Published in Chem Biodivers on January 01, 2010
Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. J Comput Chem (2011) 1.81
The structural diversity of artificial genetic polymers. Nucleic Acids Res (2015) 0.89
The many twists and turns of DNA: template, telomere, tool, and target. Curr Opin Struct Biol (2010) 0.85
The conformationally constrained N-methanocarba-dT analogue adopts an unexpected C4'-exo sugar pucker in the structure of a DNA hairpin. Biochemistry (2012) 0.81
Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity. J Am Chem Soc (2012) 0.81
Synthesis, structure and imaging of oligodeoxyribonucleotides with tellurium-nucleobase derivatization. Nucleic Acids Res (2011) 0.80
Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease. Nucleic Acids Res (2016) 0.75
UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem (2004) 112.47
The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J (1992) 21.67
Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J Am Chem Soc (1972) 9.83
Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide. Proc Natl Acad Sci U S A (1978) 7.90
Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. J Biol Chem (1982) 5.63
Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Cell (2005) 5.43
Inhibition of Rous sarcoma viral RNA translation by a specific oligodeoxyribonucleotide. Proc Natl Acad Sci U S A (1978) 4.65
Chemical etiology of nucleic acid structure: the alpha-threofuranosyl-(3'-->2') oligonucleotide system. Science (2000) 3.11
The ups and downs of nucleic acid duplex stability: structure-stability studies on chemically-modified DNA:RNA duplexes. Nucleic Acids Res (1997) 3.00
Role of RNase H in hybrid-arrested translation by antisense oligonucleotides. Proc Natl Acad Sci U S A (1988) 2.98
Estimates of the ab initio limit for pi-pi interactions: the benzene dimer. J Am Chem Soc (2002) 2.53
DNA structure from A to Z. Methods Enzymol (1992) 2.45
Enzyme from calf thymus degrading the RNA moiety of DNA-RNA Hybrids: effect on DNA-dependent RNA polymerase. Science (1969) 2.41
A crystalline fragment of the double helix: the structure of the dinucleoside phosphate guanylyl-3',5'-cytidine. Proc Natl Acad Sci U S A (1973) 2.39
Antitumor activity of a phosphorothioate antisense oligodeoxynucleotide targeted against C-raf kinase. Nat Med (1996) 2.39
Current concepts in antisense drug design. J Med Chem (1993) 2.28
RNA double-helical fragments at atomic resolution. II. The crystal structure of sodium guanylyl-3',5'-cytidine nonahydrate. J Mol Biol (1976) 2.07
Nucleic-acid therapeutics: basic principles and recent applications. Nat Rev Drug Discov (2002) 2.06
Molecular structure of r(GCG)d(TATACGC): a DNA--RNA hybrid helix joined to double helical DNA. Nature (1982) 2.03
Efficient replication between non-hydrogen-bonded nucleoside shape analogs. Nat Struct Biol (1998) 1.97
RNA hydration: a detailed look. Biochemistry (1996) 1.93
A review of the issues in the pharmacokinetics and toxicology of phosphorothioate antisense oligonucleotides. Biochim Biophys Acta (1999) 1.92
AT base pairs are less stable than GC base pairs in Z-DNA: the crystal structure of d(m5CGTAm5CG). Cell (1984) 1.91
Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes. Biochemistry (1993) 1.91
Structure of a DNA:RNA hybrid duplex. Why RNase H does not cleave pure RNA. J Mol Biol (1993) 1.90
Experimental Measurement of Aromatic Stacking Affinities in the Context of Duplex DNA. J Am Chem Soc (1996) 1.85
Oligonucleotide N3'-->P5' phosphoramidates. Proc Natl Acad Sci U S A (1995) 1.74
2'-carbohydrate modifications in antisense oligonucleotide therapy: importance of conformation, configuration and conjugation. Biochim Biophys Acta (1999) 1.73
Pharmacokinetic properties of 2'-O-(2-methoxyethyl)-modified oligonucleotide analogs in rats. J Pharmacol Exp Ther (2001) 1.73
Crystal structure and improved antisense properties of 2'-O-(2-methoxyethyl)-RNA. Nat Struct Biol (1999) 1.65
Dynamics of photoinduced charge transfer and hole transport in synthetic DNA hairpins. Acc Chem Res (2001) 1.63
Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing. J Mol Biol (1999) 1.63
A single 2'-hydroxyl group converts B-DNA to A-DNA. Crystal structure of the DNA-RNA chimeric decamer duplex d(CCGGC)r(G)d(CCGG) with a novel intermolecular G-C base-paired quadruplet. J Mol Biol (1994) 1.58
Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments. Nucleic Acids Res (2001) 1.49
Chiral phosphorothioate analogues of B-DNA. The crystal structure of Rp-d[Gp(S)CpGp(S)CpGp(S)C]. J Mol Biol (1986) 1.43
X-ray crystallographic analysis of the hydration of A- and B-form DNA at atomic resolution. Biopolymers (1998) 1.40
A simple glycol nucleic acid. J Am Chem Soc (2005) 1.37
The difluorotoluene debate--a decade later. Chem Commun (Camb) (2006) 1.36
Gene silencing activity of siRNAs with a ribo-difluorotoluyl nucleotide. ACS Chem Biol (2006) 1.33
Stabilizing effects of the RNA 2'-substituent: crystal structure of an oligodeoxynucleotide duplex containing 2'-O-methylated adenosines. Chem Biol (1994) 1.32
Crystal structures of B-DNA with incorporated 2'-deoxy-2'-fluoro-arabino-furanosyl thymines: implications of conformational preorganization for duplex stability. Nucleic Acids Res (1998) 1.29
Binding affinity and specificity of Escherichia coli RNase H1: impact on the kinetics of catalysis of antisense oligonucleotide-RNA hybrids. Biochemistry (1997) 1.23
Synthesis of oligodeoxyribonucleotide N3'-->P5' phosphoramidates. Nucleic Acids Res (1995) 1.23
Structural requirements at the catalytic site of the heteroduplex substrate for human RNase H1 catalysis. J Biol Chem (2004) 1.22
DNA-cation interactions: quo vadis? Chem Biol (2002) 1.20
Internal derivatization of oligonucleotides with selenium for X-ray crystallography using MAD. J Am Chem Soc (2002) 1.20
Methylation of the EcoRI recognition site does not alter DNA conformation: the crystal structure of d(CGCGAm6ATTCGCG) at 2.0-A resolution. J Biol Chem (1988) 1.19
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 (2007) 1.16
Covalent incorporation of selenium into oligonucleotides for X-ray crystal structure determination via MAD: proof of principle. Multiwavelength anomalous dispersion. Biochimie (2002) 1.15
B-form to A-form conversion by a 3'-terminal ribose: crystal structure of the chimera d(CCACTAGTG)r(G). Nucleic Acids Res (2000) 1.13
Selenium-assisted nucleic acid crystallography: use of phosphoroselenoates for MAD phasing of a DNA structure. J Am Chem Soc (2002) 1.11
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 (2007) 1.11
Solvation of the left-handed hexamer d(5BrC-G-5BrC-G-5 BrC-G) in crystals grown at two temperatures. J Mol Biol (1986) 1.10
Inter-strand C-H...O hydrogen bonds stabilizing four-stranded intercalated molecules: stereoelectronic effects of O4' in cytosine-rich DNA. Proc Natl Acad Sci U S A (1996) 1.09
High resolution structure of the RNA duplex [U(U-A)6A]2. Nature (1988) 1.09
Crystal structure of an Okazaki fragment at 2-A resolution. Proc Natl Acad Sci U S A (1992) 1.09
Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system. J Am Chem Soc (2006) 1.06
Duplex structure of a minimal nucleic acid. J Am Chem Soc (2008) 1.06
The crystal structure of r(CCCCGGGG) in two distinct lattices. Biochemistry (1995) 1.04
Chemically modified hammerhead ribozymes with improved catalytic rates. Biochemistry (1996) 1.03
Large scale chemical synthesis, purification and crystallization of RNA-DNA chimeras. Nucleic Acids Res (1992) 1.01
2'-Fluoroarabino- and arabinonucleic acid show different conformations, resulting in deviating RNA affinities and processing of their heteroduplexes with RNA by RNase H. Biochemistry (2006) 1.00
Synthesis and physical and physiological properties of 4'-thioRNA: application to post-modification of RNA aptamer toward NF-kappaB. Nucleic Acids Res (2004) 1.00
Hydrophobic Groups Stabilize the Hydration Shell of 2'-O-Methylated RNA Duplexes. Angew Chem Int Ed Engl (2001) 0.98
Structural basis of cleavage by RNase H of hybrids of arabinonucleic acids and RNA. Biochemistry (2000) 0.98
Watson-Crick base-pairing properties of tricyclo-DNA. J Am Chem Soc (2002) 0.98
Crystal structure of a Z-DNA fragment containing thymine/2-aminoadenine base pairs. J Biomol Struct Dyn (1986) 0.97
The influence of antisense oligonucleotide-induced RNA structure on Escherichia coli RNase H1 activity. J Biol Chem (1997) 0.94
Structural origins of the exonuclease resistance of a zwitterionic RNA. Proc Natl Acad Sci U S A (1999) 0.93
4'-Thio-RNA: synthesis of mixed base 4'-thio-oligoribonucleotides, nuclease resistance, and base pairing properties with complementary single and double strand. Antisense Res Dev (1995) 0.92
Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex. Cell Cycle (2008) 0.92
Stability of stereoregular oligo(nucleoside phosphorothioate)s in human plasma: diastereoselectivity of plasma 3'-exonuclease. Antisense Nucleic Acid Drug Dev (1997) 0.92
Conformational preorganization, hydration, and nucleic acid duplex stability. Antisense Nucleic Acid Drug Dev (1998) 0.92
Correlating structure and stability of DNA duplexes with incorporated 2'-O-modified RNA analogues. Biochemistry (1998) 0.91
Crystal structure of a B-form DNA duplex containing (L)-alpha-threofuranosyl (3'-->2') nucleosides: a four-carbon sugar is easily accommodated into the backbone of DNA. J Am Chem Soc (2002) 0.91
Synthesis and Structure of 1-Deoxy-1-phenyl-beta-D-ribofuranose and Its Incorporation into Oligonucleotides. J Org Chem (1996) 0.91
The crystal structure analysis of d(CGCGAASSCGCG)2, a synthetic DNA dodecamer duplex containing four 4'-thio-2'-deoxythymidine nucleotides. Nucleic Acids Res (1996) 0.91
Crystal structure of 2'-O-Me(CGCGCG)2, an RNA duplex at 1.30 A resolution. Hydration pattern of 2'-O-methylated RNA. Nucleic Acids Res (1997) 0.90
Antisense properties of tricyclo-DNA. Nucleic Acids Res (2002) 0.90
Functional groups on the cleavage site pyrimidine nucleotide are required for stabilization of the hammerhead transition state. RNA (1997) 0.89
Structure of 11-deoxydaunomycin bound to DNA containing a phosphorothioate. J Mol Biol (1990) 0.88
Selenium modification of nucleic acids: preparation of oligonucleotides with incorporated 2'-SeMe-uridine for crystallographic phasing of nucleic acid structures. Nat Protoc (2007) 0.88
Structural RNA mimetics: N3'-->P5' phosphoramidate DNA analogs of HIV-1 RRE and TAR RNA form A-type helices that bind specifically to Rev and Tat-related peptides. Biochemistry (1997) 0.87
Why does TNA cross-pair more strongly with RNA than with DNA? an answer from X-ray analysis. Angew Chem Int Ed Engl (2003) 0.87
Stabilizing contributions of sulfur-modified nucleotides: crystal structure of a DNA duplex with 2'-O-[2-(methoxy)ethyl]-2-thiothymidines. Nucleic Acids Res (2005) 0.86
RNA-Binding affinities and crystal structure of oligonucleotides containing five-atom amide-based backbone structures. Biochemistry (2006) 0.86
Insights from crystallographic studies into the structural and pairing properties of nucleic acid analogs and chemically modified DNA and RNA oligonucleotides. Annu Rev Biophys Biomol Struct (2007) 0.85
2'-O-[2-(methylthio)ethyl]-modified oligonucleotide: an analogue of 2'-O-[2-(methoxy)-ethyl]-modified oligonucleotide with improved protein binding properties and high binding affinity to target RNA. Biochemistry (2002) 0.85
Syntheses of 4'-thioribonucleosides and thermodynamic stability and crystal structure of RNA oligomers with incorporated 4'-thiocytosine. Nucleic Acids Res (2005) 0.85
Crystallization and preliminary X-ray analysis of Escherichia coli RNase HI-dsRNA complexes. Acta Crystallogr Sect F Struct Biol Cryst Commun (2007) 0.84
A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution. Chem Commun (Camb) (2009) 0.84
Synthesis and properties of 4'-ThioDNA: unexpected RNA-like behavior of 4'-ThioDNA. Nucleic Acids Res (2006) 0.84
Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing. Nucleic Acids Res (2007) 0.84
2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] modified oligonucleotides: symbiosis of charge interaction factors and stereoelectronic effects. Org Lett (2003) 0.83
Crystal structure of tricyclo-DNA: an unusual compensatory change of two adjacent backbone torsion angles. Chem Commun (Camb) (2007) 0.83
Towards the structure-based design of oligonucleotide therapeutics. Adv Enzyme Regul (1998) 0.83
2'-O-[2-(guanidinium)ethyl]-modified oligonucleotides: stabilizing effect on duplex and triplex structures. Org Lett (2004) 0.82
Reinforced HNA backbone hydration in the crystal structure of a decameric HNA/RNA hybrid. J Am Chem Soc (2005) 0.82
Face-to-face and edge-to-face pi-pi interactions in a synthetic DNA hairpin with a stilbenediether linker. J Am Chem Soc (2003) 0.82
Unique gene-silencing and structural properties of 2'-fluoro-modified siRNAs. Angew Chem Int Ed Engl (2011) 1.20
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 (2007) 1.16
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 (2007) 1.11
Interplay of structure, hydration and thermal stability in formacetal modified oligonucleotides: RNA may tolerate nonionic modifications better than DNA. J Am Chem Soc (2009) 1.07
Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system. J Am Chem Soc (2006) 1.06
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 (2011) 1.02
An exocyclic methylene group acts as a bioisostere of the 2'-oxygen atom in LNA. J Am Chem Soc (2010) 0.99
Synthesis and antisense properties of fluoro cyclohexenyl nucleic acid (F-CeNA), a nuclease stable mimic of 2'-fluoro RNA. J Org Chem (2012) 0.86
Insights from crystallographic studies into the structural and pairing properties of nucleic acid analogs and chemically modified DNA and RNA oligonucleotides. Annu Rev Biophys Biomol Struct (2007) 0.85
The many twists and turns of DNA: template, telomere, tool, and target. Curr Opin Struct Biol (2010) 0.85
Syntheses of 4'-thioribonucleosides and thermodynamic stability and crystal structure of RNA oligomers with incorporated 4'-thiocytosine. Nucleic Acids Res (2005) 0.85
Replication of N2,3-ethenoguanine by DNA polymerases. Angew Chem Int Ed Engl (2012) 0.83
Differential stabilities and sequence-dependent base pair opening dynamics of Watson-Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine. Biochemistry (2015) 0.83
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 (2011) 0.82
The long and winding road to the structure of homo-DNA. Chem Soc Rev (2006) 0.78
Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction. Nucleic Acids Res (2013) 0.76
Generating Crystallographic Models of DNA Dodecamers from Structures of RNase H:DNA Complexes. Methods Mol Biol (2016) 0.76
Synthesis, duplex stabilization and structural properties of a fluorinated carbocyclic LNA analogue. Chembiochem (2012) 0.75
Correction to differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine. Biochemistry (2015) 0.75
Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs. Nucleic Acids Res (2012) 0.75