Nucleic Acids Quiz 6

• Absorbance scale of nucleic bases: at 260 nm

  Adenine ~ 15,400 > Guanine ~ 11,700 > Uracil ~ 9,900 > Thymine ~ 9,200 > Cytosine ~ 7,500
• Properties that allow nucleic acids to be good at UV absorption: conjugated heterocycles, and delocalized electrons
• Nucleic acids absorb best at 260 nm
• Base stacking forces compose of LDF's and hydrophobic interactions - the strongest interactions occur between C - G | C - G, while weakest are pyrimidines A - T | A - T
• Base pairs per helical turn of A form: 11 at 28 Å, B form: 10.5, and Z form: 12
• Helix rise per form A: 2.6 Å, B form: 3.4 Å (wider spacing), Z form: 3.7 Å
• poly A regions (AAAAAA) create 18° arc in major groove
• Palindromic DNA/RNA - ends of single strand DNA/RNA that can conform with each other to make double strand, with hairpin loop of unconforming nucleotides in between
• Hoogsteen base pairing occurs on A-T pair or G-C⁺ pair on other side away from watson crick pair
• Triplex DNA occurs with Watson-Crick and Hoogsteen pairs found both on one purine
• G-quadruplex occurs when four guanosines are paired together by Hoogsteen pairs
• Tm = fraction = 0.5 of folded vs. unfolded DNA
• Watson Crick pairs localize electrons making dsDNA less absorbent in UV vis
• ATP has energy value at about 30 KJ/mol
• Pyrimidine dimers are caused by UV light, causing crosslinks like cyclobutane or 6-4 base stacking covalent bonds in between two stacked pyrimidines : genetic info becomes inaccessible
• Chemotheraputic and other DNA damaging agents like cisplatin or mustard gas cause kinks in DNA structure to induce apoptosis in cells