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Items: 1 to 20 of 109

1.

DNA multiplex hybridization on microarrays and thermodynamic stability in solution: a direct comparison.

Fish DJ, Horne MT, Brewood GP, Goodarzi JP, Alemayehu S, Bhandiwad A, Searles RP, Benight AS.

Nucleic Acids Res. 2007;35(21):7197-208. Epub 2007 Oct 18.

2.

Influence of buffer species on the thermodynamics of short DNA duplex melting: sodium phosphate versus sodium cacodylate.

Alemayehu S, Fish DJ, Brewood GP, Horne MT, Manyanga F, Dickman R, Yates I, Benight AS.

J Phys Chem B. 2009 Mar 5;113(9):2578-86.

PMID:
19708201
4.

Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches.

Peyret N, Seneviratne PA, Allawi HT, SantaLucia J Jr.

Biochemistry. 1999 Mar 23;38(12):3468-77.

PMID:
10090733
5.

Thermodynamic characterization of single mismatches found in naturally occurring RNA.

Davis AR, Znosko BM.

Biochemistry. 2007 Nov 20;46(46):13425-36. Epub 2007 Oct 24.

PMID:
17958380
6.

Melting studies of short DNA hairpins: influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability.

Vallone PM, Paner TM, Hilario J, Lane MJ, Faldasz BD, Benight AS.

Biopolymers. 1999 Oct 5;50(4):425-42.

PMID:
10423551
7.

Position dependent mismatch discrimination on DNA microarrays - experiments and model.

Naiser T, Kayser J, Mai T, Michel W, Ott A.

BMC Bioinformatics. 2008 Dec 1;9:509. doi: 10.1186/1471-2105-9-509.

8.

Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes.

Watkins NE Jr, SantaLucia J Jr.

Nucleic Acids Res. 2005 Nov 1;33(19):6258-67. Print 2005.

9.

DNA sequence context and multiplex hybridization reactions: melting studies of heteromorphic duplex DNA complexes.

Riccelli PV, Hall TS, Pancoska P, Mandell KE, Benight AS.

J Am Chem Soc. 2003 Jan 8;125(1):141-50.

PMID:
12515515
10.

Nearest neighbor thermodynamic parameters for internal G.A mismatches in DNA.

Allawi HT, SantaLucia J Jr.

Biochemistry. 1998 Feb 24;37(8):2170-9.

PMID:
9485363
11.
12.

Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond.

Hadiwikarta WW, Walter JC, Hooyberghs J, Carlon E.

Nucleic Acids Res. 2012 Oct;40(18):e138. doi: 10.1093/nar/gks475. Epub 2012 May 31.

13.

Thermodynamic contributions of single internal rA·dA, rC·dC, rG·dG and rU·dT mismatches in RNA/DNA duplexes.

Watkins NE Jr, Kennelly WJ, Tsay MJ, Tuin A, Swenson L, Lee HR, Morosyuk S, Hicks DA, Santalucia J Jr.

Nucleic Acids Res. 2011 Mar;39(5):1894-902. doi: 10.1093/nar/gkq905. Epub 2010 Nov 10.

14.
15.

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs.

Xia T, SantaLucia J Jr, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH.

Biochemistry. 1998 Oct 20;37(42):14719-35.

PMID:
9778347
16.

Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops.

Blose JM, Manni ML, Klapec KA, Stranger-Jones Y, Zyra AC, Sim V, Griffith CA, Long JD, Serra MJ.

Biochemistry. 2007 Dec 25;46(51):15123-35. Epub 2007 Nov 30.

17.

Correcting for heat capacity and 5'-TA type terminal nearest neighbors improves prediction of DNA melting temperatures using nearest-neighbor thermodynamic models.

Hughesman CB, Turner RF, Haynes C.

Biochemistry. 2011 Apr 5;50(13):2642-9. doi: 10.1021/bi101653z. Epub 2011 Mar 8.

PMID:
21323352
18.

Positional and neighboring base pair effects on the thermodynamic stability of RNA single mismatches.

Davis AR, Znosko BM.

Biochemistry. 2010 Oct 12;49(40):8669-79. doi: 10.1021/bi100146z. Epub 2010 Sep 21.

19.

Thermodynamic stability of DNA tandem mismatches.

Bourdélat-Parks BN, Wartell RM.

Biochemistry. 2004 Aug 3;43(30):9918-25.

PMID:
15274646
20.

Stability of DNA duplexes containing GG, CC, AA, and TT mismatches.

Tikhomirova A, Beletskaya IV, Chalikian TV.

Biochemistry. 2006 Sep 5;45(35):10563-71.

PMID:
16939208

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