3P4D
| Alternatingly modified 2'Fluoro RNA octamer f/rC4G4 | Descriptor: | 5'-R(*(CFZ)P*CP*(CFZ)P*CP*(GF2)P*GP*(GF2)P*G)-3' | Authors: | Pallan, P.S, Greene, E.M, Jicman, P.A, Pandey, R.K, Manoharan, M, Rozners, E, Egli, M. | Deposit date: | 2010-10-06 | Release date: | 2011-01-05 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Unexpected origins of the enhanced pairing affinity of 2'-fluoro-modified RNA. Nucleic Acids Res., 39, 2011
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4DKZ
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7UCR
| Joint X-ray/neutron structure of the Sarcin-Ricin loop RNA | Descriptor: | SULFATE ION, Sarcin-Ricin loop RNA | Authors: | Harp, J.M, Egli, M.E, Pallan, P.S, Coates, L. | Deposit date: | 2022-03-17 | Release date: | 2022-07-20 | Last modified: | 2024-04-03 | Method: | NEUTRON DIFFRACTION (1 Å), X-RAY DIFFRACTION | Cite: | Cryo neutron crystallography demonstrates influence of RNA 2'-OH orientation on conformation, sugar pucker and water structure. Nucleic Acids Res., 50, 2022
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2H9S
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3HR3
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3I8D
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7JJF
| Sarcin-ricin loop with modified residue. | Descriptor: | MAGNESIUM ION, RNA/DNA (27-mer) | Authors: | Harp, J.M, Pallan, P.S, Egli, M. | Deposit date: | 2020-07-25 | Release date: | 2020-12-23 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.2 Å) | Cite: | Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost. Biochemistry, 59, 2020
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2M11
| Structure of perimidinone-derived synthetic nucleoside paired with guanine in DNA duplex | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(D3N)P*GP*CP*G)-3') | Authors: | Kowal, E.A, Lad, R, Pallan, P.S, Muffly, E, Wawrzak, Z, Egli, M, Sturla, S.J, Stone, M.P. | Deposit date: | 2012-11-09 | Release date: | 2013-06-12 | Last modified: | 2024-05-01 | Method: | SOLUTION NMR | Cite: | Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction. Nucleic Acids Res., 41, 2013
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2VA3
| Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *CP*TP*A)-3', 5'-D(*TP*TP*CP*AP*DFTP*TP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3', ... | Authors: | Irimia, A, Pallan, P.S, Egli, M. | Deposit date: | 2007-08-28 | Release date: | 2007-10-30 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.98 Å) | Cite: | Structure and Activity of Y-Class DNA Polymerase Dpo4 from Sulfolobus Solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4-Difluorotoluene. J.Biol.Chem., 282, 2007
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2Q1O
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4PWM
| Crystal structure of Dickerson Drew Dodecamer with 5-carboxycytosine | Descriptor: | 5'-[CGCGAATT(5CC)GCG]-3' | Authors: | Szulik, M.W, Pallan, P, Banerjee, S, Voehler, M, Egli, M, Stone, M.P. | Deposit date: | 2014-03-20 | Release date: | 2015-02-11 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine. Biochemistry, 54, 2015
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4QC7
| Dodecamer structure of 5-formylcytosine containing DNA | Descriptor: | short DNA strands | Authors: | Szulik, M.W, Pallan, P, Egli, M, Stone, M.P. | Deposit date: | 2014-05-09 | Release date: | 2015-02-11 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine. Biochemistry, 54, 2015
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2V9W
| Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand | Descriptor: | 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *CP*TP*G)-3', 5'-D(*TP*TP*CP*AP*GP*DFTP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3', ... | Authors: | Irimia, A, Pallan, P.S, Egli, M. | Deposit date: | 2007-08-27 | Release date: | 2007-10-30 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Structure and Activity of Y-Class DNA Polymerase Dpo4 from Sulfolobus Solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4-Difluorotoluene. J.Biol.Chem., 282, 2007
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2VA2
| Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand | Descriptor: | 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *CP*TP*A)-3', 5'-D(*TP*TP*CP*AP*GP*DFTP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3', ... | Authors: | Irimia, A, Pallan, P.S, Egli, M. | Deposit date: | 2007-08-28 | Release date: | 2007-10-30 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Structure and Activity of Y-Class DNA Polymerase Dpo4 from Sulfolobus Solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4- Difluorotoluene. J.Biol.Chem., 282, 2007
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4HQH
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2Q1R
| Crystal Structure Analysis of the RNA Dodecamer CGCGAAUUAGCG, with a G-A mismatch. | Descriptor: | MAGNESIUM ION, RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*AP*GP*CP*G)-3') | Authors: | Li, F, Pallan, P.S. | Deposit date: | 2007-05-25 | Release date: | 2007-10-30 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (1.12 Å) | Cite: | Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme. Nucleic Acids Res., 35, 2007
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3EY3
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3EY1
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3EY2
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4HQI
| Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex | Descriptor: | SPERMINE, STRONTIUM ION, Short modified nucleic acids | Authors: | Kowal, E.A, Lad, R, Pallan, P.S, Muffly, E, Wawrzak, Z, Egli, M, Sturla, S.J, Stone, M.P. | Deposit date: | 2012-10-25 | Release date: | 2013-07-10 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction. Nucleic Acids Res., 41, 2013
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3OZ3
| Vinyl Carbocyclic LNA | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*GP*CP*GP*TP*AP*(UVX)P*AP*CP*GP*C)-3') | Authors: | Seth, P.R, Allerson, C.A, Berdeja, A, Siwkowski, A, Pallan, P.S, Gaus, H, Prakash, T.P, Watt, A.T, Egli, M, Swayze, E.E. | Deposit date: | 2010-09-24 | Release date: | 2010-11-24 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (1.57 Å) | Cite: | An exocyclic methylene group acts as a bioisostere of the 2'-oxygen atom in LNA. J.Am.Chem.Soc., 132, 2010
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3OZ5
| S-Methyl Carbocyclic LNA | Descriptor: | DNA (5'-D(*GP*CP*GP*TP*AP*(UMX)P*AP*CP*GP*C)-3'), SPERMINE | Authors: | Seth, P.R, Allerson, C.A, Berdeja, A, Siwkowski, A, Pallan, P.S, Gaus, H, Prakash, T.P, Watt, A.T, Egli, M, Swayze, E.E. | Deposit date: | 2010-09-24 | Release date: | 2010-11-24 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (1.36 Å) | Cite: | An exocyclic methylene group acts as a bioisostere of the 2'-oxygen atom in LNA. J.Am.Chem.Soc., 132, 2010
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3OZ4
| R-Methyl Carbocyclic LNA | Descriptor: | DNA (5'-D(*GP*CP*GP*TP*AP*(URX)P*AP*CP*GP*C)-3') | Authors: | Seth, P.R, Allerson, C.A, Berdeja, A, Siwkowski, A, Pallan, P.S, Gaus, H, Prakash, T.P, Watt, A.T, Egli, M, Swayze, E.E. | Deposit date: | 2010-09-24 | Release date: | 2010-11-24 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (1.59 Å) | Cite: | An exocyclic methylene group acts as a bioisostere of the 2'-oxygen atom in LNA. J.Am.Chem.Soc., 132, 2010
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3OPI
| 7-DEAZA-2'-DEOXYADENOSINE modification in B-FORM DNA | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*AP*(7DA)P*TP*TP*CP*GP*CP*G)-3'), MAGNESIUM ION, SODIUM ION | Authors: | Kowal, E.A, Ganguly, M, Pallan, P.S, Marky, L.A, Gold, B, Egli, M, Stone, M.P. | Deposit date: | 2010-09-01 | Release date: | 2011-08-31 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (1.1 Å) | Cite: | Altering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2'-deoxyadenosine:dT Base Pairing in DNA. J.Phys.Chem.B, 115, 2011
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3Q61
| 3'-Fluoro Hexitol Nucleic Acid DNA Structure | Descriptor: | DNA (5'-D(*GP*CP*GP*TP*AP*(F3H)P*AP*CP*GP*C)-3') | Authors: | Seth, P.R, Allerson, C.R, Prakash, T.P, Siwkowski, A, Berdeja, A, Yu, J, Pallan, P.S, Watt, A.T, Gaus, H, Bhat, B, Egli, M, Swayze, E.E. | Deposit date: | 2010-12-30 | Release date: | 2012-01-18 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (1.56 Å) | Cite: | Synthesis, improved antisense activity and structural rationale for the divergent RNA affinities of 3'-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides. J.Am.Chem.Soc., 133, 2011
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