このページはRCSBの David S. Goodsell博士による「Molecule of the Month」2001年11月の記事を日本語に訳したものです。転載・引用については利用規約をご覧下さい。
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:翻訳 工藤高裕 (PDBj)

B型DNA2重らせん

あなたの身体にあるそれぞれの細胞は約1.5ギガバイトの遺伝情報を持っている。この情報量はCD ROM2枚、あるいは小さなハードディスクドライブをいっぱいにするだけの量に匹敵する。驚くべきことに、この情報は適切な卵細胞にある時、呼吸をし考える完全なヒトを作り上げるのに十分な量の情報となる。国際ヒトゲノム配列プロジェクトの成果によって、現在この情報を見ることができる。大部分の生物学研究社会だけでなく、あなたもこの情報の複雑さに驚き、その意味を理解しようとすることができる。また同時に、ヒトの身体の複雑さに比べた時のこの情報の単純さに驚くこともできる。

読み取り専用メモリ(ROM)

DNAは読み取り専用のメモリ(記憶媒体)で、細胞内に安全に保管されている。遺伝情報はDNA鎖の中に規則正しく納められている。DNAは何百万個ものヌクレオチドが連なった長い鎖でできており、多くの場合相手となる鎖と組になって存在している。これらの鎖はお互いに包み合って、右図のようなよく知られる二重らせんの形をとる。この中の遺伝暗号は極めて簡単に読むことができる。あなたはDNA鎖を1ヌクレオチドずつたどり、塩基がA、T、C、Gのいずれであるかを読み取りさえすればよいのである。この作業はあなたの細胞が正確に行っている。細胞はメッセンジャーRNAに遺伝情報を読み取り(DNAに情報をコピーして)、その情報に基づきリボソームを使ってタンパク質を作り出している。またこの方法は研究者がDNA鎖の配列を決定する方法でもある。彼らは1つずつヌクレオチドを切り取り、それが何であるのかを確かめている。

あなたの相続財産

あなたの遺伝情報は、両親から受け継いだ、あなたにとって最も大切な財産である。人生最初の9ヶ月間あなたの身体形成を指示し、その後も生命の基本的な機能の全てを制御し続けている。あなたの身体を構成する各細胞は絶えずこの情報を使い、血糖値や体温をどのように制御するのか、いろいろな食べ物をどのようにして消化するのか、新しい環境における課題をどう処理するのか、などその他にも何千とある重要な問題を尋ねている。その答えはDNAの中にある。この情報交換のため、何百種類ものタンパク質が作られる。あるものは情報を読み取り新しいタンパク質を作るために、あるものは細胞分裂の際情報をコピーするために、あるものはDNAが活発に使われていない時に貯蔵して保護するために、あるものは化学物質や放射線によってDNAが破壊され始めたとき情報を修復するために。

中心的象徴

DNAは生きた細胞の中にある最も美しい分子の一つと言ってほぼ間違いないだろう。その優雅ならせんは目を楽しませてくれる。またDNAは最もよく知られている分子の一つでもあり、みんなが簡単に認める分子生物学の中心的象徴である。人によっては、遺伝的に改変された産物に対抗する活動家の間で普及している象徴として、否定的な含みを持つように聞こえるかもしれない。また、よく最近話題となる裁判で使われるDNA鑑定(DNA指紋法)のような犯罪科学上の進歩を思い出す人もいるかもしれない。恐竜を作ったり、異星人からの謎めいたメッセージを保存したりするためDNAが修正されるのを空想科学小説(SF)で見た人もいるかもしれない。全てにとってDNAとは、人体やヒト近縁種への理解を深めることと、DNAの知識に直面した時解決しなければならない道徳的、倫理的問題に対するよく知られた象徴である。

分子の情報

DNA二重らせん(左)とその部分拡大図(右)、赤矢印は塩基対を形成する水素結合、AとDは遺伝外情報における水素結合受容体と水素結合供与体、矢印とアスタリスクは特徴的な化学基を示す。

DNAは情報の蓄積と読み出しにとっては完璧である。DNAには情報がいっぱい詰め込まれている。分子の表面および末端はそれぞれ情報を保持している。DNAが遺伝情報を保持し伝えているという基本的機構が、1950年代にワトソン(Watson)とクリック(Crick)によって発見された。この基本情報は、二重らせんの相手鎖にある塩基と対合させ相補的な水素結合を形成する方法で保持されている。なお、対合する組み合わせはアデニン(adenine)とチミン(thymine)、グアニン(guanine)とシトシン(cytosine)である。上図ではこの水素結合を赤い矢印で示している。

追加の「遺伝外」情報は、二重らせんの中あって外に露出している表面から読み取られる。主要な溝(左に示す構造中にある2つの溝のうち広い方)では、異なる塩基対が特徴的なパターンの化学基を持っていて、そこには情報が保持されている。上図右の拡大図では緑の矢印で示されている。また図には、アデニン-チミン塩基対にある大きなグループ(大きなアスタリスク)またはグアニン-シトシン塩基対にある小さなグループ(小さなアスタリスク)に加え水素結合の供与体(donor, D)と受容体(acceptor, A)も示されている。小さい方の溝には、別の化学基の配列があって、そこには追加情報が保持されている。上図右では青い矢印、上図左では青い文字で示されている。PDBでは何百個ものエントリーでそのことが明らかにされており、この遺伝外情報は二重らせんをほどかずDNAの遺伝情報を読み取るタンパク質によって利用される。その情報はDNAを攻撃する多くの毒物や薬剤の対象ともなっている。

テーマの変化

A-DNA(左:PDB:1ana)、B-DNA(中央:PDB:1bna)、Z-DNA(右:PDB:2dcg)

生きた細胞で見られる典型的条件下において、DNAは「Bらせん」とよばれるなじみのある滑らかな二重らせんの形をとる。左図中央に示したのが、PDBエントリー 1bna の結晶構造によって明らかにされたBらせんの例である。この図は上部にある構造を重ね合わせて理想的なBらせんを作ったものである。ところがDNAは、別の条件下ではまた違った構造をとることができる。2つの結晶構造が早くに明らかとなっており、一方は左に示した PDBエントリー 1ana 、もう一方は右に示した PDBエントリー 2dcg である。左に示した構造は、塩基が傾いて深く大きな溝を持つ構造で、A-DNAと呼ばれる。この構造は脱水条件下で形成される。またRNAもこの構造をとることが多い。なぜならRNAはDNAよりも糖の水酸基が多く、これが邪魔をして安定なB型を作ることができない(例えば、以前の今月の分子で紹介した 運搬RNA のらせん構造を見て欲しい)。右に示す構造は、A-DNAやB-DNAとは逆方向にねじれており、Z-DNAと呼ばれる。この構造は高濃度の塩がある条件下で見られ、しかもシトシン-グアニン塩基対とグアニン-シトシン塩基対が交互に何度も現れるという特別な型の塩基配列を必要とする。

構造をみる

B-DNA(PDB:1bna)分子上部にはらせんのゆがみが、分子下部には塩基のねじれば見られる。

我々はDNAは完全で、滑らかな二重らせんであると考えることが多い。ところが実際は、DNAには多くの局所構造が見られる。ここに示したDNAの小さな断片は PDBエントリー 1bna の構造で、よく見られる変異を示している。上部では、らせんが左に曲がり、らせんが結晶の中に押し込められてゆがんでいる。下部では、2つの塩基が大きくねじれて、1つの完全な平面上にはない状態になっている。この状態が、お互いの鎖に沿って鎖上部に塩基を積み重ねる方法を改善し、二重らせん全体を安定化させる。DNA構造の研究が進むにつれ、DNAは動的な分子で、かなり柔軟性があり、DNAと相互作用するタンパク質によって曲げられ、ねじられ、むすばれたり解かれたりされ、ほどかれたり巻き直されたりされることが明らかになってきた。

詳細条件検索を使ってRCSB-PDBでDNA構造を探すには、「Molecule / Chain Type」で「Contains DNA」でYESを選択し、その他はNOを選択してください(PDBjの場合は「Contains Chain Type」で「polydeoxyribonucleotide」をYesに、その他をNoに設定して検索を行ってください)。2001年11月時点でPDBに登録されていた全てのDNA構造のリストをこちらのリストに掲載しています。

2001年11月 のキーワード検索による関連PDBエントリー一覧
このリストを閉じるには右上の×をクリックして下さい
PDB ID Title Authors Publication Year Journal Name Volume No First Page
101d Refinement of netropsin bound to DNA: bias and feedback in electron density map interpretation. D.S.Goodsell, M.L.Kopka, R.E.Dickerson 1995 Biochemistry 34 4983
102d Sequence-dependent drug binding to the minor groove of DNA: crystal structure of the DNA dodecamer d(CGCAAATTTGCG)2 complexed with propamidine. C.M.Nunn, S.Neidle 1995 J Med Chem 38 2317
103d The unusual structure of the human centromere (GGA)2 motif. Unpaired guanosine residues stacked between sheared G.A pairs. S.H.Chou, L.Zhu, B.R.Reid 1994 J Mol Biol 244 259
105d Solution structures of the i-motif tetramers of d(TCC), d(5methylCCT) and d(T5methylCC): novel NOE connections between amino protons and sugar protons. J.L.Leroy, M.Gueron 1995 Structure 3 101
106d
107d Solution structure of the covalent duocarmycin A-DNA duplex complex. C.H.Lin, D.J.Patel 1995 J Mol Biol 248 162
108d Solution structure of a DNA complex with the fluorescent bis- intercalator TOTO determined by NMR spectroscopy. H.P.Spielmann, D.E.Wemmer, J.P.Jacobsen 1995 Biochemistry 34 8542
109d ANALYSIS OF VAN-DER-WAALS AND ELECTROSTATIC CONTRIBUTIONS IN THE INTERACTIONS OF MINOR-GROOVE BINDING BENZIMIDAZOLES WITH DNA. A.Czarny, D.W.Boykin, A.A.Wood, C.M.Nunn, S.Neidle, M.Zhao, W.D.Wilson 1995 J Am Chem Soc 117 4716
110d ANTHRACYCLINE DNA INTERACTIONS AT UNFAVORABLE BASE-PAIR TRIPLET-BINDING SITES - STRUCTURES OF D(CGGCCG) DAUNOMYCIN AND D(TGGCCA) ADRIAMYCIN COMPLEXES. G.A.Leonard, T.W.Hambley, K.Mcauleyhecht, T.Brown, W.N.Hunter 1993 Acta Crystallogr
D Biol Crystallogr
49 458
1da9
111d Crystal structure and stability of a DNA duplex containing A(anti).G(syn) base-pairs. T.Brown, G.A.Leonard, E.D.Booth, J.Chambers 1989 J Mol Biol 207 455
112d Molecular structure of the G.A base pair in DNA and its implications for the mechanism of transversion mutations. T.Brown, W.N.Hunter, G.Kneale, O.Kennard 1986 Proc. Nat. Acad.
Sci. USA
83 2402
113d The structure of guanosine-thymidine mismatches in B-DNA at 2.5-A resolution. W.N.Hunter, T.Brown, G.Kneale, N.N.Anand, D.Rabinovich, O.Kennard 1987 J Biol Chem 262 9962
114d Inosine.adenine base pairs in a B-DNA duplex. P.W.Corfield, W.N.Hunter, T.Brown, P.Robinson, O.Kennard 1987 Nucleic Acids Res 15 7935
115d Ordered water structure in an A-DNA octamer at 1.7 A resolution. O.Kennard, W.B.Cruse, J.Nachman, T.Prange, Z.Shakked, D.Rabinovich 1986 J Biomol Struct Dyn 3 623
116d Crystal and molecular structure of the A-DNA dodecamer d(CCGTACGTACGG). Choice of fragment helical axis. C.A.Bingman, G.Zon, M.Sundaralingam 1992 J Mol Biol 227 738
117d Crystal and molecular structure of the alternating dodecamer d(GCGTACGTACGC) in the A-DNA form: comparison with the isomorphous non-alternating dodecamer d(CCGTACGTACGG). C.Bingman, S.Jain, G.Zon, M.Sundaralingam 1992 Nucleic Acids Res 20 6637
118d Crystal and molecular structure of d(GTGCGCAC): investigation of the effects of base sequence on the conformation of octamer duplexes. C.Bingman, X.Li, G.Zon, M.Sundaralingam 1992 Biochemistry 31 12803
119d Crystal and molecular structure of d(CGTAGATCTACG) at 2.25 A resolution. G.A.Leonard, W.N.Hunter 1993 J Mol Biol 234 198
121d Molecular structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor groove binding drug netropsin. L.Tabernero, N.Verdaguer, M.Coll, I.Fita, G.A.van der Marel, J.H.van Boom, A.Rich, J.Aymami 1993 Biochemistry 32 8403
122d DNA HELIX STRUCTURE AND REFINEMENT ALGORITHM - COMPARISON OF MODELS FOR D(CCAGGCM(5)CTGG) DERIVED FROM NUCLSQ, TNT AND X-PLOR. M.Hahn, U.Heinemann 1993 Acta Crystallogr
D Biol Crystallogr
49 468
123d
126d Crystal structure of CATGGCCATG and its implications for A-tract bending models. D.S.Goodsell, M.L.Kopka, D.Cascio, R.E.Dickerson 1993 Proc. Nat. Acad.
Sci. USA
90 2930
127d Conformation of B-DNA containing O6- ethyl- G-C base pairs stabilized by minor groove binding drugs: molecular structure of d(CGC[e6G]AATTCGCG complexed with Hoechst 33258 or Hoechst 33342. M.Sriram, G.A.van der Marel, H.L.Roelen, J.H.van Boom, A.H.Wang 1992 EMBO J 11 225
128d
129d
130d
131d The low-temperature crystal structure of the pure-spermine form of Z-DNA reveals binding of a spermine molecule in the minor groove. D.Bancroft, L.D.Williams, A.Rich, M.Egli 1994 Biochemistry 33 1073
132d Solution structure of the TnAn DNA duplex GCCGTTAACGCG containing the HpaI restriction site. S.G.Kim, B.R.Reid 1992 Biochemistry 31 12103
133d The crystal structure of N4- methylcytosine.guanosine base- pairs in the synthetic hexanucleotide d(CGCGm4CG). A.R.Cervi, A.Guy, G.A.Leonard, R.Teoule, W.N.Hunter 1993 Nucleic Acids Res 21 5623
134d Solution structure of a purine.purine.pyrimidine DNA triplex containing G.GC and T.AT triples. I.Radhakrishnan, D.J.Patel 1993 Structure 1 135
135d
136d
137d Evidence for crystal environment dominating base sequence effects on DNA conformation: crystal structures of the orthorhombic and hexagonal polymorphs of the A-DNA decamer d(GCGGGCCCGC) and comparison with their isomorphous crystal structures. B.Ramakrishnan, M.Sundaralingam 1993 Biochemistry 32 11458
138d
139d Solution structure of a parallel-stranded G-quadruplex DNA. Y.Wang, D.J.Patel 1993 J Mol Biol 234 1171
140d Solution structure of a conserved DNA sequence from the HIV-1 genome: restrained molecular dynamics simulation with distance and torsion angle restraints derived from two-dimensional NMR spectra. A.Mujeeb, S.M.Kerwin, G.L.Kenyon, T.L.James 1993 Biochemistry 32 13419
141d
142d
143d Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex. Y.Wang, D.J.Patel 1993 Structure 1 263
144d Minor groove binding of SN6999 to an alkylated DNA: molecular structure of d(CGC[e6G]AATTCGCG)- SN6999 complex. Y.G.Gao, M.Sriram, W.A.Denny, A.H.Wang 1993 Biochemistry 32 9639
145d Structure and thermodynamics of nonalternating C.G base pairs in Z-DNA: the 1.3-A crystal structure of the asymmetric hexanucleotide d(m5CGGGm5CG).d(m5CGCCm5CG). G.P.Schroth, T.F.Kagawa, P.S.Ho 1993 Biochemistry 32 13381
146d Solution structure of the mithramycin dimer-DNA complex. M.Sastry, D.J.Patel 1993 Biochemistry 32 6588
148d Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG). P.Schultze, R.F.Macaya, J.Feigon 1994 J Mol Biol 235 1532
149d Solution structure of a pyrimidine.purine.pyrimidine DNA triplex containing T.AT, C+.GC and G.TA triples. I.Radhakrishnan, D.J.Patel 1994 Structure 2 17
150d Guanine- 1, N6- ethenoadenine base pairs in the crystal structure of d(CGCGAATT(epsilon dA)GCG). G.A.Leonard, K.E.McAuley- Hecht, N.J.Gibson, T.Brown, W.P.Watson, W.N.Hunter 1994 Biochemistry 33 4755
151d Water ring structure at DNA interfaces: hydration and dynamics of DNA- anthracycline complexes. L.A.Lipscomb, M.E.Peek, F.X.Zhou, J.A.Bertrand, D.VanDerveer, L.D.Williams 1994 Biochemistry 33 3649
152d
153d Crystal structure of a mispaired dodecamer, d(CGAGAATTC(O6Me)GCG)2, containing a carcinogenic O6-methylguanine. S.L.Ginell, J.Vojtechovsky, B.Gaffney, R.Jones, H.M.Berman 1994 Biochemistry 33 3487
154d DNA distortion in bis-intercalated complexes. M.E.Peek, L.A.Lipscomb, J.A.Bertrand, Q.Gao, B.P.Roques, C.Garbay- Jaureguiberry, L.D.Williams 1994 Biochemistry 33 3794
156d Refined solution structure of the dimeric quadruplex formed from the Oxytricha telomeric oligonucleotide d(GGGGTTTTGGGG). P.Schultze, F.W.Smith, J.Feigon 1994 Structure 2 221
158d Crystallographic analysis of C- C- A- A- G- C- T- T- G- G and its implications for bending in B-DNA. K.Grzeskowiak, D.S.Goodsell, M.Kaczor- Grzeskowiak, D.Cascio, R.E.Dickerson 1993 Biochemistry 32 8923
159d Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex. X.Chen, B.Ramakrishnan, S.T.Rao, M.Sundaralingam 1994 Nat Struct Biol 1 169
160d High resolution crystal structure of the A-DNA decamer d(CCCGGCCGGG). Novel intermolecular base-paired G*(G.C) triplets. B.Ramakrishnan, M.Sundaralingam 1993 J Mol Biol 231 431
166d Crystal structure of gamma-oxapentamidine complexed with d(CGCGAATTCGCG)2. The effects of drug structural change on DNA minor-groove recognition. C.M.Nunn, T.C.Jenkins, S.Neidle 1994 Eur J Biochem 226 953
167d The crystal structure of C- C- A- T- T- A- A- T- G- G. Implications for bending of B-DNA at T-A steps. D.S.Goodsell, M.Kaczor- Grzeskowiak, R.E.Dickerson 1994 J Mol Biol 239 79
171d Solution structure of a DNA dodecamer containing the anti- neoplastic agent arabinosylcytosine: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement. B.I.Schweitzer, T.Mikita, G.W.Kellogg, K.H.Gardner, G.P.Beardsley 1994 Biochemistry 33 11460
172d MULTIPLE BINDING MODES OF ANTICANCER DRUG ACTINOMYCIN-D - X-RAY, MOLECULAR MODELING, AND SPECTROSCOPIC STUDIES OF D(GAAGCTTC)(2)- ACTINOMYCIN- D COMPLEXES AND ITS HOST DNA. S.Kamitori, F.Takusagawa 1994 J Am Chem Soc 116 4154
173d
175d DNA sequence GCGAATGAGC containing the human centromere core sequence GAAT forms a self- complementary duplex with sheared G.A pairs in solution. S.H.Chou, J.W.Cheng, O.Fedoroff, B.R.Reid 1994 J Mol Biol 241 467
177d Solution structure and hydration patterns of a pyrimidine.purine.pyrimidine DNA triplex containing a novel T.CG base- triple. I.Radhakrishnan, D.J.Patel 1994 J Mol Biol 241 600
178d Crystal structure of a DNA duplex containing 8- hydroxydeoxyguanine- adenine base pairs. K.E.McAuley- Hecht, G.A.Leonard, N.J.Gibson, J.B.Thomson, W.P.Watson, W.N.Hunter, T.Brown 1994 Biochemistry 33 10266
179d Solution structure of the d(T- C- G- A) duplex at acidic pH. A parallel- stranded helix containing C+ .C, G.G and A.A pairs. Y.Wang, D.J.Patel 1994 J Mol Biol 242 508
180d Sequence- dependent microheterogeneity of Z-DNA: the crystal and molecular structures of d(CACGCG).d(CGCGTG) and d(CGCACG).d(CGTGCG). C.Sadasivan, N.Gautham 1995 J Mol Biol 248 918
181d
182d DNA- nogalamycin interactions: the crystal structure of d(TGATCA) complexed with nogalamycin. C.K.Smith, G.J.Davies, E.J.Dodson, M.H.Moore 1995 Biochemistry 34 415
183d X-ray structure of a DNA decamer containing 7, 8- dihydro- 8- oxoguanine. L.A.Lipscomb, M.E.Peek, M.L.Morningstar, S.M.Verghis, E.M.Miller, A.Rich, J.M.Essigmann, L.D.Williams 1995 Proc. Nat. Acad.
Sci. USA
92 719
184d Self- association of a DNA loop creates a quadruplex: crystal structure of d(GCATGCT) at 1.8 A resolution. G.A.Leonard, S.Zhang, M.R.Peterson, S.J.Harrop, J.R.Helliwell, W.B.Cruse, B.L.d'Estaintot, O.Kennard, T.Brown, W.N.Hunter 1995 Structure 3 335
186d Solution structure of the Tetrahymena telomeric repeat d(T2G4)4 G- tetraplex. Y.Wang, D.J.Patel 1994 Structure 2 1141
187d Hydration patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition. M.Eisenstein, Z.Shakked 1995 J Mol Biol 248 662
188d
189d
190d Crystal structure of a four- stranded intercalated DNA: d(C4). L.Chen, L.Cai, X.Zhang, A.Rich 1994 Biochemistry 33 13540
191d Crystal structure of intercalated four- stranded d(C3T) at 1.4 A resolution. C.H.Kang, I.Berger, C.Lockshin, R.Ratliff, R.Moyzis, A.Rich 1994 Proc. Nat. Acad.
Sci. USA
91 11636
192d Recombination- like structure of d(CCGCGG). L.Malinina, L.Urpi, X.Salas, T.Huynh- Dinh, J.A.Subirana 1994 J Mol Biol 243 484
194d X-RAY STRUCTURES OF THE B-DNA DODECAMER D(CGCGTTAACGCG) WITH AN INVERTED CENTRAL TETRANUCLEOTIDE AND ITS NETROPSIN COMPLEX. K.Balendiran, S.T.Rao, C.Y.Sekharudu, G.Zon, M.Sundaralingam 1995 Acta Crystallogr
D Biol Crystallogr
51 190
195d
196d Crystal structure of C- T- C- T- C- G- A- G- A- G. Implications for the structure of the Holliday junction. D.S.Goodsell, K.Grzeskowiak, R.E.Dickerson 1995 Biochemistry 34 1022
197d Orthorhombic crystal structure of the A-DNA octamer d(GTACGTAC). Comparison with the tetragonal structure. B.Langlois d'Estaintot, A.Dautant, C.Courseille, G.Precigoux 1993 Eur J Biochem 213 673
198d A trigonal form of the idarubicin:d(CGATCG) complex; crystal and molecular structure at 2.0 A resolution. A.Dautant, B.Langlois d'Estaintot, B.Gallois, T.Brown, W.N.Hunter 1995 Nucleic Acids Res 23 1710
199d Solution structure of the monoalkylated mitomycin C-DNA complex. M.Sastry, R.Fiala, R.Lipman, M.Tomasz, D.J.Patel 1995 J Mol Biol 247 338
1a6h Solution structure of a DNA quadruplex containing the fragile X syndrome triplet repeat. A.Kettani, R.A.Kumar, D.J.Patel 1995 J Mol Biol 254 638
1a83 An intramolecular i-motif: the solution structure and base- pair opening kinetics of d(5mCCT3CCT3ACCT3CC). X.Han, J.L.Leroy, M.Gueron 1998 J Mol Biol 278 949
1a84 NMR solution structure of a DNA dodecamer duplex containing a cis- diammineplatinum(II) d(GpG) intrastrand cross- link, the major adduct of the anticancer drug cisplatin. A.Gelasco, S.J.Lippard 1998 Biochemistry 37 9230
1a8n Solution structure of a Na cation stabilized DNA quadruplex containing G.G.G.G and G.C.G.C tetrads formed by G-G-G-C repeats observed in adeno- associated viral DNA. A.Kettani, S.Bouaziz, A.Gorin, H.Zhao, R.A.Jones, D.J.Patel 1998 J Mol Biol 282 619
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1ac9 Solution structure of a DNA decamer containing the antiviral drug ganciclovir: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement. M.Foti, S.Marshalko, E.Schurter, S.Kumar, G.P.Beardsley, B.I.Schweitzer 1997 Biochemistry 36 5336
1af1 Styrene oxide adducts in an oligodeoxynucleotide containing the human N-ras codon 12 sequence: structural refinement of the minor groove R(12, 2)- and S(12, 2)- alpha- (N2- guanyl) stereoisomers from 1H NMR. I.S.Zegar, F.R.Setayesh, B.L.DeCorte, C.M.Harris, T.M.Harris, M.P.Stone 1996 Biochemistry 35 4334
1aff Bombyx mori single repeat telomeric DNA sequence forms a G-quadruplex capped by base triads. A.Kettani, S.Bouaziz, W.Wang, R.A.Jones, D.J.Patel 1997 Nat Struct Biol 4 382
1afz Solution structure of an oligodeoxynucleotide containing the human N-ras codon 12 sequence refined from 1H NMR using molecular dynamics restrained by nuclear Overhauser effects. I.S.Zegar, M.P.Stone 1996 Chem Res Toxicol 9 114
1ag3 Structure of a duplex oligodeoxynucleotide containing propanodeoxyguanosine opposite a two-base deletion in the (CpG)3 frame shift hotspot of Salmonella typhimurium hisD3052 determined by 1H NMR and restrained molecular dynamics. J.P.Weisenseel, J.G.Moe, G.R.Reddy, L.J.Marnett, M.P.Stone 1995 Biochemistry 34 50
1ag5 Refined solution structure of 8, 9- dihydro- 8- (N7- guanyl)- 9- hydroxyaflatoxin B1 opposite CpA in the complementary strand of an oligodeoxynucleotide duplex as determined by 1H NMR. D.S.Johnston, M.P.Stone 1995 Biochemistry 34 14037
1agh Solution structure of an oligodeoxynucleotide containing the human n-ras codon 61 sequence refined from 1H NMR using molecular dynamics restrained by nuclear Overhauser effects. B.Feng, M.P.Stone 1995 Chem Res Toxicol 8 821
1agk Major groove (R)- alpha-(N6- adenyl)styrene oxide adducts in an oligodeoxynucleotide containing the human N-ras codon 61 sequence: conformations of the R(61, 2) and R(61, 3) sequence isomers from 1H NMR. B.Feng, L.Zhou, M.Passarelli, C.M.Harris, T.M.Harris, M.P.Stone 1995 Biochemistry 34 14021
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1ago Major groove (S)- alpha-(N6- adenyl)styrene oxide adducts in an oligodeoxynucleotide containing the human N-ras codon 61 sequence: conformations of the S(61, 2) and S(61, 3) sequence isomers from 1H NMR. B.Feng, M.Voehler, L.Zhou, M.Passarelli, C.M.Harris, T.M.Harris, M.P.Stone 1996 Biochemistry 35 7316
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1au5 Structure and isomerization of an intrastrand cisplatin- cross- linked octamer DNA duplex by NMR analysis. D.Yang, S.S.van Boom, J.Reedijk, J.H.van Boom, A.H.Wang 1995 Biochemistry 34 12912
1au6 A novel DNA structure induced by the anticancer bisplatinum compound crosslinked to a GpC site in DNA. D.Yang, S.S.van Boom, J.Reedijk, J.H.van Boom, N.Farrell, A.H.Wang 1995 Nat Struct Biol 2 577
1aul Solution structure of a highly stable DNA duplex conjugated to a minor groove binder. S.Kumar, M.W.Reed, H.B.Gamper Jr., V.V.Gorn, E.A.Lukhtanov, M.Foti, J.West, R.B.Meyer Jr., B.I.Schweitzer 1998 Nucleic Acids Res 26 831
1aw4 Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP. C.H.Lin, D.J.Patel 1997 Chem Biol 4 817
1ax6 Solution structure of the aminofluorene- intercalated conformer of the syn [AF]- C8- dG adduct opposite a––2 deletion site in the NarI hot spot sequence context. B.Mao, A.Gorin, Z.Gu, B.E.Hingerty, S.Broyde, D.J.Patel 1997 Biochemistry 36 14479
1ax7 Solution structure of the aminofluorene- stacked conformer of the syn [AF]- C8- dG adduct positioned at a template- primer junction. B.Mao, Z.Gu, A.Gorin, B.E.Hingerty, S.Broyde, D.J.Patel 1997 Biochemistry 36 14491
1axl Solution conformation of the (-)- trans- anti- [BP]dG adduct opposite a deletion site in a DNA duplex: intercalation of the covalently attached benzo[a]pyrene into the helix with base displacement of the modified deoxyguanosine into the minor groove. B.Feng, A.Gorin, A.Kolbanovskiy, B.E.Hingerty, N.E.Geacintov, S.Broyde, D.J.Patel 1997 Biochemistry 36 13780
1axo Structural alignment of the (+)- trans- anti- benzo [a] pyrene- dG adduct positioned opposite dC at a DNA template-primer junction. B.Feng, A.Gorin, B.E.Hingerty, N.E.Geacintov, S.Broyde, D.J.Patel 1997 Biochemistry 36 13769
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1axu Solution Structure of the N- (Deoxyguanosin- 8- Yl)- 1- Aminopyrene ([Ap]Dg) Adduct Opposite Da in a DNA Duplex Z.Gu, A.Gorin, R.Krishnasami, B.E.Hingerty, A.K.Basu, S.Broyde, D.J.Patel n/a To be Published n/a n/a
1axv Solution Structure of the (+)- Cis- Anti- Benzo[A]Pyrene ([Bp]Da) Adduct Opposite Dt in a DNA Duplex B.Mao, Z.Gu, A.A.Gorin, J.Chen, B.E.Hingerty, S.Amid, S.Broyde, N.E.Geacintov, D.J.Patel n/a To be Published n/a n/a
1b0s Binding of Ar-1-144, a Tri-Imidazole DNA Minor Groove Binder, to Ccgg Sequence Analyzed by NMR Spectroscopy X.-L.Yang, C.Kaenzig, M.Lee, A.H.-J.Wang 1999 Eur.J.Biochem. 263 646
1b3p Interlocked Mismatch- Aligned Arrowhead DNA Motifs A.Kettani, S.Bouaziz, E.Skripkin, A.Majumdar, W.Wang, R.A.Jones, D.J.Patel 1999 Structure (London) 7 803
1b4y Structure and Mechanism of Formation of the H-Y5 Isomer of an Intramolecular DNA Triple Helix M.J.P.Van Dongen, J.F.Doreleijers, G.A.Van Der Marel, J.H.Van Boom, C.W.Hilbers, S.S.Wijmenga 1999 Nat.Struct.Biol. 6 854
1b5k NMR solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3, N4- etheno- 2'- deoxycytidine opposite thymidine: comparison with the duplex containing deoxyadenosine opposite the adduct. D.Cullinan, A.Korobka, A.P.Grollman, D.J.Patel, M.Eisenberg, C.de los Santos 1996 Biochemistry 35 13319
1b60 Solution Structure of an 11-mer Duplex Containing the 3, N4- Ethenocytosine Adduct Opposite 2'- Deoxycytidine: Implications for the Recognition of Exocyclic Lesions by DNA Glycosylases D.Cullinan, F.Johnson, C.De Los Santos 2000 J.Mol.Biol. 296 851
1b6x Solution structure of a DNA duplex containing the exocyclic lesion 3, N4- etheno- 2'- deoxycytidine opposite 2'- deoxyguanosine. D.Cullinan, F.Johnson, A.P.Grollman, M.Eisenberg, C.de los Santos 1997 Biochemistry 36 11933
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1bcb The contribution of cytosine protonation to the stability of parallel DNA triple helices. J.L.Asensio, A.N.Lane, J.Dhesi, S.Bergqvist, T.Brown 1998 J Mol Biol 275 811
1bce Comparison of the solution structures of intramolecular DNA triple helices containing adjacent and non-adjacent CG.C+ triplets. J.L.Asensio, T.Brown, A.N.Lane 1998 Nucleic Acids Res 26 3677
1bd1 Crystallographic study of one turn of G/C-rich B-DNA. U.Heinemann, C.Alings 1989 J Mol Biol 210 369
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1bdz NMR structure of the extended Myb cognate sequence and modeling studies on specific DNA-Myb complexes. P.K.Radha, P.K.Patel, R.V.Hosur 1998 Biochemistry 37 9952
1be5 Structural studies of a stable parallel-stranded DNA duplex incorporating isoguanine:cytosine and isocytosine:guanine basepairs by nuclear magnetic resonance spectroscopy. X.L.Yang, H.Sugiyama, S.Ikeda, I.Saito, A.H.Wang 1998 Biophys J 75 1163
1bhr 2'- Deoxyisoguanosine adopts more than one tautomer to form base pairs with thymidine observed by high-resolution crystal structure analysis. H.Robinson, Y.G.Gao, C.Bauer, C.Roberts, C.Switzer, A.H.Wang 1998 Biochemistry 37 10897
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1bn9 Solution Structure of the Orphan Nuclear Receptor Rev-Erb Beta Response Element by 1H, 31P NMR and Molecular Simulation C.Castagne, H.Terenzi, M.M.Zakin, M.Delepierre n/a To be Published n/a n/a
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1bp8 The Three Dimensional Structure of the 4:1 Mithramycin: D(Acccgggt)2 Complex: Evidence for an Interaction between the E Saccharides M.A.Keniry, E.A.Owen, R.H.Shafer n/a To be Published n/a n/a
1bps Solution structure of the minor conformer of a DNA duplex containing a dG mismatch opposite a benzo[a]pyrene diol epoxide/dA adduct: glycosidic rotation from syn to anti at the modified deoxyadenosine. J.L.Schwartz, J.S.Rice, B.A.Luxon, J.M.Sayer, G.Xie, H.J.Yeh, X.Liu, D.M.Jerina, D.G.Gorenstein 1997 Biochemistry 36 11069
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1c11 Centromeric pyrimidine strands fold into an intercalated motif by forming a double hairpin with a novel T:G:G:T tetrad: solution structure of the d(TCCCGTTTCCA) dimer. J.Gallego, S.H.Chou, B.R.Reid 1997 J Mol Biol 273 840
1c32 Structures of the Potassium- Saturated, 2:1, And Intermediate, 1:1, Forms of a Quadruplex DNA V.M.Marathias, P.H.Bolton 2000 Nucleic Acids Res. 28 1969
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1c9z Effects of Cationic Charge on Three- Dimensional Structures of Intercalative Complexes: Structure of a Bis- Intercalated DNA Complex Solved by MAD Phasing X.Shui, M.E Peek, L.A.Lipscomb, A.P.Wilkinson, L.D.Williams, M.Gao, C.Ogata, B.P.Roques, C.Garbay- Jaureguiberry 2000 Curr.Med.Chem. 7 59
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1coc Solution- state structure of a DNA dodecamer duplex containing a Cis- syn thymine cyclobutane dimer, the major UV photoproduct of DNA. K.McAteer, Y.Jing, J.Kao, J.S.Taylor, M.A.Kennedy 1998 J Mol Biol 282 1013
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1cqo NMR Structure of the Palindromic DNA Decamer D(Gcgttaacgc)2 J.A.Smith, V.T.Tsui, W.J.Chazin, D.A.Case n/a To be Published n/a n/a
1cr3 Solution Conformation of the (+)- Trans- Anti- Benzo[G]Chrysene- Da Adduct Opposite Dt in a DNA Duplex A.K.Suri, B.Mao, S.Amin, N.E.Geacintov, D.J.Patel 1999 J.Mol.Biol. 292 289
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1cs7 Structure and Photoinduced Electron Transfer in Exceptionally Stable Synthetic DNA Hairpins with Stilbenediether Linkers F.D.Lewis, X.Liu, Y.Wu, S.E.Miller, M.R.Wasielewski, R.L.Letsinger, R.Sanishvili, A.Joachimiak, V.Tereshko, M.Egli 1999 J.Am.Chem.Soc. 121 9905
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1cx3 Solution Structure and Dynamics of a Complex between DNA and the Antitumor Bisnaphthalimide Lu- 79553: Intercalated Ring Flipping on the Millisecond Time Scale J.Gallego, B.R.Reid 1999 Biochemistry 38 15104
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1d54 Anthracycline binding to DNA. High-resolution structure of d(TGTACA) complexed with 4'-epiadriamycin. G.A.Leonard, T.Brown, W.N.Hunter 1992 Eur J Biochem 204 69
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1d58 The molecular structure of a 4'- epiadriamycin complex with d(TGATCA) at 1.7A resolution: comparison with the structure of 4'- epiadriamycin d(TGTACA) and d(CGATCG) complexes. B.Langlois d'Estaintot, B.Gallois, T.Brown, W.N.Hunter 1992 Nucleic Acids Res 20 3561
1d59 Crystal structure of four-stranded Oxytricha telomeric DNA. C.Kang, X.Zhang, R.Ratliff, R.Moyzis, A.Rich 1992 Nature 356 126
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1d62 The Structure of a /B-DNA Decamer with an I(Slash)A Mismatch and Comparison with the G(Slash)A Mismatch A.A.Lipanov, M.L.Kopka, M.Kaczor- Grzeskowiak, R.E.Dickerson n/a To be Published n/a n/a
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1dcv The Holliday Junction in an Inverted Repeat DNA Sequence: Sequence Effects on the Structure of Four-Way Junctions B.F.Eichman, J.M.Vargason, B.H.M.Mooers, P.S.Ho 2000 Proc. Nat. Acad.
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1dcw The Holliday Junction in an Inverted Repeat Sequence: Sequence Effects on the Structure of Four-Way Junctions B.F.Eichman, J.M.Vargason, B.H.M.Mooers, P.S.Ho 2000 Proc. Nat. Acad.
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1ddp Solution structure of a cisplatin-induced DNA interstrand cross-link. H.Huang, L.Zhu, B.R.Reid, G.P.Drobny, P.B.Hopkins 1995 Science 270 1842
1dgo Structural Basis for Uracil DNA Glycosylase (Udg) Interaction with DNA: NMR Characterization M.Ghosh, N.V.Kumar, U.Varshney, K.V.R.Chary 2000 Nucleic Acids Res. 9 1906
1dj6 Crystal Structure of a Molecular Complex of a Left-Handed Z-DNA Hexamer, D(Cg) 3, with Synthetic Polyamine: Polyamine Binding in the Minor Groove at Room Temperature H.Ohishi, K.-I.Tomita, I.Nakanishi, M.Ohtsuchi, T.Hakoshima, A.Rich n/a To be Published n/a n/a
1djd Role of a Polycyclic Aromatic Hydrocarbon Bay Region Ring in Modulating DNA Adduct Structure: The Non-Bay Region (8S, 9R, 10S, 11R)- N(6)- [11- (8, 9, 10, 11- Tetrahydro- 8, 9, 10- Trihydroxybenz[A]Anthracenyl)]- 2'- Deoxyadenosyl Adduct in Codon 61 of the Human N-Ras Protooncogene Z.Li, H.Y.Kim, P.J.Tamura, C.M.Harris, T.M.Harris, M.P.Stone 1999 Biochemistry 38 14820
1dk6 NMR Structure Analysis of the DNA Nine Base Pair Duplex D(Catgagtac) D(Gtac( Np3)Catg) D.A.Klewer, A.Hoskins, V.J.Davisson, D.E.Bergstrom, A.C.Liwang n/a To be Published n/a n/a
1dk9 Structure of a DNA Duplex Containing Nucleoside Analog 1- (2'- Deoxy- Beta-D- Ribofuranosyl)- 3- Nitropyrrole and the Structure of the Unmodified Control D.A.Klewer, A.Hoskins, P.Zhang, V.J.Davisson, D.E.Bergstrom, A.C.Liwang 2000 Nucleic Acids Res. 28 4514
1dl4 Intercalation of the 1S, 2R, 3S, 4R- N6- [1- (1, 2, 3, 4- Tetrahydro- 2, 3, 4- Trihydroxy- Benz[A]Anthracenyl)]- 2'- Deoxyadenosyl Adduct in an Oligodeoxynucleotide Containing the Human N-Ras Codon 61 Sequence Z.Li, H.-Y.Kim, P.J.Tamura, C.M.Harris, T.M.Harris, M.P.Stone 1999 Biochemistry 38 16045
1dl8 Acridinecarboxamide Topoisomerase Poisons: Structural and Kinetic Studies of the DNA Complexes of 5- Substituted 9- Amino- (N- (2- Dimethylamino)Ethyl)Acridine- 4- Carboxamides A.Adams, J.M.Guss, C.A.Collyer, W.A.Denny, A.S.Prakash, L.P.G.Wakelin 2000 Mol.Pharmacol. 58 649
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1dn6 The crystal structure of d(GGATGGGAG): an essential part of the binding site for transcription factor IIIA. M.McCall, T.Brown, W.N.Hunter, O.Kennard 1986 Nature 322 661
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1dnf Effects of 5- fluorouracil/ guanine wobble base pairs in Z-DNA: molecular and crystal structure of d(CGCGFG). M.Coll, D.Saal, C.A.Frederick, J.Aymami, A.Rich, A.H.Wang 1989 Nucleic Acids Res 17 911
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1dnm Crystal structure and sequence- dependent conformation of the A.G mispaired oligonucleotide d(CGCAAGCTGGCG). G.D.Webster, M.R.Sanderson, J.V.Skelly, S.Neidle, P.F.Swann, B.F.Li, I.J.Tickle 1990 Proc. Nat. Acad.
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1dnn Smooth Bending of /DNA in Chromatin E.N.Trifonov, J.L.Sussman 1979 Molecular Mechanisms of Biological Recognition n/a 227
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1dnz Hexahydrated Magnesium Ions Bind in the Deep Major Groove and at the Outer Mouth of the A-Form Nucleic Acid Duplexes H.Robinson, Y.-G.Gao, R.Sanishvili, A.Joachimiak, A.H.-J.Wang 2000 Nucleic Acids Res. 28 1760
1dou Monovalent Cations Sequester within the A-Tract Minor Groove of [D(Cgcgaattcgcg)]2 K.K.Woods, L.Mcfail-Isom, C.C.Sines, S.B.Howerton, R.K.Stephens, L.D.Williams 2000 J.Am.Chem.Soc. 122 1546
1dpn X-Ray Crystallographic Analysis of the Hydration of A-and B-Form DNA at Atomic Resolution M.Egli, V.Tereshko, M.Teplova, G.Minasov, A.Joachimiak, R.Sanishvili, C.M.Weeks, R.Miller, M.A.Maier, H.An, P.Dan Cook, M.Manoharan 1998 Biopolymers 48 234
1dsa High resolution solution structure of a DNA duplex alkylated by the antitumor agent duocarmycin SA. P.S.Eis, J.A.Smith, J.M.Rydzewski, D.A.Case, D.L.Boger, W.J.Chazin 1997 J Mol Biol 272 237
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1duf The NMR Structure of a DNA Dodecamer in an Aqueous Dilute Liquid Crystalline Phase N.Tjandra, S.Tate, A.Ono, M.Kainosho, A.Bax 2000 J.Am.Chem.Soc. 122 6190
1dxa NMR solution structure of a nonanucleotide duplex with a dG mismatch opposite a 10S adduct derived from trans addition of a deoxyadenosine N6- amino group to (+)- (7R, 8S, 9S, 10R)- 7, 8- dihydroxy- 9, 10- epoxy- 7, 8, 9, 10- tetrahydrobenzo[a]pyrene: an unusual syn glycosidic torsion angle at the modified dA. H.J.Yeh, J.M.Sayer, X.Liu, A.S.Altieri, R.A.Byrd, M.K.Lakshman, H.Yagi, E.J.Schurter, D.G.Gorenstein, D.M.Jerina 1995 Biochemistry 34 13570
1ecu Solution Structure of E2F Binding DNA Fragment Gcgcgaaac- T- Gtttcgcgc Studied by Molecular Dynamics Simulation and Two Dimensional NMR Experiment J.H.Wu, C.Chang, J.M.Pei, Q.Xiao, Y.Y.Shi 2000 To be Published n/a n/a
1edr Crystallographic Studies on Damaged Dnas. II. N6- Methoxyadenine Can Present Two Alternate Faces for Watson- Crick Base- Pairing, Leading to Pyrimidine Transition Mutagenesis T.Chatake, T.Hikima, A.Ono, Y.Ueno, A.Matsuda, A.Takenaka 1999 J.Mol.Biol. 294 1223
1eeg A Dimeric DNA Interface Stabilized by Stacked A(Gggg)A Hexads and Coordinated Monovalent Cations A.Kettani, A.Gorin, A.Majumdar, T.Hermann, E.Skripkin, H.Zhao, R.Jones, D.J.Patel 2000 J.Mol.Biol. 297 627
1eek Solution Structure of a Nonpolar, Non Hydrogen Bonded Base Pair Surrogate in DNA. E.T.Kool, T.R.Krugh, K.M.Guckian 2000 To be Published n/a n/a
1eel Structure of Dcgcgaattcgcg Bis[Piperidino- Ethyl]- Furamidine Complex S.Neidle, I.J.Simpson n/a To be Published n/a n/a
1ehv A New Crystal Form for the Dodecamer
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1ei4 Structural Basis of Cleavage by Rnase H of Hybrids of Arabinonucleic Acids and RNA G.Minasov, M.Teplova, P.Nielsen, J.Wengel, M.Egli 2000 Biochemistry 39 3525
1ekh A High-Resolution Structure of a DNA- Chromomycin- Co(II) Complex Determined from Pseudocontact Shifts in Nuclear Magnetic Resonance M.Gochin 2000 Structure Fold Des. 8 441
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1ekw Hybrid- Hybrid Matrix Structural Refinement of a DNA Three-Way Junction from 3D Noesy-Noesy V.Thiviyanathan, B.A.Luxon, N.B.Leontis, D.Donne, D.G.Gorenstein 1999 J.Biomol.NMR 14 209
1el2 The Solution Structure and Internal Motions of a Fragment of the Cytidine- Rich Strand of the Human Telomere A.T.Phan, M.Gueron, J.-L.Leroy 2000 J.Mol.Biol. 299 123
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1em0 A DNA-Porphyrin Minor-Groove Complex at Atomic Resolution: The Structural Consequences of Porphyrin Ruffling M.Bennett, A.Krah, F.Wien, E.Garman, R.McKenna, M.Sanderson, S.Neidle 2000 Proc. Nat. Acad.
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1emq NMR Observation of T-Tetrads in a Parallel Stranded DNA Quadruplex Formed by Saccharomyces Cerevisiae Telomere Sequence R.V.Hosur, P.K.Patel 1999 Nucleic Acids Res. 27 2457
1en1 Structure of the HIV-1 Minus Strand Primer Binding Site P.E.Johnson, R.B.Turner, Z.R.Wu, J.G.Levin, M.F.Summers n/a To be Published n/a n/a
1en3 1 a Crystal Structures of B-DNA Reveal Sequence-Specific Binding and Groove-Specific Bending of DNA by Magnesium and Calcium T.K.Chiu, R.E.Dickerson 2000 J.Mol.Biol. 301 915
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1enn Solvent Organization in an Oligonucleotide Crystal: The Structure of D(Gcgaattcg)2 at Atomic Resolution M.Soler-Lopez, L.Malinina, J.A.Subirana 2000 J.Biol.Chem. 275 23034
1ess The NMR structure of estrone (Es)- tethered tandem DNA duplex:
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1eu2 Dimeric Solution Structure of Two Cyclic Octamers: Four-Stranded DNA Structures Stabilized by A:T:A:T and G:C:G:C N.Escaja, E.Pedroso, M.Rico, C.Gonzalez 2000 J.Am.Chem.Soc. 122 12732
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1evm NMR Studies on Truncated Sequences of Human Telomeric DNA: Observation of a Novel A-Tetrad P.K.Patel, A.S.R.Koti, R.V.Hosur 1999 Nucleic Acids Res. 27 3836
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1evo NMR Observation of a Novel C-Tetrad in the Structure of the Sv40 Repeat Sequence Gggcgg P.K.Patel, N.S.Bhavesh, R.V.Hosur 2000 Biochem. Biophys.
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1ew1 An Extended DNA Structure Through Deoxyribose-Base Stacking Induced by Reca Protein T.Nishinaka, Y.Ito, S.Yokoyama, T.Shibata 1997 Proc. Nat. Acad.
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1exl Structure of an 11-mer DNA Duplex Containing the Carbocyclic Nucleotide Analog: 2'- Deoxyaristeromycin. S.Smirnov, F.Johnson, R.Marumoto, C.De Los Santos 2000 To be Published n/a n/a
1ez5 Bending of DNA Upon Binding of Ecteinascidin 743 and Phthalascidin 650 Studied by Unrestrained Molecular Dynamics Simulations R.Garcia-Nieto, I.Manzanares, C.Cuevas, F.Gago 2000 J.Am.Chem.Soc. 122 7172
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1ezn Solution Structure of a DNA Three-Way Junction Containing Two Unpaired Thymidine Bases. Identification of Sequence Features that Decide Conformer Selection B.N.M.Van Buuren, F.J.Overmars, J.H.Ippel, C.Altona, S.S.Wijmenga 2000 J.Mol.Biol. 304 371
1f3s A Two-Stranded Template-Based Approach to G.(C-A) Triad Formation: Designing Novel Structural Elements Into an Existing DNA Framework A.Kettani, G.Basu, A.Gorin, A.Majumdar, E.Skripkin, D.J.Patel 2000 J.Mol.Biol. 301 129
1f69 The Extended and Eccentric E-DNA Structure Induced by Cytosine Methylation or Bromination J.M.Vargason, B.F.Eichman, P.S.Ho 2000 Nat.Struct.Biol. 7 758
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1fd5 Binding of a Macrocyclic Bisacridine and Ametantrone to Cgtacg Involves Similar Unusual Intercalation Platforms X.-L.Yang, H.Robinson, Y.-G.Gao, A.H.-J.Wang 2000 Biochemistry 39 10950
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1fhy The Crystal Structures of Psoralen Cross-Linked Dnas: Drug-Dependent Formation of Holliday Junctions B.F.Eichman, B.H.M.Mooers, M.Alberti, J.E.Hearst, P.S.Ho 2001 J.Mol.Biol. 308 15
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1fj5 Accomodation of S- Cis- Tamoxifen- N2- Guanine Adduct within a Bent and Widened DNA Minor Groove S.Shimotakahara, A.Gorin, A.Kolbanovskiy, A.Kettani, B.E.Hingerty, S.Amin, S.Broyde, N.Geacintov, D.J.Patel 2000 J.Mol.Biol. 302 375
1fjb Structural studies of the ionizing radiation adduct 7, 8- dihydro- 8- oxoadenine (A(oxo)) positioned opposite thymine in a DNA duplex. H.F.Chen, F.Johnson, A.P.Grollman, D.J.Patel 1996 MAGNETIC RESONANCE IN CHEMISTRY 34 23
1fky Solution structure as a function of pH of two central mismatches, C . T and C . C, in the 29 to 39 K-ras gene sequence, by nuclear magnetic resonance and molecular dynamics. Y.Boulard, J.A.Cognet, G.V.Fazakerley 1997 J Mol Biol 268 331
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1fmq DNA Minor Groove Interactions and the Biological Activity of 2, 5- Bis- [4- (N- Alkylamidino)Phenyl] Furans I.J.Simpson, M.Lee, A.Kumar, D.W.Boykin, S.Neidle 2000 To be Published n/a n/a
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1fn1 A Novel Form of Interaclation Involving Four DNA Duplexes in an Acridine- 4- Carboxamide Complex of D(Cgtacg)2 A.Adams, J.M.Guss, C.A.Collyer, W.A.Denny, L.P.G.Wakelin 2000 Nucleic Acids Res. 28 4244
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1fq2 Cations Mediate B-DNA Conformational Heterogeneity C.C.Sines, L.Mcfail-Isom, S.B.Howerton, D.Vanderveer, L.D.Williams 2000 J.Am.Chem.Soc. 122 11048
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206d Base-pair opening and spermine binding––B-DNA features displayed in the crystal structure of a gal operon fragment: implications for protein-DNA recognition. L.W.Tari, A.S.Secco 1995 Nucleic Acids Res 23 2065
207d Solution structure of mithramycin dimers bound to partially overlapping sites on DNA. M.Sastry, R.Fiala, D.J.Patel 1995 J Mol Biol 251 674
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214d Structure of a DNA duplex containing a single 2'- O- methyl- beta-D- araT: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement. C.H.Gotfredsen, H.P.Spielmann, J.Wengel, J.P.Jacobsen 1996 Bioconjug Chem 7 680
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230d Solution structures of unimolecular quadruplexes formed by oligonucleotides containing Oxytricha telomere repeats. F.W.Smith, P.Schultze, J.Feigon 1995 Structure 3 997
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337d Structural Parameters from Single-Crystal Structures for Accurate Models of A- DNA B.H.M.Mooers, B.F.Eichman, P.S.Ho n/a To be Published n/a n/a
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344d Determination by MAD-DM of the structure of the DNA duplex d[ACGTACG(5- BrU)]2 at 1.46 A and 100 K. A.K.Todd, A.Adams, H.R.Powell, D.J.Wilcock, J.H.Thorpe, A.Lausi, F.Zanini, L.P.Wakelin, C.J.Cardin 1999 Acta Crystallogr
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423d Structural Code for DNA Recognition Revealed in Crystal Structures of Papillomavirus E2-DNA Targets H.Rozenberg, D.Rabinovich, F.Frolow, R.S.Hegde, Z.Shakked 1998 Proc. Nat. Acad.
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442d Structures of M-Iodo Hoechst-DNA Complexes in Crystals with Reduced Solvent Content: Implications for Minor Goove Binder Drug Design C.J.Squire, L.J.Baker, G.R.Clark, R.F.Martin, J.White 2000 Nucleic Acids Res. 28 1252
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476d Atomic- Resolution Crystal Structures of B-DNA Reveal Specific Influences of Divalent Metal Ions on Conformation and Packing G.Minasov, V.Tereshko, M.Egli 1999 J.Mol.Biol. 291 83
477d
478d Atomic- Resolution Crystal Structures of B-DNA Reveal Specific Influence of Divalent Metal Ions on Conformation and Packing G.Minasov, V.Tereshko, M.Egli 1999 J.Mol.Biol. 291 83
482d Release of the Cyano Moiety in the Crystal Structure of N- Cyanomethyl- N- (2- Methoxyethyl)- Daunomycin Complexed with D(Cgatcg) P.Saminadin, A.Dautant, M.Mondon, B.Langlois D'Estaintot, C.Courseille, G.Precigoux 2000 Eur.J.Biochem. 267 457
4dnb Methylation of the EcoRI recognition site does not alter DNA conformation: the crystal structure of d(CGCGAm6ATTCGCG) at 2.0-A resolution. C.A.Frederick, G.J.Quigley, G.A.van der Marel, J.H.van Boom, A.H.Wang, A.Rich 1988 J Biol Chem 263 17872
5ana The crystal structure of d(GTACGTAC) at 2.25 A resolution: are the A-DNA's always unwound approximately 10 degrees at the C-G steps? F.Takusagawa 1990 J Biomol Struct Dyn 7 795
5bna The primary mode of binding of cisplatin to a B-DNA dodecamer: C-G-C-G-A-A-T-T-C-G-C-G. R.M.Wing, P.Pjura, H.R.Drew, R.E.Dickerson 1984 EMBO J 3 1201
5dnb Structure of the B-DNA Decamer C-C-A-A-C-G-T-T-G-G and Comparison with Isomorphous Decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G G.G.Prive, K.Yanagi, R.E.Dickerson 1991 J.Mol.Biol. 217 177
5zna Evidence for a new Z-type left-handed DNA helix: properties of Z(WC)- DNA. A.T.Ansevin, A.H.Wang 1990 Nucleic Acids Res 18 6119
6bna Binding of an antitumor drug to DNA, Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G. M.L.Kopka, C.Yoon, D.Goodsell, P.Pjura, R.E.Dickerson 1985 J Mol Biol 183 553
7bna Anisotropic Thermal- Parameter Refinement of the DNA Dodecamer Cgcgaattcgcg by the Segmented Rigid-Body Method S.R.Holbrook, R.E.Dickerson, S.-H.Kim 1985 Acta Crystallogr.,Sect.B 41 255
8bna Binding of Hoechst 33258 to the minor groove of B-DNA. P.E.Pjura, K.Grzeskowiak, R.E.Dickerson 1987 J Mol Biol 197 257
9bna Re-refinement of the B-dodecamer d(CGCGAATTCGCG) with a comparative analysis of the solvent in it and in the Z-hexamer d(5BrCG5BrCG5BrCG). E.Westhof 1987 J Biomol Struct Dyn 5 581
9dna Crystal structure analysis of an A-DNA fragment at 1.8 A resolution: d(GCCCGGGC). U.Heinemann, H.Lauble, R.Frank, H.Blocker 1987 Nucleic Acids Res 15 9531

DNAについて更に知りたい方へ

以下の文献も参照してください。

  • Richard E. Dickerson (1983) The DNA Helix and How it is Read. Scientific American 249 (December), pp 94-111.
  • Wolfram Saenger (1994) Principles of Nucleic Acid Structure (Springer-Verlag, New York).
  • The Nucleic Acid Database, http://ndbserver.rutgers.edu/



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