Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2′-deoxyadenosine

Nucleic Acids Research

Volumn 32, Issue 7, 2004, Pages 2241-2250

  Hendrickson, Cynthia L ^a,c   Devine, Kevin G ^a,b   Benner, Steven A ^a  

^a University of Florida   (United States)

^b UNIVERSITY COLLEGE DUBLIN   (Ireland)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

3 DEAZAADENOSINE; ADENINE; CYTOSINE; DEOXYADENOSINE; DEOXYRIBONUCLEOTIDE; EXONUCLEASE; GUANINE; HYDROGEN; NUCLEIC ACID BASE; OLIGONUCLEOTIDE; PRIMER DNA; RNA DIRECTED DNA POLYMERASE; THYMINE; 2'-DEOXYADENOSINE TRIPHOSPHATE; 3 DEAZA 2' DEOXYADENOSINE; 3-DEAZA-2'-DEOXYADENOSINE; DEOXYADENOSINE PHOSPHATE; DEOXYADENOSINE TRIPHOSPHATE; DNA; DNA DIRECTED DNA POLYMERASE; DRUG DERIVATIVE; TUBERCIDIN;

ARTICLE; CONTROLLED STUDY; CRYSTALLOGRAPHY; DNA HELIX; ENZYME ACTIVITY; ENZYME SPECIFICITY; HYDROGEN BOND; MOLECULAR RECOGNITION; PLASTICITY; PRIORITY JOURNAL; BASE MISPAIRING; BINDING SITE; CHEMISTRY; CLASSIFICATION; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE;

BASE PAIR MISMATCH; BASE SEQUENCE; BINDING SITES; DEOXYADENINE NUCLEOTIDES; DNA; DNA-DIRECTED DNA POLYMERASE; EXONUCLEASES; RNA-DIRECTED DNA POLYMERASE; SUBSTRATE SPECIFICITY; TUBERCIDIN;

EID: 2342572250     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh542     Document Type: Article

References (32)

1. Switzer,C.Y., Moroney,S.E. and Benner,S.A. (1989) Enzymatic incorporation of a new base pair into DNA and RNA. J. Am. Chem. Soc., 111, 8322-8323.
2. Kool,E.T. (2000) Roles of Watson-Crick and minor groove hydrogen bonds in DNA replication. Cold Spring Harb. Symp. Quant. Biol., 63, 93-102.
3. McMinn,D.L., Ogawa,A.K., Wu,Y., Liu,J., Schultz,P.G. and Romesberg,F.E. (1999) Efforts toward expansion of the genetic alphabet: DNA polymerase recognition of a highly stable self-pairing hydrophobic base. J. Am. Chem. Soc., 121, 11585-11586.
4. Geyer,C.R., Battersby,T.R. and Benner,S.A. (2003) Rules for designing artificial genetic systems. The nucleobases. Structure, 11, 1485-1498.
5. Benner,S.A. (2003) Synthetic biology. Nature, 421, 118.
6. Seeman,N.C. Rosenberg,J.M. and Rich,A. (1976) Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl Acad. Sci. USA, 73, 804-808.
7. Eom,S.H., Wang,J. and Steitz,T.A. (1996) Structure of Taq polymerase with DNA at the polymerase active site. Nature, 382, 278-281.
8. Li,Y., Korolev,S. and Waksman,G. (1998) Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. EMBO J., 17, 7514-7525.
9. Kiefer,J.R., Mao,C., Braman,J.C. and Beese,L.S. (1998) Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature, 391, 304-307.
10. Franklin,M.C., Wang,J.M. and Steitz,T.A. (2001) Structure of the replicating complex of a Pol alpha family DNA polymerase. Cell, 105, 657-667.
11. Braithwaite,D.K. and Ito,J. (1993) Compilation, alignment and phylogenetic relationships of DNA polymerases. Nucleic Acids Res., 21, 787-802.
12. Singh,K. and Modak,M.J. (2003) Presence of 18-Å long hydrogen bond track in the active site of Escherichia coli DNA polymerase I (Klenow fragment). J. Biol. Chem., 278, 11289-11302.
13. Spratt,T.E. (2001) Identification of hydrogen bonds between Escherichia coli DNA polymerase I (Klenow Fragment) and the minor groove of DNA by amino acid substitution of the polymerase and atomic substitution of the DNA. Biochemistry, 40, 2647-2652.
14. Thompson,E.H.Z., Bailey,M.F., van der Schans,E.J.C., Joyce,C.M. and Millar,D.P. (2002) Determinants of DNA mismatch recognition within the polymerase domain of the Klenow fragment. Biochemistry, 41, 713-722.
15. Wang,J., Sattar,A.K.M.A., Wang,C.C., Karam,J.D., Konigsberg,W.H. and Steitz,T.A. (1997) Crystal structure of a pol α family replication DNA polymerase from bacteriophage RB69. Cell, 89, 1087-1099.
16. Joyce,C.M. and Steitz,T.A. (1994) Function and structure relationships in DNA polymerases. Annu. Rev. Biochem., 63, 777-822.
17. Patel,P.H. and Loeb,L.L. (2001) Getting a grip on how DNA polymerases function. Nature Struct. Biol., 8, 656-659.
18. Steitz,T.A., Smerdon,S., Jäger,J., Wang,J., Kohlstaedt,L.A., Friedman,J.M., Beese,L.S. and Rice,P.A. (1993) Two DNA polymerases: HIV reverse transcriptase and the Klenow fragment of Escherichia coli DNA polymerase I. Cold Spring Harb. Symp. Quant. Biol., 58, 495-504.
19. Huang,H., Chopra,R., Verdine,G.L. and Harrison,S.C. (1998) Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science, 282, 1669-1675.
20. Jacobo-Molina,A., Ding,J., Nanni,R.G., Clark,A.D.,Jr, Lu,X., Tantillo,C., Williams,R.L., Kamer,G., Ferris,A.L., Clark,P., Hizi,A.; Hughes,S.H. and Arnold,E. (1990) Crystal structure of human immunodeficiency virus Type-1 reverse transcriptase complexed with double-stranded DNA at 3.0 Angstrom resolution shows bent DNA. Proc. Natl Acad. Sci. USA, 90, 6320-6324.
21. Najmudin,S., Coté,M.L., Sun,D., Yohannan,S., Montano,S.P., Gu,J. and Feorgiadis,M.M. (2000) Crystal structures of an N-terminal fragment from moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain. J. Mol. Biol., 296, 613-632.
22. Cosstick,R., Li,X. Tuli,D.K. Williams,D.M., Connolly,B.A. and Newman,P.C. (1990) Molecular recognition in the minor groove of the DNA helix. Studies on the synthesis of oligonucleotides and polynucleotides containing 3-deaza-2′-deoxyadenosine. Interaction of the oligonucleotides with the restriction endonuclease EcoRV. Nucleic Acids Res., 18, 4771-4778.
23. Guo,M.-J., Hildbrand,S., Leumann,C.J., McLaughlin,L.W. and Waring,M.J. (1998) Inhibition of DNA polymerase reactions by pyrimidine nucleotide analogues lacking the 2-keto group. Nucleic Acids Res., 26, 1863-1869.
24. Hoops,G.C., Zhang,P., Johnson,W.T., Paul,N., Bergstrom,D.E. and Davisson,V.J. (1997) Template directed incorporation of nucleotide mixtures using azole-nucleobase analogs. Nucleic Acids Res., 25, 4866-4871.
25. Wu,U., Ogawa,A.K., Berger,M., McMinn,D.L., Schultz,P.G. and Romesberg,F.E. (2000) Efforts toward expansion of the genetic alphabet: optimization of interbase hydrophobic interactions. J. Am. Chem. Soc., 122, 7621-7632.
26. Morales,J.C. and Kool,E.T. (1999) Minor groove interactions between polymerase and DNA: more essential to replication than Watson-Crick hydrogen bonds? J. Am. Chem. Soc., 121, 2323-2324.
27. Morales,J.C. and Kool,E.T. (2000) Functional hydrogen-bonding map of the minor groove binding tracks of six DNA polymerases. Biochemistry, 39, 12979-12988.
28. Ludwig,J. and Eckstein,F. (1989) Rapid and efficient synthesis of nucleoside 5′-o-(1-thiotriphosphates), 5′ -triphosphates and 2′,3′-cyclophosphorothioates using 2-chloro-4H-1,3,2-benzodioxaphosphorin-4-one. J. Org. Chem., 54, 631-635.
29. Hu,G.X. (1993) DNA polymerase-catalyzed addition of nontemplated extra nucleotides to the 3′-end of a DNA fragment. DNA Cell Biol., 12, 763-770.
30. Minikawa,N., Kojima,N. and Matsuda,A. (1999) Nucleosides and nucleotides. 184. Synthesis and conformational investigation of antifixed 3-deaza-3-halopurine ribonucleotides. J. Org. Chem., 64, 7158-7172.
31. Lever,C., Li,X., Cosstick,R., Ebel,S. and Brown,T. (1993) Thermodynamic stability and drug-binding properties of oligodeoxyribonucleotide duplexes containing 3-deazaadenine-thymine base-pairs. Nucleic Acids Res., 21, 1743-1746
32. Benner,S.A., Caraco,M.D., Thomson,J.M. and Gaucher,E.A. (2002) Planetary biology. Paleontological, geological and molecular histories of life. Science, 293, 864-868.