Author results

1Y9S
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CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-PROPARGYL THYMIDINE (T*)
Descriptor:5'-D(*GP*CP*GP*TP*AP*(2GT)P*AP*CP*GP*C)-3')
Authors:Egli, M., Minasov, G., Tereshko, V., Pallan, P.S., Teplova, M., Inamati, G.B., Lesnik, E.A., Owens, S.R., Ross, B.S., Prakash, T.P., Manoharan, M.
Deposit date:2004-12-16
Release date:2005-06-28
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications.
Biochemistry, 44, 2005
1YB9
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CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2-(N,N-DIMETHYLAMINOOXY)ETHYL] THYMIDINE (T*)
Descriptor:5'-D(*GP*CP*GP*TP*AP*(2OT)P*AP*CP*GP*C)-3'), SPERMINE
Authors:Egli, M., Minasov, G., Tereshko, V., Pallan, P.S., Teplova, M., Inamati, G.B., Lesnik, E.A., Owens, S.R., Ross, B.S., Prakash, T.P., Manoharan, M.
Deposit date:2004-12-20
Release date:2005-06-28
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications.
Biochemistry, 44, 2005
1YBC
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CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2-(BENZYLOXY)ETHYL] THYMIDINE (T*)
Descriptor:5'-D(*GP*CP*GP*TP*AP*(BOE)P*AP*CP*GP*C)-3'), STRONTIUM ION
Authors:Egli, M., Minasov, G., Tereshko, V., Pallan, P.S., Teplova, M., Inamati, G.B., Lesnik, E.A., Owens, S.R., Ross, B.S., Prakash, T.P., Manoharan, M.
Deposit date:2004-12-20
Release date:2005-06-28
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications.
Biochemistry, 44, 2005
2A0P
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CRYSTAL STRUCTURE OF RNA OLIGOMER CONTAINING 4'-THIORIBOSE
Descriptor:5'-R(*CP*CP*(S4C)P*CP*GP*GP*GP*G)-3'
Authors:Haeberli, P., Berger, I., Pallan, P.S., Egli, M.
Deposit date:2005-06-16
Release date:2005-08-16
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Syntheses of 4'-thioribonucleosides and thermodynamic stability and crystal structure of RNA oligomers with incorporated 4'-thiocytosine
Nucleic Acids Res., 33, 2005
2H9S
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CRYSTAL STRUCTURE OF HOMO-DNA AND NATURE'S CHOICE OF PENTOSE OVER HEXOSE IN THE GENETIC SYSTEM
Descriptor:5'-D(*(XCT)P*(XGU)P*(XAD)P*(XAD)P*(XTH)P*(XTH)P*(XCT)P*(XGU))-3', MAGNESIUM ION
Authors:Egli, M., Pallan, P.S.
Deposit date:2006-06-11
Release date:2006-12-12
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system.
J.Am.Chem.Soc., 128, 2006
2M11
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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:2013-09-11
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
2Q1O
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CRYSTAL STRUCTURE ANALYSIS OF THE RNA DODECAMER CGC-NF2-AAUUGGCG, WITH AN INCORPORATED 2,4-DIFLUOROTOLUYL RESIDUE (NF2)
Descriptor:RNA (5'-R(*CP*GP*CP*(NF2)P*AP*AP*UP*UP*GP*GP*CP*G)-3')
Authors:Li, F., Pallan, P.S.
Deposit date:2007-05-25
Release date:2007-10-30
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.1 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
2Q1R
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CRYSTAL STRUCTURE ANALYSIS OF THE RNA DODECAMER CGCGAAUUAGCG, WITH A G-A MISMATCH.
Descriptor:RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*AP*GP*CP*G)-3'), MAGNESIUM ION
Authors:Li, F., Pallan, P.S.
Deposit date:2007-05-25
Release date:2007-10-30
Last modified:2011-07-13
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
2V9W
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COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND
Descriptor:DNA POLYMERASE IV, 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:2011-07-13
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
2VA2
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COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND
Descriptor:DNA POLYMERASE IV, 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:2014-04-09
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
2VA3
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COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND
Descriptor:DNA POLYMERASE IV, 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:2011-07-13
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
3HR3
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INTERPLAY OF STRUCTURE, HYDRATION AND THERMAL STABILITY IN FORMACETAL MODIFIED OLIGONUCLEOTIDES: RNA MAY TOLERATE HYDROPHOBIC MODIFICATIONS BETTER THAN DNA
Descriptor:5'-D(*GP*CP*GP*(US4)P*(OMU))P*AP*CP*GP*C)-3'
Authors:Egli, M., Pallan, P.S.
Deposit date:2009-06-08
Release date:2009-10-27
Last modified:2015-03-25
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Interplay of structure, hydration and thermal stability in formacetal modified oligonucleotides: RNA may tolerate nonionic modifications better than DNA.
J.Am.Chem.Soc., 131, 2009
3OPI
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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:2017-11-08
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
3OZ3
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VINYL CARBOCYCLIC LNA
Descriptor:DNA (5'-D(*GP*CP*GP*TP*AP*(UVX)P*AP*CP*GP*C)-3'), (4S)-2-METHYL-2,4-PENTANEDIOL
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:2011-07-13
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
3OZ4
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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:2011-07-13
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
3OZ5
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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:2017-11-08
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
3Q61
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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
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
3SD8
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CRYSTAL STRUCTURE OF ARA-FHNA DECAMER DNA
Descriptor:5'-D(*GP*CP*GP*TP*AP*(F4H)P*AP*CP*GP*C)-3', STRONTIUM ION
Authors:Egli, M., Pallan, P.S.
Deposit date:2011-06-08
Release date:2012-08-29
Method:X-RAY DIFFRACTION (1.67 Å)
Cite:Structural Origins of Opposite Effects on Stability by Axial and Equatorial 3'-Fluoro Modifications of Hexitol Nucleic Acid (HNA)
To be Published
4HQH
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DECAMER FLUORO CARBOCYCLIC LNA (R-F-CLNA) CRYSTAL STRUCTURE
Descriptor:DNA (5'-D(*GP*CP*GP*TP*AP*(ULF)P*AP*CP*GP*C)-3')
Authors:Seth, P.P., Pallan, P.S., Swayze, E.E., Egli, M.
Deposit date:2012-10-25
Release date:2013-11-20
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Properties of a Fluorinated Carbocyclic LNA Analog
To be Published
4HQI
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STRUCTURE OF O6-BENZYL-2'-DEOXYGUANOSINE OPPOSITE PERIMIDINONE-DERIVED SYNTHETIC NUCLEOSIDE IN DNA DUPLEX
Descriptor:Short modified nucleic acids, SPERMINE, STRONTIUM ION
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:2013-09-11
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
4PWM
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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:2015-02-25
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
4QC7
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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:2015-02-25
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
3V6H
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REPLICATION OF N2,3-ETHENOGUANINE BY DNA POLYMERASES
Descriptor:DNA (5'-D(*TP*CP*AP*CP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'), DNA (5'-D(*GP*G*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC))-3'), DNA polymerase IV, ...
Authors:Zhao, L.
Deposit date:2011-12-19
Release date:2012-04-25
Last modified:2012-06-06
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Replication of n(2) ,3-ethenoguanine by DNA polymerases.
Angew.Chem.Int.Ed.Engl., 51, 2012
3V6J
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REPLICATION OF N2,3-ETHENOGUANINE BY DNA POLYMERASES
Descriptor:DNA polymerase IV, DNA (5'-D(*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC))-3'), DNA (5'-D(*TP*CP*AP*TP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*C)-3'), ...
Authors:Zhao, L.
Deposit date:2011-12-19
Release date:2012-04-25
Last modified:2012-06-06
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Replication of n(2) ,3-ethenoguanine by DNA polymerases.
Angew.Chem.Int.Ed.Engl., 51, 2012
3V6K
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REPLICATION OF N2,3-ETHENOGUANINE BY DNA POLYMERASES
Descriptor:DNA polymerase IV, DNA (5'-D(P*GP*AP*AP*GP*GP*AP*TP*TP*CP*(2DT))-3'), DNA (5'-D(*TP*CP*AP*CP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*C)-3'), ...
Authors:Zhao, L.
Deposit date:2011-12-20
Release date:2012-04-25
Last modified:2012-06-06
Method:X-RAY DIFFRACTION (3.6 Å)
Cite:Replication of n(2) ,3-ethenoguanine by DNA polymerases.
Angew.Chem.Int.Ed.Engl., 51, 2012