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Assigned Article: xDNA

References/Resources

Resources and References from Databases are stored here for easy access.

^[1]^[2]^[3]^[4]^[5]^[6]^[7]^[8]^[9]^[10]^[11]^[12]^[13]

^ Varsano, Daniele; Garbesi, Anna; Di Felice, Rosa (2007-12-01). "Ab Initio Optical Absorption Spectra of Size-Expanded xDNA Base Assemblies". The Journal of Physical Chemistry B. 111 (50): 14012–14021. doi:10.1021/jp075711z. ISSN 1520-6106.
^ Krueger, Andrew T.; Lu, Haige; Lee, Alex H. F.; Kool, Eric T. (2007-02-01). "Synthesis and Properties of Size-Expanded DNAs: Toward Designed, Functional Genetic Systems". Accounts of Chemical Research. 40 (2): 141–150. doi:10.1021/ar068200o. ISSN 0001-4842.
^ Heckel, Alexander (2004-06-07). "A New DNA Analogue with Expanded Size and Scope". ChemBioChem. 5 (6): 765–767. doi:10.1002/cbic.200400001. ISSN 1439-7633.
^ Winnacker, Malte; Kool, Eric T. (2013-11-25). "Artificial Genetic Sets Composed of Size-Expanded Base Pairs". Angewandte Chemie International Edition. 52 (48): 12498–12508. doi:10.1002/anie.201305267. ISSN 1521-3773.
^ Fuentes-Cabrera, Miguel; Zhao, Xiongce; Kent, P. R. C.; Sumpter, Bobby G. (2007-08-01). "Electronic Structure of xDNA". The Journal of Physical Chemistry B. 111 (30): 9057–9061. doi:10.1021/jp0729056. ISSN 1520-6106.
^ Varghese, Mathew K.; Thomas, Renjith; Unnikrishnan, N. V.; Sudarsanakumar, C. (2009-05-01). "Molecular dynamics simulations of xDNA". Biopolymers. 91 (5): 351–360. doi:10.1002/bip.21137. ISSN 1097-0282.
^ Sharma, Purshotam; Lait, Linda A.; Wetmore, Stacey D. (2013-08-28). "Exploring the limits of nucleobase expansion: computational design of naphthohomologated (xx-) purines and comparison to the natural and xDNA purines". Physical Chemistry Chemical Physics. 15 (37). doi:10.1039/c3cp52656a. ISSN 1463-9084.
^ Liu, Haibo; Lynch, Stephen R.; Kool, Eric T. (2004-06-01). "Solution Structure of xDNA: A Paired Genetic Helix with Increased Diameter". Journal of the American Chemical Society. 126 (22): 6900–6905. doi:10.1021/ja0497835. ISSN 0002-7863.
^ Gao, Jianmin; Liu, Haibo; Kool, Eric T. (2005-05-13). "Assembly of the Complete Eight-Base Artificial Genetic Helix, xDNA, and Its Interaction with the Natural Genetic System". Angewandte Chemie International Edition. 44 (20): 3118–3122. doi:10.1002/anie.200500069. ISSN 1521-3773.
^ McConnell, Tom L.; Wetmore, Stacey D. (2007-03-01). "How Do Size-Expanded DNA Nucleobases Enhance Duplex Stability? Computational Analysis of the Hydrogen-Bonding and Stacking Ability of xDNA Bases". The Journal of Physical Chemistry B. 111 (11): 2999–3009. doi:10.1021/jp0670079. ISSN 1520-6106.
^ Krueger, Andrew T.; Lu, Haige; Højland, Torben; Liu, Haibo; Gao, Jianmin; Kool, Eric T. (2008-09-01). "Towards the Replication of xDNA, a Size-expanded Unnatural Genetic System". Nucleic Acids Symposium Series. 52 (1): 455–456. doi:10.1093/nass/nrn231. ISSN 0261-3166.
^ Jarchow-Choy, Sarah K.; Krueger, Andrew T.; Liu, Haibo; Gao, Jianmin; Kool, Eric T. (2011-03-01). "Fluorescent xDNA nucleotides as efficient substrates for a template-independent polymerase". Nucleic Acids Research. 39 (4): 1586–1594. doi:10.1093/nar/gkq853. ISSN 0305-1048.
^ Lait, Linda A.; Rutledge, Lesley R.; Millen, Andrea L.; Wetmore, Stacey D. (2008-10-02). "yDNA versus xDNA Pyrimidine Nucleobases: Computational Evidence for Dependence of Duplex Stability on Spacer Location". The Journal of Physical Chemistry B. 112 (39): 12526–12536. doi:10.1021/jp805547p. ISSN 1520-6106.

Structure Planning

Origin

Synthesis

Features

Functions

Limitations

Research Using xDNA

Article Evaluation

Assigned article: Quenching (Fluorescence)

This article is "start" class. It is relatively short but provides a basic overview of the concept. There are several links to other pages but not many references. There are some under-represented sections, for example the Exciplex section which is one sentence and is not cited. There are a couple links for the "see also" which link to other pages on wikipedia. Some articles or more academic further readings may be more helpful. The introduction section provides a good overview of the subject and the rest of the article.

[1] Varsano, Daniele; Garbesi, Anna; Di Felice, Rosa (2007-12-01). "Ab Initio Optical Absorption Spectra of Size-Expanded xDNA Base Assemblies". The Journal of Physical Chemistry B. 111 (50): 14012–14021. doi:10.1021/jp075711z. ISSN 1520-6106.

[2] Krueger, Andrew T.; Lu, Haige; Lee, Alex H. F.; Kool, Eric T. (2007-02-01). "Synthesis and Properties of Size-Expanded DNAs: Toward Designed, Functional Genetic Systems". Accounts of Chemical Research. 40 (2): 141–150. doi:10.1021/ar068200o. ISSN 0001-4842.

[3] Heckel, Alexander (2004-06-07). "A New DNA Analogue with Expanded Size and Scope". ChemBioChem. 5 (6): 765–767. doi:10.1002/cbic.200400001. ISSN 1439-7633.

[4] Winnacker, Malte; Kool, Eric T. (2013-11-25). "Artificial Genetic Sets Composed of Size-Expanded Base Pairs". Angewandte Chemie International Edition. 52 (48): 12498–12508. doi:10.1002/anie.201305267. ISSN 1521-3773.

[5] Fuentes-Cabrera, Miguel; Zhao, Xiongce; Kent, P. R. C.; Sumpter, Bobby G. (2007-08-01). "Electronic Structure of xDNA". The Journal of Physical Chemistry B. 111 (30): 9057–9061. doi:10.1021/jp0729056. ISSN 1520-6106.

[6] Varghese, Mathew K.; Thomas, Renjith; Unnikrishnan, N. V.; Sudarsanakumar, C. (2009-05-01). "Molecular dynamics simulations of xDNA". Biopolymers. 91 (5): 351–360. doi:10.1002/bip.21137. ISSN 1097-0282.

[7] Sharma, Purshotam; Lait, Linda A.; Wetmore, Stacey D. (2013-08-28). "Exploring the limits of nucleobase expansion: computational design of naphthohomologated (xx-) purines and comparison to the natural and xDNA purines". Physical Chemistry Chemical Physics. 15 (37). doi:10.1039/c3cp52656a. ISSN 1463-9084.

[8] Liu, Haibo; Lynch, Stephen R.; Kool, Eric T. (2004-06-01). "Solution Structure of xDNA: A Paired Genetic Helix with Increased Diameter". Journal of the American Chemical Society. 126 (22): 6900–6905. doi:10.1021/ja0497835. ISSN 0002-7863.

[9] Gao, Jianmin; Liu, Haibo; Kool, Eric T. (2005-05-13). "Assembly of the Complete Eight-Base Artificial Genetic Helix, xDNA, and Its Interaction with the Natural Genetic System". Angewandte Chemie International Edition. 44 (20): 3118–3122. doi:10.1002/anie.200500069. ISSN 1521-3773.

[10] McConnell, Tom L.; Wetmore, Stacey D. (2007-03-01). "How Do Size-Expanded DNA Nucleobases Enhance Duplex Stability? Computational Analysis of the Hydrogen-Bonding and Stacking Ability of xDNA Bases". The Journal of Physical Chemistry B. 111 (11): 2999–3009. doi:10.1021/jp0670079. ISSN 1520-6106.

[11] Krueger, Andrew T.; Lu, Haige; Højland, Torben; Liu, Haibo; Gao, Jianmin; Kool, Eric T. (2008-09-01). "Towards the Replication of xDNA, a Size-expanded Unnatural Genetic System". Nucleic Acids Symposium Series. 52 (1): 455–456. doi:10.1093/nass/nrn231. ISSN 0261-3166.

[12] Jarchow-Choy, Sarah K.; Krueger, Andrew T.; Liu, Haibo; Gao, Jianmin; Kool, Eric T. (2011-03-01). "Fluorescent xDNA nucleotides as efficient substrates for a template-independent polymerase". Nucleic Acids Research. 39 (4): 1586–1594. doi:10.1093/nar/gkq853. ISSN 0305-1048.

[13] Lait, Linda A.; Rutledge, Lesley R.; Millen, Andrea L.; Wetmore, Stacey D. (2008-10-02). "yDNA versus xDNA Pyrimidine Nucleobases: Computational Evidence for Dependence of Duplex Stability on Spacer Location". The Journal of Physical Chemistry B. 112 (39): 12526–12536. doi:10.1021/jp805547p. ISSN 1520-6106.

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