메뉴 건너뛰기




Volumn 292, Issue 2, 1999, Pages 309-320

Stable formation of a pyrimidine-rich loop hairpin in a cruciform promoter

Author keywords

Cruciform; N4 virion RNAP; NMR structure; Purine rich loop; Pyrimidine rich loop

Indexed keywords

PYRIMIDINE DERIVATIVE; RNA POLYMERASE; VIRUS DNA;

EID: 0033578827     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3066     Document Type: Article
Times cited : (21)

References (43)
  • 1
    • 0000265069 scopus 로고
    • Conformational analysis of nucleic acids. Determination of backbone geometry of single-helical RNA and DNA in aqueous solution
    • Altona C. Conformational analysis of nucleic acids. Determination of backbone geometry of single-helical RNA and DNA in aqueous solution. Recl. Trav. Chim. Pays-Bas. 101:1982;413-433.
    • (1982) Recl. Trav. Chim. Pays-Bas. , vol.101 , pp. 413-433
    • Altona, C.1
  • 2
    • 0015511563 scopus 로고
    • Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation
    • Altona C., Sundaralingam M. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc. 94:1972;8205-8212.
    • (1972) J. Am. Chem. Soc. , vol.94 , pp. 8205-8212
    • Altona, C.1    Sundaralingam, M.2
  • 3
    • 0027185318 scopus 로고
    • Conformational properties of DNA hairpins with TTT and TTTT loops
    • Baxter S. M., Greizerstein M. B., Kushlan D. M., Ashley G. W. Conformational properties of DNA hairpins with TTT and TTTT loops. Biochemistry. 32:1993;8702-8711.
    • (1993) Biochemistry , vol.32 , pp. 8702-8711
    • Baxter, S.M.1    Greizerstein, M.B.2    Kushlan, D.M.3    Ashley, G.W.4
  • 5
    • 0016189342 scopus 로고
    • Stability of ribonucleic acid double-stranded helices
    • Borer P. N., Dengler B., Tinoco I. J. Stability of ribonucleic acid double-stranded helices. J. Mol. Biol. 86:1974;843-853.
    • (1974) J. Mol. Biol. , vol.86 , pp. 843-853
    • Borer, P.N.1    Dengler, B.2    Tinoco, I.J.3
  • 6
    • 0026045275 scopus 로고
    • The solution structure of a DNA hairpin containing a loop of three thymidines determined by nuclear magnetic resonance and molecular mechanics
    • Boulard Y., Gabarro-Arpa J., Cognet J. A. H., Bret M. L., Guy A., Teoule R., Guschlbauer W., Fazakerley G. V. The solution structure of a DNA hairpin containing a loop of three thymidines determined by nuclear magnetic resonance and molecular mechanics. Nucl. Acids Res. 19:1991;5159-5167.
    • (1991) Nucl. Acids Res. , vol.19 , pp. 5159-5167
    • Boulard, Y.1    Gabarro-Arpa, J.2    Cognet, J.A.H.3    Bret, M.L.4    Guy, A.5    Teoule, R.6    Guschlbauer, W.7    Fazakerley, G.V.8
  • 7
    • 0033534369 scopus 로고    scopus 로고
    • Cross-strand pruine-pyrimidine stack and sheared purine:pyrimidine pairing in the human HIV-1 reverse transcriptase inhibitors
    • Chou S.-H., Tseng Y.-Y. Cross-strand pruine-pyrimidine stack and sheared purine:pyrimidine pairing in the human HIV-1 reverse transcriptase inhibitors. J. Mol. Biol. 285:1999;41-48.
    • (1999) J. Mol. Biol. , vol.285 , pp. 41-48
    • Chou, S.-H.1    Tseng, Y.-Y.2
  • 9
    • 0028146180 scopus 로고
    • DNA sequence GCGAATGAGC containing the human centromere core sequence GAAT forms a self-complementary duplex with sheared G:A pairs in solution
    • Chou S.-H., Cheng J.-W., Fedoroff O., Reid B. R. DNA sequence GCGAATGAGC containing the human centromere core sequence GAAT forms a self-complementary duplex with sheared G:A pairs in solution. J. Mol. Biol. 241:1994a;467-479.
    • (1994) J. Mol. Biol. , vol.241 , pp. 467-479
    • Chou, S.-H.1    Cheng, J.-W.2    Fedoroff, O.3    Reid, B.R.4
  • 10
    • 0028063442 scopus 로고
    • 2motif: Unpaired guanosines stacked between sheared GA pairs
    • 2motif: unpaired guanosines stacked between sheared GA pairs. J. Mol. Biol. 244:1994b;259-268.
    • (1994) J. Mol. Biol. , vol.244 , pp. 259-268
    • Chou, S.-H.1    Zhu, L.2    Reid, B.R.3
  • 11
    • 17544394367 scopus 로고    scopus 로고
    • Hairpin loops consisting of single adenine residues closed by sheared A:A and G:G pairs formed by the DNA triplets AAA and GAG: Solution structure of the d(GTACAAAGTAC) hairpin
    • Chou S.-H., Zhu L., Gao Z., Cheng J.-W., Reid B. R. Hairpin loops consisting of single adenine residues closed by sheared A:A and G:G pairs formed by the DNA triplets AAA and GAG: solution structure of the d(GTACAAAGTAC) hairpin. J. Mol. Biol. 264:1996a;981-1001.
    • (1996) J. Mol. Biol. , vol.264 , pp. 981-1001
    • Chou, S.-H.1    Zhu, L.2    Gao, Z.3    Cheng, J.-W.4    Reid, B.R.5
  • 12
    • 0029951996 scopus 로고    scopus 로고
    • On the relative ability of centromeric GNA triplets to form hairpins versus self-paired duplexes
    • Chou S.-H., Zhu L., Reid R. R. On the relative ability of centromeric GNA triplets to form hairpins versus self-paired duplexes. J. Mol. Biol. 259:1996b;445-457.
    • (1996) J. Mol. Biol. , vol.259 , pp. 445-457
    • Chou, S.-H.1    Zhu, L.2    Reid, R.R.3
  • 13
    • 0031576896 scopus 로고    scopus 로고
    • Sheared purine:purine pairing in biology
    • Chou S.-H., Zhu L., Reid B. R. Sheared purine:purine pairing in biology. J. Mol. Biol. 267:1997;1055-1067.
    • (1997) J. Mol. Biol. , vol.267 , pp. 1055-1067
    • Chou, S.-H.1    Zhu, L.2    Reid, B.R.3
  • 14
    • 0033030742 scopus 로고    scopus 로고
    • Structural studies of symmetric DNA undecamers containing non-symmetrical sheared (PuGAPu):(PyGAPy) motifs
    • Chou S.-H., Tseng Y.-Y., Chen Y.-R., Cheng J.-W. Structural studies of symmetric DNA undecamers containing non-symmetrical sheared (PuGAPu):(PyGAPy) motifs. J. Biomol. NMR. 14:1999a;157-167.
    • (1999) J. Biomol. NMR , vol.14 , pp. 157-167
    • Chou, S.-H.1    Tseng, Y.-Y.2    Chen, Y.-R.3    Cheng, J.-W.4
  • 15
    • 0033605418 scopus 로고    scopus 로고
    • Stable sheared A:C pair in DNA hairpins
    • Chou S.-H., Tseng Y.-Y., Wang S.-W. Stable sheared A:C pair in DNA hairpins. J. Mol. Biol. 287:1999b;301-313.
    • (1999) J. Mol. Biol. , vol.287 , pp. 301-313
    • Chou, S.-H.1    Tseng, Y.-Y.2    Wang, S.-W.3
  • 17
    • 0032538282 scopus 로고    scopus 로고
    • Sequence-dependent extrusion of a small DNA hairpin at the N4 virion RNA polymerase promoters
    • Dai X., Kloster M., Rothman-Denes L. B. Sequence-dependent extrusion of a small DNA hairpin at the N4 virion RNA polymerase promoters. J. Mol. Biol. 283:1998;43-58.
    • (1998) J. Mol. Biol. , vol.283 , pp. 43-58
    • Dai, X.1    Kloster, M.2    Rothman-Denes, L.B.3
  • 18
    • 0031574326 scopus 로고    scopus 로고
    • The loop E - loop D region of Escherichia coli 5S rRNA: The solution structure reveals an unusual loop that may be important for binding ribosomal proteins
    • Dallas A., Moore P. B. The loop E - loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins. Structure. 5:1997;1639-1653.
    • (1997) Structure , vol.5 , pp. 1639-1653
    • Dallas, A.1    Moore, P.B.2
  • 19
    • 0028938599 scopus 로고
    • Stereoelectronic effects of deoxyribose O4' on DNA conformation
    • Egli M., Gessner R. V. Stereoelectronic effects of deoxyribose O4' on DNA conformation. Proc. Natl Acad. Sci. USA. 92:1995;180-184.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 180-184
    • Egli, M.1    Gessner, R.V.2
  • 20
    • 0345311136 scopus 로고
    • Practical aspects of the E. COSY technique. Measurement of scalar spin-spin coupling constants in peptides
    • Griesinger C., Sorensen O. W., Ernst R. R. Practical aspects of the E. COSY technique. Measurement of scalar spin-spin coupling constants in peptides. J. Magn. Res. 75:1987;474-492.
    • (1987) J. Magn. Res. , vol.75 , pp. 474-492
    • Griesinger, C.1    Sorensen, O.W.2    Ernst, R.R.3
  • 21
    • 20444483055 scopus 로고
    • The relationship between proton-proton NMR coupling constants and substituent electronegativities
    • Haasnoot C. A. G., de Leeuv F. A. A. M., Altona C. The relationship between proton-proton NMR coupling constants and substituent electronegativities. Tetrahedron. 36:1980;2783-2792.
    • (1980) Tetrahedron , vol.36 , pp. 2783-2792
    • Haasnoot, C.A.G.1    De Leeuv, F.A.A.M.2    Altona, C.3
  • 22
    • 0021105577 scopus 로고
    • Assignment of the non-exchangeable proton resonances of d(CGCGAATTCGCG) using two-dimensional nuclear magnetic resonance methods
    • Hare D. R., Wemmer D. E., Chou S.-H., Drobny G., Reid B. R. Assignment of the non-exchangeable proton resonances of d(CGCGAATTCGCG) using two-dimensional nuclear magnetic resonance methods. J. Mol. Biol. 171:1983;319-336.
    • (1983) J. Mol. Biol. , vol.171 , pp. 319-336
    • Hare, D.R.1    Wemmer, D.E.2    Chou, S.-H.3    Drobny, G.4    Reid, B.R.5
  • 23
    • 0028247062 scopus 로고
    • Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: An extraordinarily stable structure resistant to nucleases and heat
    • Hirao I., Kawai G., Yoshizawa S., Nishimura Y., Ishido Y., Watanabe K., Miura K.-I. Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: an extraordinarily stable structure resistant to nucleases and heat. Nucl. Acids Res. 22:1994;576-582.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 576-582
    • Hirao, I.1    Kawai, G.2    Yoshizawa, S.3    Nishimura, Y.4    Ishido, Y.5    Watanabe, K.6    Miura, K.-I.7
  • 24
    • 0031835535 scopus 로고    scopus 로고
    • The telomeres of streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures
    • Huang C.-H., Lin Y.-S., Yang Y.-L., Huang S.-W., Chen C. W. The telomeres of streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures. Mol. Microbiol. 28:1998;905-916.
    • (1998) Mol. Microbiol. , vol.28 , pp. 905-916
    • Huang, C.-H.1    Lin, Y.-S.2    Yang, Y.-L.3    Huang, S.-W.4    Chen, C.W.5
  • 25
    • 0023057151 scopus 로고
    • Altered DNA conformations in the gene regulatory region of torsionally-stressed SV40 DNA
    • Iacono-Connors L., Kowalski D. Altered DNA conformations in the gene regulatory region of torsionally-stressed SV40 DNA. Nucl. Acids Res. 14:1986;8949-8962.
    • (1986) Nucl. Acids Res. , vol.14 , pp. 8949-8962
    • Iacono-Connors, L.1    Kowalski, D.2
  • 27
    • 0028866812 scopus 로고
    • Solution structure of the CUUG hairpin loop: A novel RNA tetraloop motif
    • Jucker F. M., Pardi A. Solution structure of the CUUG hairpin loop: a novel RNA tetraloop motif. Biochemistry. 34:1995;14416-14427.
    • (1995) Biochemistry , vol.34 , pp. 14416-14427
    • Jucker, F.M.1    Pardi, A.2
  • 29
    • 0026053768 scopus 로고
    • NMR and molecular modeling evidence for a GA mismatch base pair in a purine-rich DNA duplex
    • Li Y., Zon G., Wilson W. D. NMR and molecular modeling evidence for a GA mismatch base pair in a purine-rich DNA duplex. Proc. Natl Acad. Sci. USA. 88:1991;26-30.
    • (1991) Proc. Natl Acad. Sci. USA , vol.88 , pp. 26-30
    • Li, Y.1    Zon, G.2    Wilson, W.D.3
  • 30
    • 0023406843 scopus 로고
    • Calculating thermodynamic data for transitions of any molecularity from equilibirum melting curves
    • Marky L. A., Breslauer K. J. Calculating thermodynamic data for transitions of any molecularity from equilibirum melting curves. Biopolymers. 26:1987;1601-1620.
    • (1987) Biopolymers , vol.26 , pp. 1601-1620
    • Marky, L.A.1    Breslauer, K.J.2
  • 31
    • 0027427531 scopus 로고
    • A base-paired hairpin structure essential for the functional priming signal for DNA replication of the broad host range plasmid RSF1010
    • Miao D. M., Honda Y., Tanaka K., Higashi A., Nakamura T., Taguchi Y., Sakai H., Komano T., Bagdaraian M. A base-paired hairpin structure essential for the functional priming signal for DNA replication of the broad host range plasmid RSF1010. Nucl. Acids Res. 21:1993;4900-4903.
    • (1993) Nucl. Acids Res. , vol.21 , pp. 4900-4903
    • Miao, D.M.1    Honda, Y.2    Tanaka, K.3    Higashi, A.4    Nakamura, T.5    Taguchi, Y.6    Sakai, H.7    Komano, T.8    Bagdaraian, M.9
  • 33
    • 0028860964 scopus 로고
    • Improved RNA structure determination by detection of NOE contacts to exchange-broadened amino protons
    • Mueller L., Legault P., Pardi A. Improved RNA structure determination by detection of NOE contacts to exchange-broadened amino protons. J. Am. Chem. Soc. 117:1995;11043-11048.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 11043-11048
    • Mueller, L.1    Legault, P.2    Pardi, A.3
  • 34
    • 33845555707 scopus 로고
    • Exchangeable proton NMR without base-line distortion, using new strong-pulse sequences
    • Plateau P., Gueron M. Exchangeable proton NMR without base-line distortion, using new strong-pulse sequences. J. Am. Chem. Soc. 104:1982;7310-7311.
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 7310-7311
    • Plateau, P.1    Gueron, M.2
  • 35
    • 0027190862 scopus 로고
    • The DNA strand in DNA/RNA hybrid duplexes is neither B -form nor A -form in solution
    • Salazar M., Fedoroff O. L., Miller J. M., Ribeiro S., Reid B. R. The DNA strand in DNA/RNA hybrid duplexes is neither B -form nor A -form in solution. Biochemistry. 32:1993;4207-4215.
    • (1993) Biochemistry , vol.32 , pp. 4207-4215
    • Salazar, M.1    Fedoroff, O.L.2    Miller, J.M.3    Ribeiro, S.4    Reid, B.R.5
  • 38
    • 0003093870 scopus 로고    scopus 로고
    • Systematic NMR assignment pathways for DNA exchangeable protons
    • Tseng Y.-Y., Chou S.-H. Systematic NMR assignment pathways for DNA exchangeable protons. J. Chin. Chem. Soc. in the press:1999.
    • (1999) J. Chin. Chem. Soc.
    • Tseng, Y.-Y.1    Chou, S.-H.2
  • 41
    • 0028800948 scopus 로고
    • Structure of a single-cytidine hairpin loop formed by the DNA Triplet GCA
    • Zhu L., Chou S.-H., Reid B. R. Structure of a single-cytidine hairpin loop formed by the DNA Triplet GCA. Nature Struct. Biol. 2:1995a;1012-1017.
    • (1995) Nature Struct. Biol. , vol.2 , pp. 1012-1017
    • Zhu, L.1    Chou, S.-H.2    Reid, B.R.3
  • 42
    • 0029593488 scopus 로고
    • The structure of a novel DNA duplex formed by human centromere d(TGGAA) repeats with possible implications for chromosome attachment during mitosis
    • Zhu L., Chou S.-H., Reid R. B. The structure of a novel DNA duplex formed by human centromere d(TGGAA) repeats with possible implications for chromosome attachment during mitosis. J. Mol. Biol. 254:1995b;623-637.
    • (1995) J. Mol. Biol. , vol.254 , pp. 623-637
    • Zhu, L.1    Chou, S.-H.2    Reid, R.B.3
  • 43
    • 0029861326 scopus 로고    scopus 로고
    • A single G-to-C change causes human centromere TGGAA repeats to fold back into hairpins
    • Zhu L., Chou S.-H., Reid B. R. A single G-to-C change causes human centromere TGGAA repeats to fold back into hairpins. Proc. Natl Acad. Sci. USA. 93:1996;12159-12164.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 12159-12164
    • Zhu, L.1    Chou, S.-H.2    Reid, B.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.