메뉴 건너뛰기




Volumn 24, Issue 1, 2014, Pages 72-80

Increasing occurrences and functional roles for high energy purine-pyrimidine base-pairs in nucleic acids

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; PURINE; PYRIMIDINE; DNA; PURINE DERIVATIVE; PYRIMIDINE DERIVATIVE; ADENINE; GUANINE; NUCLEIC ACID; THYMINE;

EID: 84891899586     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2013.12.003     Document Type: Review
Times cited : (11)

References (55)
  • 1
    • 0000403995 scopus 로고
    • The crystal and molecular structure of a hydrogen-bonded complex between 1-methylthymine and 9-methyladenine
    • Hoogsteen K. The crystal and molecular structure of a hydrogen-bonded complex between 1-methylthymine and 9-methyladenine. Acta Cryst 1963, 16:907-916.
    • (1963) Acta Cryst , vol.16 , pp. 907-916
    • Hoogsteen, K.1
  • 4
    • 80055079975 scopus 로고    scopus 로고
    • Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis
    • Wang W., Hellinga H.W., Beese L.S. Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Proc Natl Acad Sci U S A 2011, 108:17644-17648.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 17644-17648
    • Wang, W.1    Hellinga, H.W.2    Beese, L.S.3
  • 5
    • 84879702721 scopus 로고    scopus 로고
    • Expanded use of sense codons is regulated by modified cytidines in tRNA
    • Cantara W.A., Murphy F.V., Demirci H., Agris P.F. Expanded use of sense codons is regulated by modified cytidines in tRNA. Proc Natl Acad Sci U S A 2013, 110:10964-10969.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 10964-10969
    • Cantara, W.A.1    Murphy, F.V.2    Demirci, H.3    Agris, P.F.4
  • 6
    • 0038497542 scopus 로고
    • Molecular structure of nucleic acids
    • Watson J.D., Crick F.H. Molecular structure of nucleic acids. Nature 1953, 171:737-738.
    • (1953) Nature , vol.171 , pp. 737-738
    • Watson, J.D.1    Crick, F.H.2
  • 7
    • 33749048664 scopus 로고
    • Genetical implications of the structure of deoxyribonucleic acid
    • Watson J.D., Crick F.H. Genetical implications of the structure of deoxyribonucleic acid. Nature 1953, 171:964-967.
    • (1953) Nature , vol.171 , pp. 964-967
    • Watson, J.D.1    Crick, F.H.2
  • 9
    • 25144479978 scopus 로고    scopus 로고
    • DNA polymerases: Hoogsteen base-pairing in DNA replication?
    • Wang J. DNA polymerases: Hoogsteen base-pairing in DNA replication?. Nature 2005, 437:E6-E7.
    • (2005) Nature , vol.437
    • Wang, J.1
  • 10
    • 0027510365 scopus 로고
    • Base-pair induced shifts in the tautomeric equilibrium of a modified DNA base
    • Fazakerley G.V., Gdaniec Z., Sowers L.C. Base-pair induced shifts in the tautomeric equilibrium of a modified DNA base. J Mol Biol 1993, 230:6-10.
    • (1993) J Mol Biol , vol.230 , pp. 6-10
    • Fazakerley, G.V.1    Gdaniec, Z.2    Sowers, L.C.3
  • 11
    • 0028004616 scopus 로고
    • In situ probing of adenine protonation in RNA by 13C NMR
    • Legault P., Pardi A. In situ probing of adenine protonation in RNA by 13C NMR. J Am Chem Soc 1994, 116:8390-8391.
    • (1994) J Am Chem Soc , vol.116 , pp. 8390-8391
    • Legault, P.1    Pardi, A.2
  • 12
    • 77950939360 scopus 로고    scopus 로고
    • a shifting in an A+·C wobble: effects of helix position, temperature, and ionic strength
    • a shifting in an A+·C wobble: effects of helix position, temperature, and ionic strength. Biochemistry 2010, 49:3225-3236.
    • (2010) Biochemistry , vol.49 , pp. 3225-3236
    • Siegfried, N.A.1    O'Hare, B.2    Bevilacqua, P.C.3
  • 13
    • 84878709257 scopus 로고    scopus 로고
    • Direct observation of ground-state lactam-lactim tautomerization using temperature-jump transient 2D IR spectroscopy
    • Peng C.S., Baiz C.R., Tokmakoff A. Direct observation of ground-state lactam-lactim tautomerization using temperature-jump transient 2D IR spectroscopy. Proc Natl Acad Sci U S A 2013, 110:9243-9248.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 9243-9248
    • Peng, C.S.1    Baiz, C.R.2    Tokmakoff, A.3
  • 14
    • 0037162169 scopus 로고    scopus 로고
    • Tautomerism of the DNA base guanine and its methylated derivatives as studied by gas-phase infrared and ultraviolet spectroscopy
    • Mons M., Dimicoli I., Piuzzi F., Tardivel B., Elhanine M. Tautomerism of the DNA base guanine and its methylated derivatives as studied by gas-phase infrared and ultraviolet spectroscopy. J Phys Chem A 2002, 106:5088-5094.
    • (2002) J Phys Chem A , vol.106 , pp. 5088-5094
    • Mons, M.1    Dimicoli, I.2    Piuzzi, F.3    Tardivel, B.4    Elhanine, M.5
  • 16
    • 84881450365 scopus 로고    scopus 로고
    • NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers
    • Sekhar A., Kay L.E. NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers. Proc Natl Acad Sci U S A 2013, 110:12867-12874.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 12867-12874
    • Sekhar, A.1    Kay, L.E.2
  • 17
    • 33744908076 scopus 로고    scopus 로고
    • Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy
    • Palmer A.G., Massi F. Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem Rev 2006, 106:1700-1719.
    • (2006) Chem Rev , vol.106 , pp. 1700-1719
    • Palmer, A.G.1    Massi, F.2
  • 19
    • 84857725677 scopus 로고    scopus 로고
    • Probing transient hoogsteen hydrogen bonds in canonical duplex DNA using NMR relaxation dispersion and single-atom substitution
    • Nikolova E.N., Gottardo F.L., Al-Hashimi H.M. Probing transient hoogsteen hydrogen bonds in canonical duplex DNA using NMR relaxation dispersion and single-atom substitution. J Am Chem Soc 2012, 134:3667-3670.
    • (2012) J Am Chem Soc , vol.134 , pp. 3667-3670
    • Nikolova, E.N.1    Gottardo, F.L.2    Al-Hashimi, H.M.3
  • 20
    • 79952143760 scopus 로고    scopus 로고
    • Replication infidelity via a mismatch with Watson-Crick geometry
    • Bebenek K., Pedersen L.C., Kunkel T.A. Replication infidelity via a mismatch with Watson-Crick geometry. Proc Natl Acad Sci U S A 2011, 108:1862-1867.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 1862-1867
    • Bebenek, K.1    Pedersen, L.C.2    Kunkel, T.A.3
  • 21
    • 84859593945 scopus 로고    scopus 로고
    • A new understanding of the decoding principle on the ribosome
    • Demeshkina N., Jenner L., Westhof E., Yusupov M., Yusupova G. A new understanding of the decoding principle on the ribosome. Nature 2012, 484:256-259.
    • (2012) Nature , vol.484 , pp. 256-259
    • Demeshkina, N.1    Jenner, L.2    Westhof, E.3    Yusupov, M.4    Yusupova, G.5
  • 24
    • 84879897415 scopus 로고    scopus 로고
    • Observing a DNA polymerase choose right from wrong
    • Freudenthal B.D., Beard W.A., Shock D.D., Wilson S.H. Observing a DNA polymerase choose right from wrong. Cell 2013, 154:157-168.
    • (2013) Cell , vol.154 , pp. 157-168
    • Freudenthal, B.D.1    Beard, W.A.2    Shock, D.D.3    Wilson, S.H.4
  • 25
    • 79952820128 scopus 로고    scopus 로고
    • Femtosecond two-dimensional infrared spectroscopy of adenine-thymine base pairs in DNA oligomers
    • Yang M., Szyc Ł., Elsaesser T. Femtosecond two-dimensional infrared spectroscopy of adenine-thymine base pairs in DNA oligomers. J Phys Chem B 2011, 115:1262-1267.
    • (2011) J Phys Chem B , vol.115 , pp. 1262-1267
    • Yang, M.1    Szyc, Ł.2    Elsaesser, T.3
  • 27
    • 84891896950 scopus 로고    scopus 로고
    • Direct observation of multiple tautomers of oxythiamine and their recognition by the thiamine pyrophosphate riboswitch
    • Article ASAP
    • Singh V., Peng C.S., Li D., Mitra K., Silvestre K.J., Tokmakoff A., Essigmann J.M. Direct observation of multiple tautomers of oxythiamine and their recognition by the thiamine pyrophosphate riboswitch. ACS Chem Biol 2013, Article ASAP.
    • (2013) ACS Chem Biol
    • Singh, V.1    Peng, C.S.2    Li, D.3    Mitra, K.4    Silvestre, K.J.5    Tokmakoff, A.6    Essigmann, J.M.7
  • 29
    • 33947470407 scopus 로고
    • Formation of a three-stranded polynucleotide molecule
    • Felsenfeld G., Davies D.R., Rich A. Formation of a three-stranded polynucleotide molecule. J Am Chem Soc 1957, 79:2023-2024.
    • (1957) J Am Chem Soc , vol.79 , pp. 2023-2024
    • Felsenfeld, G.1    Davies, D.R.2    Rich, A.3
  • 32
    • 0033573008 scopus 로고    scopus 로고
    • TATA element recognition by the TATA box-binding protein has been conserved throughout evolution
    • Patikoglou G.A., Kim J.L., Sun L., Yang S.-H., Kodadek T., Burley S.K. TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev 1999, 13:3217-3230.
    • (1999) Genes Dev , vol.13 , pp. 3217-3230
    • Patikoglou, G.A.1    Kim, J.L.2    Sun, L.3    Yang, S.-H.4    Kodadek, T.5    Burley, S.K.6
  • 33
    • 0030451819 scopus 로고    scopus 로고
    • Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn
    • Rice P.A., Yang S-w, Mizuuchi K., Nash H.A. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell 1996, 87:1295-1306.
    • (1996) Cell , vol.87 , pp. 1295-1306
    • Rice, P.A.1    Yang, S.-W.2    Mizuuchi, K.3    Nash, H.A.4
  • 34
    • 59649112203 scopus 로고    scopus 로고
    • Crystal structure of a p53 core tetramer bound to DNA
    • Malecka K.A., Ho W.C., Marmorstein R. Crystal structure of a p53 core tetramer bound to DNA. Oncogene 2008, 28:325-333.
    • (2008) Oncogene , vol.28 , pp. 325-333
    • Malecka, K.A.1    Ho, W.C.2    Marmorstein, R.3
  • 35
    • 75849126765 scopus 로고    scopus 로고
    • Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer
    • Chen Y., Dey R., Chen L. Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer. Structure 2010, 18:246-256.
    • (2010) Structure , vol.18 , pp. 246-256
    • Chen, Y.1    Dey, R.2    Chen, L.3
  • 36
    • 42749086351 scopus 로고    scopus 로고
    • Effect of 1-methyladenine on double-helical DNA structures
    • Yang H., Zhan Y., Fenn D., Chi L.M., Lam S.L. Effect of 1-methyladenine on double-helical DNA structures. FEBS Lett 2008, 582:1629-1633.
    • (2008) FEBS Lett , vol.582 , pp. 1629-1633
    • Yang, H.1    Zhan, Y.2    Fenn, D.3    Chi, L.M.4    Lam, S.L.5
  • 37
    • 77955235019 scopus 로고    scopus 로고
    • Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system
    • Lu L., Yi C., Jian X., Zheng G., He C. Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system. Nucleic Acids Res 2010, 38:4415-4425.
    • (2010) Nucleic Acids Res , vol.38 , pp. 4415-4425
    • Lu, L.1    Yi, C.2    Jian, X.3    Zheng, G.4    He, C.5
  • 38
    • 0345138990 scopus 로고    scopus 로고
    • Structures of Escherichia coli DNA mismatch repair enzyme MutS in complex with different mismatches: a common recognition mode for diverse substrates
    • Natrajan G., Lamers M.H., Enzlin J.H., Winterwerp H.H., Perrakis A., Sixma T.K. Structures of Escherichia coli DNA mismatch repair enzyme MutS in complex with different mismatches: a common recognition mode for diverse substrates. Nucleic Acids Res 2003, 31:4814-4821.
    • (2003) Nucleic Acids Res , vol.31 , pp. 4814-4821
    • Natrajan, G.1    Lamers, M.H.2    Enzlin, J.H.3    Winterwerp, H.H.4    Perrakis, A.5    Sixma, T.K.6
  • 39
    • 84881477474 scopus 로고    scopus 로고
    • Unusual base pairing during the decoding of a stop codon by the ribosome
    • Fernandez I.S., Ng C.L., Kelley A.C., Wu G., Yu Y.-T., Ramakrishnan V. Unusual base pairing during the decoding of a stop codon by the ribosome. Nature 2013, 500:107-110.
    • (2013) Nature , vol.500 , pp. 107-110
    • Fernandez, I.S.1    Ng, C.L.2    Kelley, A.C.3    Wu, G.4    Yu, Y.-T.5    Ramakrishnan, V.6
  • 40
    • 26444528004 scopus 로고    scopus 로고
    • Human DNA polymerase ι incorporates dCTP opposite template G via a G, C+ Hoogsteen base pair
    • Nair D.T., Johnson R.E., Prakash L., Prakash S., Aggarwal A.K. Human DNA polymerase ι incorporates dCTP opposite template G via a G, C+ Hoogsteen base pair. Structure 2005, 13:1569-1577.
    • (2005) Structure , vol.13 , pp. 1569-1577
    • Nair, D.T.1    Johnson, R.E.2    Prakash, L.3    Prakash, S.4    Aggarwal, A.K.5
  • 41
    • 84864540063 scopus 로고    scopus 로고
    • Structure of human DNA polymerase iota and the mechanism of DNA synthesis
    • Makarova A., Kulbachinskiy A. Structure of human DNA polymerase iota and the mechanism of DNA synthesis. Biochemistry (Mosc) 2012, 77:547-561.
    • (2012) Biochemistry (Mosc) , vol.77 , pp. 547-561
    • Makarova, A.1    Kulbachinskiy, A.2
  • 42
    • 35148820034 scopus 로고    scopus 로고
    • A role for yeast and human translesion synthesis DNA polymerases in promoting replication through 3-methyl adenine
    • Johnson R.E., Yu S.-L., Prakash S., Prakash L. A role for yeast and human translesion synthesis DNA polymerases in promoting replication through 3-methyl adenine. Mol Cell Biol 2007, 27:7198-7205.
    • (2007) Mol Cell Biol , vol.27 , pp. 7198-7205
    • Johnson, R.E.1    Yu, S.-L.2    Prakash, S.3    Prakash, L.4
  • 43
    • 42449091527 scopus 로고    scopus 로고
    • Eukaryotic Y-family polymerases bypass a 3-methyl-2'-deoxyadenosine analog in vitro and methyl methanesulfonate-induced DNA damage in vivo
    • Plosky B.S., Frank E.G., Berry D.A., Vennall G.P., McDonald J.P., Woodgate R. Eukaryotic Y-family polymerases bypass a 3-methyl-2'-deoxyadenosine analog in vitro and methyl methanesulfonate-induced DNA damage in vivo. Nucleic Acids Res 2008, 36:2152-2162.
    • (2008) Nucleic Acids Res , vol.36 , pp. 2152-2162
    • Plosky, B.S.1    Frank, E.G.2    Berry, D.A.3    Vennall, G.P.4    McDonald, J.P.5    Woodgate, R.6
  • 45
    • 84877311638 scopus 로고    scopus 로고
    • Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA
    • Nikolova E.N., Goh G.B., Brooks C.L., Al-Hashimi H.M. Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA. J Am Chem Soc 2013, 135:6766-6769.
    • (2013) J Am Chem Soc , vol.135 , pp. 6766-6769
    • Nikolova, E.N.1    Goh, G.B.2    Brooks, C.L.3    Al-Hashimi, H.M.4
  • 47
    • 0017148262 scopus 로고
    • Complementary base pairing and the origin of substitution mutations
    • Topal M.D., Fresco J.R. Complementary base pairing and the origin of substitution mutations. Nature 1976, 263:285-289.
    • (1976) Nature , vol.263 , pp. 285-289
    • Topal, M.D.1    Fresco, J.R.2
  • 48
    • 84859412476 scopus 로고    scopus 로고
    • How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations
    • Kirmizialtin S., Nguyen V., Johnson K.A., Elber R. How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations. Structure 2012, 20:618-627.
    • (2012) Structure , vol.20 , pp. 618-627
    • Kirmizialtin, S.1    Nguyen, V.2    Johnson, K.A.3    Elber, R.4
  • 49
    • 0027297046 scopus 로고
    • Ionization of bromouracil and fluorouracil stimulates base mispairing frequencies with guanine
    • Yu H., Eritja R., Bloom L.B., Goodman M.F. Ionization of bromouracil and fluorouracil stimulates base mispairing frequencies with guanine. J Biol Chem 1993, 268:15935-15943.
    • (1993) J Biol Chem , vol.268 , pp. 15935-15943
    • Yu, H.1    Eritja, R.2    Bloom, L.B.3    Goodman, M.F.4
  • 50
    • 84872113855 scopus 로고    scopus 로고
    • DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase
    • Xia S., Wang J., Konigsberg W.H. DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase. J Am Chem Soc 2012, 135:193-202.
    • (2012) J Am Chem Soc , vol.135 , pp. 193-202
    • Xia, S.1    Wang, J.2    Konigsberg, W.H.3
  • 51
    • 33645657530 scopus 로고    scopus 로고
    • Adenine tautomers: relative stabilities, ionization energies, and mismatch with cytosine
    • Fonseca Guerra C., Bickelhaupt F., Saha S., Wang F. Adenine tautomers: relative stabilities, ionization energies, and mismatch with cytosine. J Phys Chem A 2006, 110:4012-4020.
    • (2006) J Phys Chem A , vol.110 , pp. 4012-4020
    • Fonseca Guerra, C.1    Bickelhaupt, F.2    Saha, S.3    Wang, F.4
  • 52
    • 84886800210 scopus 로고    scopus 로고
    • a shifting in double-stranded RNA is highly dependent upon nearest neighbors and bulge positioning
    • a shifting in double-stranded RNA is highly dependent upon nearest neighbors and bulge positioning. Biochemistry 2013, 52:7470-7476.
    • (2013) Biochemistry , vol.52 , pp. 7470-7476
    • Wilcox, J.L.1    Bevilacqua, P.C.2
  • 53
    • 84887575499 scopus 로고    scopus 로고
    • G/U and certain wobble position mismatches as possible main causes of amino acid misincorporations
    • Zhang Z., Shah B., Bondarenko P.V. G/U and certain wobble position mismatches as possible main causes of amino acid misincorporations. Biochemistry 2013, 52:8165-8176.
    • (2013) Biochemistry , vol.52 , pp. 8165-8176
    • Zhang, Z.1    Shah, B.2    Bondarenko, P.V.3
  • 54
    • 84878924244 scopus 로고    scopus 로고
    • Structural basis of the translational elongation cycle
    • Voorhees R.M., Ramakrishnan V. Structural basis of the translational elongation cycle. Annu Rev Biochem 2013, 82:203-236.
    • (2013) Annu Rev Biochem , vol.82 , pp. 203-236
    • Voorhees, R.M.1    Ramakrishnan, V.2
  • 55
    • 84878947991 scopus 로고    scopus 로고
    • New structural insights into the decoding mechanism: translation infidelity via a G-U pair with Watson-Crick geometry
    • Demeshkina N., Jenner L., Westhof E., Yusupov M., Yusupova G. New structural insights into the decoding mechanism: translation infidelity via a G-U pair with Watson-Crick geometry. FEBS Lett 2013, 587:1848-1857.
    • (2013) FEBS Lett , vol.587 , pp. 1848-1857
    • Demeshkina, N.1    Jenner, L.2    Westhof, E.3    Yusupov, M.4    Yusupova, G.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.