA replication systems. Annu Rev Biochem 52:581–615
Patel DJ, Pardi A, Itakura K (1982) DNA conformation, dynamics, and interactions in solution. Science 216:581–590
Ravishanker G, Swaminathan S, Beveridge DL, Lavery R, Sklenar H (1989) Conformational and helicoidal analysis of 30 ps of molecular dynamics on the d(CGCGAA-TTCGCG) double helix: “curves”, dials and windows. J Biomol Str Dyn 6:669–699
Sancar A, Hearst JE (1993) Molecular matchmakers. Science 259:1415–1420
Santi DV, Garrett CE, Barr PJ (1983) On the mechanism of inhibition of DNA-cytosine methyltransferases by cytosine analogs. Cell 33:9–10
Schultz SC, Shields GC, Steitz TA (1991) Crystal structure of a CAP-DNA complex: the DNA is bent by 90°. Science 253:1001–1007
Shi Y, Gamper H, Hearst JE (1988) Interaction of T7 RNA polymerase with DNA in an elongation complex arrested at a specific psoralen adduct site. J Biol Chem 263:527–534
Steitz TA (1990) Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding. Q Rev Biophys 23:205–280
Stevens SY, Swanson PC, Voss EW Jr, Glick GD (1993) Evidence for induced fit in antibody DNA complexes. J Am Chem Soc 115:1584–1586
Tomasz M, Lipman R, Chowdary D, Pawlak J, Verdine GL, Nakanishi K (1987) Isolation and structure of a covalent cross-link adduct between mitomycin C and DNA. Science 235:1204–1208
Tomic MT, Wemmer DE, Kim S-H (1987) Structure of a psoralen cross-linked DNA in solution by nuclear magnetic resonance. Science 238:1722–1725
Travers AA (1989) DNA conformation and protein binding. Annu Rev Biochem 58: 427–452
von Hippel PH, Bear DG, Morgan WD, McSwiggen JA (1984) Protein-nucleic acid interactions in transcription: a molecular analysis. Annu Rev Biochem 53:389–446
Webb TR, Matteucci MD (1986a) Sequence-specific cross-linking of deoxyoligonucleotides via hybridization-triggered alkylation. J Am Chem Soc 108:2764–2765
Webb TR, Matteucci MD (1986b) Hybridization triggered cross-linking of deoxyoligonucleotides. Nucleic Acids Res 14:7661–7674
Weidner MF, Millard JT, Hopkins PB (1989) Sequence preferences of DNA interstrand cross-linking agents: dG-to-dG cross-linking at 5′-CG by structurally simplified analogues of mitomycin C. J Am Chem Soc 111:9270–9272
Winkler FK, Banner DW, Oefner C, Tsernoglou D, Brown RS, Heathman SP, Bryan RK, Martin PD, Petratos K, Wilson KS (1993) The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J 12:1781–1795
Wolfe SA, Verdine GL (1993) Ratcheting torsional stress in duplex DNA. J Am Chem Soc (in press)
Wolfe SA, Ferentz AE, Grantcharova V, Verdine GL (1993) Changing the structure of DNA from linear to bent (submitted)
Woo J, Sigurdsson ST, Hopkins PB (1993) DNA interstrand cross-linking by reductively activated FR900482 and FR66979. J Am Chem Soc 115:1199–1200
Wu JC, Santi DV (1987) Kinetic and catalytic mechanism of Hha I methyltransferase. J Biol Chem 262:4778–4786
Zhou X-X, Chattopadhyaya J (1986) Site-specific modification of the pyrimidine residue during the deprotection of the fully protected diuridylic acid. Tetrahedron 42:5149–5156
Zuckermann RN, Corey D, Schultz PG (1987) Efficient methods for attachment of thiol specific probes to the 3′-ends of synthetic oligodeoxynucleotides. Nucleic Acids Res 15:5305–5353
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1994 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Ferentz, A.E., Verdine, G.L. (1994). The Convertible Nucleoside Approach: Structural Engineering of Nucleic Acids by Disulfide Cross-Linking. In: Eckstein, F., Lilley, D.M.J. (eds) Nucleic Acids and Molecular Biology. Nucleic Acids and Molecular Biology, vol 8. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-78666-2_2
Download citation
DOI: https://doi.org/10.1007/978-3-642-78666-2_2
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-78668-6
Online ISBN: 978-3-642-78666-2
eBook Packages: Springer Book Archive