Prosit, an online service to calculate pseudorotational parameters of nucleosides and nucleotides

Nucleosides, Nucleotides and Nucleic Acids

Volumn 24, Issue 5-7, 2005, Pages 1029-1032

  Sun, Guangyu ^a   Voigt, Johannes H ^a,b   Marquez, Victor E ^a   Nicklaus, Marc C ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE; NUCLEOSIDE; NUCLEOTIDE;

CHEMICAL ANALYSIS; COMPUTER PROGRAM; CONFERENCE PAPER; CONFORMATION; HOLLIDAY JUNCTION; ONLINE SYSTEM;

ALGORITHMS; DATABASES, NUCLEIC ACID; INTERNET; MODELS, CHEMICAL; MOLECULAR CONFORMATION; NUCLEIC ACID CONFORMATION; NUCLEOSIDES; NUCLEOTIDES; RIBONUCLEOSIDES; SOFTWARE;

EID: 26644465337     PISSN: 15257770     EISSN: 15322335     Source Type: Journal    
DOI: 10.1081/NCN-200059757     Document Type: Conference Paper

References (11)

1. Marquez, V.E.; Siddiqui, M.A.; Ezzitouni, A.; Russ, P.; Wang, J.Y.; Wagner, R.W.; Matteucci, M.D. Nucleosides with a twist. Can fixed forms of sugar ring pucker influence biological activity in nucleosides and oligonucleotides? 1996, 39, 3739-3747.
2. Marquez, V.E.; Ezzitouni, A.; Russ, P.; Siddiqui, M.A.; Ford, H.; Feldman, R.J.; Mitsuya, H.; George, C.; Barchi, J.J. HIV-1 reverse transcriptase can discriminate between two conformationally locked carbocyclic AZT triphosphate analogues. 1998, 120, 2780-2789.
3. Marquez, V.E.; Russ, P.; Alonso, R.; Siddiqui, M.A.; Hernandez, S.; George, C.; Nicklaus, M.C.; Dai, F.; Ford, H. Synthesis of conformationally restricted carbocyclic nucleosides: The role of the O(4′)-atom in the key hydration step of adenosine deaminase. Helv. Chim. Acta 1999, 82, 2119-2129.
4. Marquez, V.E.; Ben-Kasus, T.; Barchi, J.J.; Green, K.M.; Nicklaus, M.C.; Agbaria, R. Experimental and structural evidence that herpes 1 kinase and cellular DNA polymerase(s) discriminate on the basis of sugar pucker. J. Am. Chem. Soc. 2004, 126, 543-549.
5. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, NY, 1984.
6. Altona, C.; Sundaralingam, M. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc. 1972, 94, 8205-8212.
7. Sun, G.Y.; Voigt, J.H.; Filippov, I.V.; Marquez, V.E.; Nicklaus, M.C. PROSIT: pseudo-rotational online service and interactive tool, applied to a conformational survey of nucleosides and nucleotides. J. Chem. Inf. Comput. Sci. 2004, 44, 1752-1762.
8. Deleeuw, H.P.M.; Haasnoot, C.A.G.; Altona, C. Nucleic-acid constituents. 13. Empirical correlations between conformational parameters in beta-D-furanoside fragments derived from a statistical-survey of crystal-structures of nucleic-acid constituents-full description of nucleoside molecular geometries in terms of 4 parameters. Isr. J. Chem. 1980, 20, 108-126.
9. Choi, Y.S.; Sun, G.Y.; George, C.; Nicklaus, M.C.; Kelley, J.A.; Marquez, V.E. Synthesis and conformational analysis of a locked analogue of carbovir built on a bicyclo 3.1.0 hex-2-enyl template. Nucleosides Nucleotides Nucleic 2003, 22, 2077-2091.
10. Phillips, K.; Dauter, Z.; Murchie, A.I.H.; Lilley, D.M.J.; Luisi, B. The crystal structure of a parallel-stranded guanine tetraplex at 0.95 angstrom resolution. J. Mol. Biol. 1997, 273, 171-182.
11. Hays, F.A.; Vargason, J.M.; Ho, P.S. Effect of sequence on the conformation of DNA Holliday junctions. Biochemistry 2003, 42, 9586-9597.