NDLI: Thermodynamic parameters for DNA sequences with dangling ends

Content Provider	PubMed Central
Author	Bommarito, Salvatore Peyret, Nicolas Santalucia, Jr. John
Copyright Year	2000
Abstract	The thermodynamic contributions to duplex formation of all 32 possible single-nucleotide dangling ends on a Watson–Crick pair are reported. In most instances, dangling ends are stabilizing with free energy contributions ranging from +0.48 ( ) to –0.96 kcal/mol ( ). In comparison, Watson–Crick nearest-neighbor increments range from –0.58 (TA/AT) to –2.24 (GC/CG) kcal/mol. Hence, in some cases, a dangling end contributes as much to duplex stability as a Watson–Crick A-T base pair. The implications of these results for DNA probe design are discussed. Analysis of the sequence dependence of dangling-end stabilities show that the nature of the closing base pair largely determines the stabilization. For a given closing base pair, however, adenine dangling ends are always more or equally as stable as the other dangling nucleotides. Moreover, 5′ dangling ends are more or equally as stabilizing as their 3′ counterparts. Comparison of DNA with RNA dangling-end motifs shows that DNA motifs with 5′ dangling ends contribute to stability equally or more than their RNA counterparts. Conversely, RNA 3′ dangling ends contribute to stability equally or more than their DNA counterparts. This data set has been incorporated into a DNA secondary structure prediction algorithm (DNA MFOLD) (http://mfold2.wustl.edu/~mfold/dna/form1.cgi ) as well as a DNA hybridization prediction algorithm (HyTher™) (http://jsl1.chem.wayne.edu/Hyther/hythermenu.html ).
Starting Page	1929
File Format	PDF
ISSN	13624962
e-ISSN	13624962
Journal	Nucleic Acids Research
Issue Number	9
Volume Number	28
Language	English
Publisher	Oxford University Press
Publisher Date	2000-05-01
Access Restriction	Open
Rights Holder	Oxford University Press
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Thermodynamic parameters for DNA sequences with dangling ends

Thermodynamic contributions of 5’- and 3’-single strand dangling-ends to the stability of short duplex DNAs

RNA complexes with nicks and gaps: thermodynamic and kinetic effects of coaxial stacking and dangling ends

Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops.

DNA-PK-dependent binding of DNA ends to plasmids containing nuclear matrix attachment region DNA sequences: evidence for assembly of a repair complex

Design of nucleic acid sequences for DNA computing based on a thermodynamic approach

Studies of oligonucleotide interactions by hybridisation to arrays: the influence of dangling ends on duplex yield.

Chromosome ends in Drosophila without telomeric DNA sequences.

Non-consensus heptamer sequences destabilize the RAG post-cleavage complex, making ends available to alternative DNA repair pathways

Thermodynamic parameters for DNA sequences with dangling ends

Similar Documents

Thermodynamic parameters for DNA sequences with dangling ends

Thermodynamic contributions of 5’- and 3’-single strand dangling-ends to the stability of short duplex DNAs

RNA complexes with nicks and gaps: thermodynamic and kinetic effects of coaxial stacking and dangling ends

Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops.

DNA-PK-dependent binding of DNA ends to plasmids containing nuclear matrix attachment region DNA sequences: evidence for assembly of a repair complex

Design of nucleic acid sequences for DNA computing based on a thermodynamic approach

Studies of oligonucleotide interactions by hybridisation to arrays: the influence of dangling ends on duplex yield.

Chromosome ends in Drosophila without telomeric DNA sequences.

Non-consensus heptamer sequences destabilize the RAG post-cleavage complex, making ends available to alternative DNA repair pathways

Thermodynamic parameters for DNA sequences with dangling ends